Structural Classification of Proteins

Superfamily: "Winged helix" DNA-binding domain

: contains a small beta-sheet (wing)
uperfamily

Lineage:

Root: scop
Class: All alpha proteins [46456]
Fold: DNA/RNA-binding 3-helical bundle [46688]
core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
Superfamily: "Winged helix" DNA-binding domain [46785]
contains a small beta-sheet (wing)
uperfamily

Families:

Biotin repressor-like [46786] (2)
1. Biotin repressor, N-terminal domain [46787]
  the middle domain is an alpha+beta fold somewhat similar to the SH2 fold
  C-terminal domain has SH3-like common fold
  1. Escherichia coli [TaxId: 562] [46788] (5)
    1. 1bia
      1. region a:1-63 [16083]
    2. 1hxd
      complexed with btn
      1. region a:4-63 [61360]
      2. region b:4-63 [61363]
    3. 2ewn
      automatically matched to d1bia_1
      complexed with btx
      1. region a:3-63 [132470]
    4. 2ewn
      automatically matched to d1bia_1
      complexed with btx
      1. region b:3-63 [132473]
    5. 1bib
      complexed with btn
      1. region a:2-63 [16084]
2. Putative transcriptional regulator TM1602, N-terminal domain [74674]
  1. Thermotoga maritima [TaxId: 2336] [74675] (1)
    1. 1j5y
      structural genomics
      complexed with k, mse, ni
      1. region a:3-67 [71592]
LexA repressor, N-terminal DNA-binding domain [46789] (1)
1. LexA repressor, N-terminal DNA-binding domain [46790]
  1. Escherichia coli [TaxId: 562] [46791] (4)
    1. 1jhf
      complexed with so4; mutant
      1. region a:2-72 [63057]
    2. 1jhh
      complexed with so4; mutant
      1. region a:2-72 [63060]
    3. 1lea
      1. chain a [16085]
    4. 1leb
      1. chain a [16086]
Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3)
1. Arginine repressor (ArgR), N-terminal DNA-binding domain [46793]
  1. Escherichia coli [TaxId: 562] [46794] (1)
    1. 1aoy
      1. chain a [16087]
  2. Bacillus stearothermophilus [TaxId: 1422] [46795] (1)
    1. 1b4a
      1. region a:4-78 [16088]
      2. region b:4-78 [16089]
      3. region c:4-78 [16090]
      4. region d:4-78 [16091]
      5. region e:4-78 [16092]
      6. region f:4-78 [16093]
  3. Bacillus subtilis [TaxId: 1423] [68966] (6)
    1. 2p5k
      automatically matched to d1f9nb1
      1. region a:2-64 [149249]
    2. 1f9n
      1. region a:3-78 [64990]
      2. region b:1-78 [64992]
      3. region c:2-78 [64994]
      4. region d:4-78 [64996]
      5. region e:2-78 [64998]
      6. region f:1-78 [65000]
    3. 2p5l
      automatically matched to d1f9nb1
      complexed with so4
      1. region c:2-64 [149250]
    4. 2p5l
      automatically matched to d1f9nb1
      complexed with so4
      1. region d:2-64 [149251]
    5. 2p5l
      automatically matched to d1f9nb1
      complexed with so4
      1. region g:2-64 [149252]
    6. 2p5l
      automatically matched to d1f9nb1
      complexed with so4
      1. region h:2-64 [149253]
Transcriptional repressor Rex, N-terminal domain [101007] (1)
1. Transcriptional repressor Rex, N-terminal domain [101008]
  AT-rich DNA-binding protein p25
  1. Thermus aquaticus [TaxId: 271] [101009] (3)
    SQ Q9X2V5; # CASP5
    1. 2dt5
      automatically matched to d1xcba1
      complexed with cl, gol, nad, so4; mutant
      1. region a:4-77 [131708]
    2. 2dt5
      automatically matched to d1xcba1
      complexed with cl, gol, nad, so4; mutant
      1. region b:4-77 [131710]
    3. 1xcb
      complexed with ca, nad
      1. region a:4-77 [109552]
      2. region b:4-77 [109554]
      3. region c:4-77 [109556]
      4. region d:4-77 [109558]
      5. region e:4-77 [109560]
      6. region f:4-77 [109562]
      7. region g:4-77 [109564]
CAP C-terminal domain-like [46796] (9)
1. Catabolite gene activator protein (CAP), C-terminal domain [46797]
  N-terminal domain has double beta-helix fold
  1. Escherichia coli [TaxId: 562] [46798] (26)
    1. 1i5z
      complexed with cmp, trs
      1. region a:138-206 [83669]
      2. region b:138-207 [83671]
    2. 1zrf
      automatically matched to d1lb2a1
      complexed with cmp, dio
      1. region a:138-207 [125543]
    3. 1zrf
      automatically matched to d1lb2a1
      complexed with cmp, dio
      1. region b:138-207 [125545]
    4. 1g6n
      complexed with cmp
      1. region a:138-206 [16100]
      2. region b:438-507 [16101]
    5. 1hw5
      complexed with cmp; mutant
      1. region a:138-208 [16098]
      2. region b:138-205 [16099]
    6. 1i6x
      complexed with cmp, trs; mutant
      1. region a:138-206 [83673]
      2. region b:138-207 [83675]
    7. 2cgp
      protein/DNA complex; complexed with cmp
      1. region a:138-207 [16102]
    8. 2gzw
      automatically matched to d1lb2a1
      complexed with cmp
      1. region a:138-206 [135917]
    9. 2gzw
      automatically matched to d1lb2a1
      complexed with cmp
      1. region b:138-203 [135919]
    10. 2gzw
      automatically matched to d1lb2a1
      complexed with cmp
      1. region c:138-206 [135921]
    11. 2gzw
      automatically matched to d1lb2a1
      complexed with cmp
      1. region d:138-207 [135923]
    12. 1j59
      complexed with cmp
      1. region a:138-207 [71532]
      2. region b:138-205 [71534]
    13. 1zre
      automatically matched to d1lb2a1
      complexed with cmp
      1. region a:138-207 [125539]
    14. 1zre
      automatically matched to d1lb2a1
      complexed with cmp
      1. region b:138-207 [125541]
    15. 1zrc
      automatically matched to d1lb2a1
      complexed with cmp
      1. region a:138-207 [125531]
    16. 1zrc
      automatically matched to d1lb2a1
      complexed with cmp
      1. region b:138-207 [125533]
    17. 1zrd
      automatically matched to d1lb2a1
      complexed with cmp
      1. region a:138-207 [125535]
    18. 1zrd
      automatically matched to d1lb2a1
      complexed with cmp
      1. region b:138-207 [125537]
    19. 1o3r
      complexed with cmp
      1. region a:138-207 [86607]
    20. 1run
      protein/DNA complex; complexed with cmp
      1. region a:138-209 [16103]
      2. region b:138-205 [16104]
    21. 1lb2
      complexed with cmp
      1. region a:138-209 [77869]
    22. 1o3q
      complexed with cmp
      1. region a:138-207 [86605]
    23. 1o3s
      complexed with cmp; mutant
      1. region a:138-207 [86609]
    24. 1ruo
      protein/DNA complex; complexed with cmp; mutant
      1. region a:138-206 [16105]
      2. region b:138-209 [16106]
    25. 1cgp
      protein/DNA complex; complexed with cmp
      1. region a:138-205 [16096]
      2. region b:138-205 [16097]
    26. 1o3t
      complexed with cmp
      1. region a:138-207 [86611]
      2. region b:138-205 [86613]
2. CO-sensing protein CooA, C-terminal domain [46799]
  1. Rhodospirillum rubrum [TaxId: 1085] [46800] (1)
    1. 1ft9
      complexed with hem
      1. region a:134-213 [16107]
      2. region b:134-213 [16108]
3. Listeriolysin regulatory protein PrfA, C-terminal domain [88975]
  1. Bacteria (Listeria monocytogenes) [TaxId: 1639] [88976] (11)
    1. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region a:138-237 [128458]
    2. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region b:138-237 [128460]
    3. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region d:138-237 [128462]
    4. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region e:138-237 [128464]
    5. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region f:138-237 [128466]
    6. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region g:138-237 [128468]
    7. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region h:138-235 [128470]
    8. 2bgc
      automatically matched to d1omia2
      complexed with dtt, dtu; mutant
      1. region i:138-237 [128472]
    9. 2beo
      automatically matched to d1omia2
      complexed with acm, cl, gln, pg4
      1. region a:138-237 [128381]
    10. 2beo
      automatically matched to d1omia2
      complexed with acm, cl, gln, pg4
      1. region b:138-237 [128383]
    11. 1omi
      complexed with gol
      1. region a:1138-1237 [87080]
      2. region b:2138-2237 [87082]
4. Transcriptional regulator PG0396, C-terminal domain [140229]
  1. Porphyromonas gingivalis [TaxId: 837] [140230] (1)
    SQ Q7MAW7 152-232
    1. 2gau
      1. region a:152-232 [134894]
5. Probable transcription regulator BT4300, C-terminal domain [140231]
  1. Bacteroides thetaiotaomicron [TaxId: 818] [140232] (1)
    SQ Q89ZS6 148-220
    1. 1zyb
      complexed with gol
      1. region a:148-220 [125815]
6. Transcriptional regulator TTHA1359, C-terminal domain [140233]
  1. Thermus thermophilus [TaxId: 274] [140234] (1)
    SQ Q5SIL0 118-199
    1. 2coh
      complexed with mpd
      1. region a:118-199 [130677]
7. Cyclic AMP receptor-like protein Vfr [158266]
  1. Pseudomonas aeruginosa [TaxId: 287] [158267] (1)
    SQ P55222 143-213
    1. 2oz6
      complexed with cmp
      1. region a:143-213 [149103]
8. Chlorophenol reduction protein CprK [158268]
  1. Desulfitobacterium dehalogenans [TaxId: 36854] [158269] (2)
    SQ Q9LAS2 148-226
    1. 2h6c
      1. region a:148-226 [147232]
    2. 2h6c
      automatically matched to 2H6C A:148-226
      1. region b:148-226 [147234]
  2. Desulfitobacterium hafniense [TaxId: 49338] [158270] (7)
    SQ Q18R04 148-227! SQ Q18R04 148-229
    1. 3e5u
      complexed with 3c4, na, po4; mutant
      1. region a:148-227 [158022]
    2. 3e5u
      automatically matched to 3E5U A:148-227
      complexed with 3c4, na, po4; mutant
      1. region b:148-226 [158024]
    3. 3e5u
      automatically matched to 3E5U A:148-227
      complexed with 3c4, na, po4; mutant
      1. region c:148-227 [158026]
    4. 3e5u
      automatically matched to 3E5U A:148-227
      complexed with 3c4, na, po4; mutant
      1. region d:148-227 [158028]
    5. 3e6c
      automatically matched to 3E5U A:148-227
      complexed with 3c4; mutant
      1. region c:148-227 [158038]
    6. 2h6b
      complexed with 3c4, so4
      1. region a:148-229 [147228]
    7. 2h6b
      automatically matched to 2H6B A:148-229
      complexed with 3c4, so4
      1. region b:148-229 [147230]
Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4)
Swapped dimer with the "wing" C-terminal strands
1. LprA [68968]
  1. Archaeon Pyrococcus furiosus [TaxId: 2261] [68969] (1)
    1. 1i1g
      1. region a:2-61 [65982]
      2. region b:2-61 [65984]
2. Putative transcriptional regulator PH1519 [101010]
  archaeal feast/famine regulatory protein
  1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101011] (3)
    identical sequence to Pyrococcus sp. ot3 protein
    1. 2cyy
      automatically matched to d1ri7a1
      complexed with ca, gln
      1. region a:5-64 [131028]
    2. 2e1c
      automatically matched to d1ri7a1
      1. region a:25-84 [146625]
    3. 1ri7
      1. region a:25-84 [97504]
3. Regulatory protein AsnC [140235]
  1. Escherichia coli [TaxId: 562] [140236] (2)
    SQ P0ACI6 4-66
    1. 2cg4
      complexed with asn, mg; mutant
      1. region a:4-66 [130417]
    2. 2cg4
      automatically matched to 2CG4 A:4-66
      complexed with asn, mg; mutant
      1. region b:4-66 [130419]
4. Transcriptional regulator LrpC [140237]
  1. Bacillus subtilis [TaxId: 1423] [140238] (8)
    SQ P96582 1-63
    1. 2cfx
      1. region a:1-63 [130395]
    2. 2cfx
      automatically matched to 2CFX A:1-63
      1. region b:1-63 [130397]
    3. 2cfx
      automatically matched to 2CFX A:1-63
      1. region c:1-63 [130399]
    4. 2cfx
      automatically matched to 2CFX A:1-63
      1. region d:1-63 [130401]
    5. 2cfx
      automatically matched to 2CFX A:1-63
      1. region e:1-63 [130403]
    6. 2cfx
      automatically matched to 2CFX A:1-63
      1. region f:1-63 [130405]
    7. 2cfx
      automatically matched to 2CFX A:1-63
      1. region g:1-63 [130407]
    8. 2cfx
      automatically matched to 2CFX A:1-63
      1. region h:1-63 [130409]
ArsR-like transcriptional regulators [46801] (4)
The N- and C-terminal helical extensions to the common fold form the dimer interface
1. SmtB repressor [46802]
  1. Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129] [46803] (4)
    SQ P30340
    1. 1r1t
      1. chain a [104769]
      2. chain b [104770]
    2. 1r23
      complexed with zn
      1. chain a [104779]
      2. chain b [104780]
    3. 1smt
      1. chain a [16109]
      2. chain b [16110]
    4. 1r22
      complexed with zn; mutant
      1. chain a [104777]
      2. chain b [104778]
2. Metal-sensing transcriptional repressor CzrA [109664]
  1. Staphylococcus aureus [TaxId: 1280] [109665] (2)
    SQ O85142
    1. 1r1u
      1. chain a [104771]
      2. chain b [104772]
      3. chain c [104773]
      4. chain d [104774]
    2. 1r1v
      complexed with zn
      1. chain a [104775]
      2. chain b [104776]
3. Putative arsenical resistance operon repressor AF0168 [116786]
  lacks the extra C-terminal helix
  1. Archaeoglobus fulgidus [TaxId: 2234] [116787] (1)
    SQ O30069
    1. 1y0u
      Structural genomics target
      complexed with act
      1. chain a [116310]
      2. chain b [116311]
4. Cadmium efflux system accessory protein CadC [140239]
  1. Staphylococcus aureus [TaxId: 1280] [140240] (4)
    SQ P20047 12-119
    1. 1u2w
      complexed with zn; mutant
      1. region a:12-119 [119487]
    2. 1u2w
      automatically matched to 1U2W A:12-119
      complexed with zn; mutant
      1. region b:12-117 [119488]
    3. 1u2w
      automatically matched to 1U2W A:12-119
      complexed with zn; mutant
      1. region c:17-114 [119489]
    4. 1u2w
      automatically matched to 1U2W A:12-119
      complexed with zn; mutant
      1. region d:12-118 [119490]
Transcriptional regulator IclR, N-terminal domain [74676] (1)
1. Transcriptional regulator IclR, N-terminal domain [74677]
  1. Thermotoga maritima [TaxId: 2336] [74678] (1)
    1. 1mkm
      complexed with fmt, zn
      1. region a:1-75 [79242]
      2. region b:0-75 [79244]
MarR-like transcriptional regulators [63379] (20)
The N- and C-terminal helical extensions to the common fold form the dimer interface
1. Multiple antibiotic resistance repressor, MarR [68970]
  1. Escherichia coli [TaxId: 562] [68971] (1)
    1. 1jgs
      complexed with sal
      1. chain a [66683]
2. MexR repressor [81686]
  1. Pseudomonas aeruginosa [TaxId: 287] [81687] (1)
    1. 1lnw
      complexed with mse
      1. chain a [78104]
      2. chain b [78105]
      3. chain c [78106]
      4. chain d [78107]
      5. chain e [78108]
      6. chain f [78109]
      7. chain g [78110]
      8. chain h [78111]
3. Transcriptional regulator SlyA [81688]
  1. Enterococcus faecalis [TaxId: 1351] [81689] (1)
    1. 1lj9
      1. chain a [78035]
      2. chain b [78036]
  2. Salmonella typhimurium [TaxId: 90371] [158271] (2)
    SQ P40676 1-140
    1. 3deu
      complexed with sal
      1. region a:2-141 [157600]
    2. 3deu
      automatically matched to 3DEU A:2-141
      complexed with sal
      1. region b:2-141 [157601]
4. Staphylococcal accessory regulator A homolog, SarR [63472]
  1. Staphylococcus aureus [TaxId: 1280] [63473] (1)
    1. 1hsj
      Fusion protein with E. coli MBP
      complexed with glc
      1. region a:373-487 [61237]
      2. region b:373-487 [61239]
5. Staphylococcal accessory regulator A homolog, SarS [88977]
  duplication: tandem repeat of two SarR-like domains assembled together as in the SarR dimer
  1. Staphylococcus aureus [TaxId: 1280] [88978] (1)
    1. 1p4x
      1. region a:1-125 [87784]
      2. region a:126-250 [87785]
6. Pleiotropic regulator of virulence genes, SarA [48292]
  closely related to SarR but adopts a different fold; possible experimental artifact?
  1. Staphylococcus aureus [TaxId: 1280] [48293] (5)
    1. 2frh
      automatically matched to d1fzpb_
      complexed with ca
      1. region a:102-216 [133988]
    2. 2frh
      automatically matched to d1fzpb_
      complexed with ca
      1. region b:102-216 [133989]
    3. 2fnp
      1. region a:103-224 [133825]
    4. 2fnp
      automatically matched to 2FNP A:103-224
      1. region b:103-224 [133826]
    5. 1fzp
      protein/DNA complex; complexed with ca
      1. chain d [19007]
      2. chain b [19008]
7. Putative transcriptional regulator YusO [101012]
  1. Bacillus subtilis [TaxId: 1423] [101013] (1)
    1. 1s3j
      structural genomics
      1. chain a [98437]
      2. chain b [98438]
8. Hypothetical protein PH1061 [101014]
  1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101015] (1)
    1. 1ub9
      structural genomics
      1. chain a [99159]
9. Putative transcriptional regulator TM0816 [140241]
  1. Thermotoga maritima [TaxId: 2336] [140242] (2)
    SQ Q9WZS3 1-140
    1. 2eth
      complexed with cl
      1. region a:1-140 [132358]
    2. 2eth
      automatically matched to 2ETH A:1-140
      complexed with cl
      1. region b:1-140 [132359]
10. Probable transcriptional regulator PA3067 [140243]
  1. Pseudomonas aeruginosa [TaxId: 287] [140244] (4)
    SQ Q9HZE1 2-146
    1. 2hr3
      1. region a:2-146 [136678]
    2. 2hr3
      automatically matched to 2HR3 A:2-146
      1. region b:3-145 [136679]
    3. 2hr3
      automatically matched to 2HR3 A:2-146
      1. region c:3-145 [136680]
    4. 2hr3
      automatically matched to 2HR3 A:2-146
      1. region d:2-145 [136681]
11. Probable transcriptional regulator PA4135 [140245]
  1. Pseudomonas aeruginosa [TaxId: 287] [140246] (1)
    SQ Q9HWP6 5-140
    1. 2fbi
      1. region a:5-140 [133246]
12. Organic hydroperoxide resistance transcriptional regulator OhrR [140247]
  1. Bacillus subtilis [TaxId: 1423] [140248] (7)
    SQ O34777 8-144
    1. 1z91
      mutant
      1. region a:8-144 [124736]
    2. 1z9c
      automatically matched to 1Z91 A:8-144
      mutant
      1. region a:9-144 [124747]
    3. 1z9c
      automatically matched to 1Z91 A:8-144
      mutant
      1. region b:8-144 [124748]
    4. 1z9c
      automatically matched to 1Z91 A:8-144
      mutant
      1. region c:8-144 [124749]
    5. 1z9c
      automatically matched to 1Z91 A:8-144
      mutant
      1. region d:8-144 [124750]
    6. 1z9c
      automatically matched to 1Z91 A:8-144
      mutant
      1. region e:8-144 [124751]
    7. 1z9c
      automatically matched to 1Z91 A:8-144
      mutant
      1. region f:8-144 [124752]
13. Transcriptional regulator PA3341 [140249]
  1. Pseudomonas aeruginosa [TaxId: 287] [140250] (1)
    SQ Q9HYQ4 8-144
    1. 2fbh
      complexed with hg, so4, zn
      1. region a:8-144 [133245]
14. Protease production regulatory protein Hpr [140251]
  1. Bacillus subtilis [TaxId: 1423] [140252] (4)
    SQ P11065 6-167
    1. 2fxa
      complexed with 1pe, edo, p6g, pge
      1. region a:6-167 [134304]
    2. 2fxa
      automatically matched to 2FXA A:6-167
      complexed with 1pe, edo, p6g, pge
      1. region b:8-167 [134305]
    3. 2fxa
      automatically matched to 2FXA A:6-167
      complexed with 1pe, edo, p6g, pge
      1. region c:8-167 [134306]
    4. 2fxa
      automatically matched to 2FXA A:6-167
      complexed with 1pe, edo, p6g, pge
      1. region d:7-167 [134307]
15. Transcriptional regulator TM0710 [140253]
  1. Thermotoga maritima [TaxId: 2336] [140254] (4)
    SQ Q9WZG9 5-143
    1. 2a61
      1. region a:5-143 [126187]
    2. 2a61
      automatically matched to 2A61 A:5-143
      1. region b:5-143 [126188]
    3. 2a61
      automatically matched to 2A61 A:5-143
      1. region c:5-143 [126189]
    4. 2a61
      automatically matched to 2A61 A:5-143
      1. region d:5-143 [126190]
16. Transcriptional regulator DR1159 [140255]
  1. Deinococcus radiodurans [TaxId: 1299] [140256] (2)
    SQ Q9RV71 8-179
    1. 2fbk
      complexed with cl
      1. region a:8-179 [133247]
    2. 2fbk
      automatically matched to 2FBK A:8-179
      complexed with cl
      1. region b:8-179 [133248]
17. Transcriptional regulator MgrA [158272]
  1. Staphylococcus aureus [TaxId: 1280] [158273] (1)
    SQ Q7A1J9 6-141
    1. 2bv6
      complexed with so4
      1. region a:5-140 [146218]
18. Ta1064 (RFK), N-terminal domain [158274]
  1. Thermoplasma acidophilum [TaxId: 2303] [158275] (1)
    SQ Q9HJA6 5-89
    1. 3cta
      1. region a:5-89 [156979]
19. Transcriptional regulator OEOE1854 [158276]
  1. Oenococcus oeni [TaxId: 1247] [158277] (4)
    SQ Q04CY6 3-137
    1. 3bro
      complexed with cl, gol
      1. region a:3-137 [155517]
    2. 3bro
      automatically matched to 3BRO A:3-137
      complexed with cl, gol
      1. region b:3-137 [155518]
    3. 3bro
      automatically matched to 3BRO A:3-137
      complexed with cl, gol
      1. region c:4-137 [155519]
    4. 3bro
      automatically matched to 3BRO A:3-137
      complexed with cl, gol
      1. region d:4-137 [155520]
DNA-binding protein Mj223 [81690] (1)
homologous to the MarR-like family in the DNA-binding region but dimerizes differently through the N- and C-terminal helical extensions to the common fold
1. DNA-binding protein Mj223 [81691]
  1. Archaeon Methanococcus jannaschii [TaxId: 2190] [81692] (1)
    1. 1ku9
      complexed with mse
      1. chain a [77544]
      2. chain b [77545]
Penicillinase repressor [101016] (4)
homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
1. Methicillin resistance regulatory protein MecI [101017]
  1. Staphylococcus aureus [TaxId: 1280] [101018] (8)
    1. 1okr
      complexed with cl, gol
      1. chain a [93269]
      2. chain b [93270]
    2. 1sd6
      1. chain a [98803]
      2. chain b [98804]
    3. 1sd7
      1. chain a [98805]
      2. chain b [98806]
    4. 1sax
      complexed with DNA
      complexed with k
      1. chain a [98787]
      2. chain b [98788]
    5. 2d45
      automatically matched to d1okrb_
      1. region a:5-121 [131242]
    6. 2d45
      automatically matched to d1okrb_
      1. region b:5-121 [131243]
    7. 2d45
      automatically matched to d1okrb_
      1. region c:5-121 [131244]
    8. 2d45
      automatically matched to d1okrb_
      1. region d:7-121 [131245]
2. Penicillinase repressor BlaI [101019]
  1. Bacillus licheniformis [TaxId: 1402] [101020] (2)
    1. 1p6r
      DNA-binding domain only
      1. chain a [94187]
    2. 2p7c
      automatically matched to d1p6ra_
      1. region b:1-82 [139517]
  2. Staphylococcus aureus [TaxId: 1280] [109666] (2)
    SQ Q9K4N1
    1. 1sd4
      complexed with so4
      1. chain a [105428]
      2. chain b [105429]
    2. 1xsd
      automatically matched to d1sd4a_
      1. region a:5-126 [122269]
3. Hypothetical protein Rv1846c [158278]
  MT1894
  1. Mycobacterium tuberculosis [TaxId: 1773] [158279] (2)
    SQ P95163 3-124
    1. 2g9w
      complexed with cl; mutant
      1. region a:3-124 [147097]
    2. 2g9w
      automatically matched to 2G9W A:3-124
      complexed with cl; mutant
      1. region b:3-124 [147098]
GntR-like transcriptional regulators [46804] (4)
1. Fatty acid responsive transcription factor FadR, N-terminal domain [46805]
  1. Escherichia coli [TaxId: 562] [46806] (5)
    1. 1hw1
      complexed with so4, zn
      1. region a:5-78 [16111]
      2. region b:5-78 [16112]
    2. 1e2x
      CASP4
      complexed with so4
      1. region a:6-78 [16113]
    3. 1h9g
      complexed with coa, myr
      1. region a:5-78 [60827]
    4. 1hw2
      protein/DNA complex; complexed with mg
      1. region a:7-78 [16114]
      2. region b:7-78 [16115]
    5. 1h9t
      complex with fadB operator
      complexed with au, cl
      1. region a:5-78 [60847]
      2. region b:5-78 [60849]
2. Transcriptional repressor TraR, N-terminal domain [140257]
  1. Streptomyces sp. [TaxId: 1931] [140258] (1)
    SQ Q54677 1-99
    78% identity to the UniProt entry species
    1. 1v4r
      1. region a:1-100 [119835]
3. Transcriptional regulator YydK [158280]
  1. Bacillus subtilis [TaxId: 1423] [158281] (3)
    SQ Q45591 5-82
    1. 3bwg
      complexed with edo
      1. region a:5-82 [155693]
    2. 3bwg
      automatically matched to 3BWG A:5-82
      complexed with edo
      1. region b:5-81 [155695]
    3. 3bwg
      automatically matched to 3BWG A:5-82
      complexed with edo
      1. region c:5-79 [155697]
4. Putative transcriptional regulator RHA1_ro03477 [158282]
  1. Rhodococcus sp. RHA1 [TaxId: 101510] [158283] (1)
    SQ Q0SB06 25-93
    1. 2hs5
      complexed with act
      1. region a:25-93 [147379]
N-terminal domain of Bacillus PurR [101021] (1)
1. N-terminal domain of Bacillus PurR [101022]
  1. Bacillus subtilis [TaxId: 1423] [101023] (2)
    1. 1o57
      complexed with 1pe, 2pe, epe, p6g, pg4, so4
      1. region a:2-74 [92483]
      2. region b:1-74 [92485]
      3. region c:1-74 [92487]
      4. region d:2-74 [92489]
    2. 1p4a
      complexed with pcp
      1. region a:2-74 [94090]
      2. region b:2-74 [94092]
      3. region c:2-74 [94094]
      4. region d:2-74 [94096]
Replication terminator protein (RTP) [46807] (1)
1. Replication terminator protein (RTP) [46808]
  contains long helix in the C-terminal extension; forms dimer similar to the LysR-like dimer
  1. Bacillus subtilis [TaxId: 1423] [46809] (10)
    1. 1bm9
      CASP1
      1. chain a [16116]
      2. chain b [16117]
    2. 1f4k
      complexed with DNA
      mutant
      1. chain a [59646]
      2. chain b [59647]
    3. 1j0r
      mutant
      1. chain a [90745]
      2. chain b [90746]
    4. 2efw
      automatically matched to d1j0rb_
      mutant
      1. region a:8-122 [146820]
    5. 2efw
      automatically matched to d1j0rb_
      mutant
      1. region b:8-122 [146821]
    6. 2efw
      automatically matched to d1j0rb_
      mutant
      1. region f:8-122 [146822]
    7. 2efw
      automatically matched to d1j0rb_
      mutant
      1. region g:8-122 [146823]
    8. 2dpu
      automatically matched to d1j0rb_
      mutant
      1. region a:8-122 [131617]
    9. 2dpd
      automatically matched to d1j0rb_
      mutant
      1. region a:8-122 [131610]
    10. 2dpd
      automatically matched to d1j0rb_
      mutant
      1. region b:8-122 [131611]
LysR-like transcriptional regulators [88979] (2)
contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
1. LysR-type regulatory protein CbnR [88980]
  1. Ralstonia eutropha [TaxId: 106590] [88981] (2)
    1. 1ixc
      complexed with mse
      1. region a:1-89 [83764]
      2. region b:1-89 [83766]
    2. 1iz1
      1. region a:1-89 [83823]
      2. region b:1-89 [83825]
      3. region p:1-89 [83827]
      4. region q:1-89 [83829]
2. Probable LysR-type transcriptional regulator PA0477 [140259]
  1. Pseudomonas aeruginosa [TaxId: 287] [140260] (4)
    SQ Q9I641 3-91
    1. 2esn
      1. region a:3-91 [132333]
    2. 2esn
      automatically matched to 2ESN A:3-91
      1. region b:3-91 [132335]
    3. 2esn
      automatically matched to 2ESN A:3-91
      1. region c:3-91 [132337]
    4. 2esn
      automatically matched to 2ESN A:3-91
      1. region d:3-91 [132339]
N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1)
contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
1. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46811]
  1. Escherichia coli [TaxId: 562] [46812] (3)
    1. 1b9m
      complexed with ni
      1. region a:-1-126 [16118]
      2. region b:-1-126 [16119]
    2. 1b9n
      complexed with ni
      1. region a:-2-126 [16120]
      2. region b:1-126 [16121]
    3. 1o7l
      molybdate-activated form
      complexed with ca, cl, moo
      1. region a:1-126 [81147]
      2. region b:1-126 [81150]
      3. region c:2-126 [81153]
      4. region d:2-126 [81156]
Transcription factor MotA, activation domain [46813] (1)
The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)
1. Transcription factor MotA, activation domain [46814]
  1. Bacteriophage T4 [TaxId: 10665] [46815] (2)
    1. 1bja
      complexed with so4
      1. chain a [16122]
      2. chain b [16123]
    2. 1i1s
      1. chain a [16124]
Transcription factor E/IIe-alpha, N-terminal domain [101024] (1)
contains extra N-terminal helix
1. Transcription factor E/IIe-alpha, N-terminal domain [101025]
  1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101026] (1)
    1. 1q1h
      1. chain a [95580]
FUR-like [101027] (1)
contains extra N-terminal helix and an alpha+beta dimerisation subdomain
1. Ferric uptake regulation protein, FUR [101028]
  1. Pseudomonas aeruginosa [TaxId: 287] [101029] (1)
    1. 1mzb
      complexed with zn
      1. chain a [91497]
Replication initiation protein [46816] (3)
duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
1. RepE54 [46817]
  1. Escherichia coli, mini-F plasmid [TaxId: 562] [46818] (5)
    1. 1rep
      1. region c:15-143 [16125]
      2. region c:144-246 [16126]
    2. 2z9o
      automatically matched to d1repc1
      1. region a:21-143 [154260]
    3. 2z9o
      automatically matched to d1repc2
      1. region a:144-246 [154261]
    4. 2z9o
      automatically matched to d1repc1
      1. region b:21-143 [154262]
    5. 2z9o
      automatically matched to d1repc2
      1. region b:144-246 [154263]
2. Replication protein A, repA [88982]
  1. Pseudomonas syringae pv. savastanoi [TaxId: 29438] [88983] (1)
    1. 1hkq
      inactive, dimeric N-terminal domain
      complexed with box, hg, po4
      1. chain a [83555]
      2. chain b [83556]
3. Replication initiation protein PI [158284]
  1. Escherichia coli [TaxId: 562] [158285] (2)
    SQ P03067 152-268! SQ P03067 9-151
    1. 2nra
      mutant
      1. region c:9-151 [148360]
    2. 2nra
      mutant
      1. region c:152-268 [148361]
Helicase DNA-binding domain [46819] (5)
follows the extended AAA-ATPase domain
1. Holliday junction helicase RuvB [46820]
  1. Thermus thermophilus [TaxId: 274] [46821] (3)
    1. 1ixs
      complexed with anp
      1. region b:243-318 [76933]
    2. 1hqc
      complexed with ade, mg
      1. region a:243-318 [16127]
      2. region b:243-318 [16128]
    3. 1ixr
      complexed with anp; mutant
      1. region c:243-312 [76930]
  2. Thermotoga maritima [TaxId: 2336] [63474] (6)
    1. 1in4
      complexed with act, adp, co, hez
      1. region a:255-329 [62597]
    2. 1j7k
      complexed with act, atp, co, hez; mutant
      1. region a:255-329 [62695]
    3. 1in6
      complexed with act, adp, co; mutant
      1. region a:255-329 [62601]
    4. 1in7
      complexed with act, adp; mutant
      1. region a:255-329 [62603]
    5. 1in8
      complexed with adp; mutant
      1. region a:255-329 [62605]
    6. 1in5
      complexed with adp; mutant
      1. region a:255-329 [62599]
2. CDC6, C-terminal domain [46822]
  contains the N- and C-terminal helical extensions to the common fold
  1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [46823] (1)
    1. 1fnn
      complexed with adp, mg
      1. region a:277-388 [16129]
      2. region b:277-388 [16130]
3. CDC6-like protein APE0152, C-terminal domain [116788]
  1. Aeropyrum pernix [TaxId: 56636] [116789] (2)
    SQ Q9YFU8
    1. 1w5s
      complexed with adp, so4
      1. region a:300-409 [114251]
      2. region b:300-409 [114253]
    2. 1w5t
      complexed with adp, anp, mg
      1. region a:300-409 [114255]
      2. region b:300-409 [114257]
      3. region c:300-409 [114259]
4. Hypothetical protein SSO1545, C-terminal domain [140261]
  1. Sulfolobus solfataricus [TaxId: 2287] [140262] (2)
    SQ Q97Y08 284-356
    1. 2fna
      complexed with adp, edo, mg
      1. region a:284-356 [133809]
    2. 2fna
      automatically matched to 2FNA A:284-356
      complexed with adp, edo, mg
      1. region b:284-356 [133811]
RecQ helicase DNA-binding domain-like [101030] (3)
follows the tandem AAA-ATPase domain
1. DNA helicase RecQ DNA-binding domain [101031]
  1. Escherichia coli [TaxId: 562] [101032] (2)
    1. 1oyw
      complexed with mn, zn
      1. region a:407-516 [93760]
    2. 1oyy
      complexed with ags, mn, zn
      1. region a:407-516 [93772]
2. Werner syndrome ATP-dependent helicase WRN [140263]
  1. Human (Homo sapiens) [TaxId: 9606] [140264] (1)
    SQ Q14191 949-1092
    1. 2axl
      1. region a:1-144 [127495]
3. Hel308 helicase [158286]
  1. Archaeoglobus fulgidus [TaxId: 2234] [158287] (2)
    1. 2p6r
      1. region a:404-488 [149270]
    2. 2p6u
      automatically matched to 2P6R A:404-488
      complexed with po4
      1. region a:404-488 [149274]
SCF ubiquitin ligase complex WHB domain [74679] (4)
1. Anaphase promoting complex (APC) [74680]
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74681] (1)
    1. 1ldd
      1. chain a [73841]
      2. chain b [73842]
      3. chain c [73843]
      4. chain d [73844]
  2. Human (Homo sapiens) [TaxId: 9606] [74682] (3)
    SQ Q13616 17-776
    1. 1ldj
      complexed with zn
      1. region a:687-776 [73847]
    2. 1u6g
      complexed with zn
      1. region a:687-775 [113062]
    3. 1ldk
      complexed with zn
      1. region b:687-776 [73852]
2. Cullin-3 homologue [101033]
  1. Mouse (Mus musculus) [TaxId: 10090] [101034] (1)
    1. 1iuy
      1. chain a [90705]
3. Cullin-4A [158288]
  1. Human (Homo sapiens) [TaxId: 9606] [158289] (1)
    SQ Q13619 676-759
    1. 2hye
      complexed with zn
      1. region c:676-759 [145414]
C-terminal fragment of elongation factor SelB [74683] (1)
1. C-terminal fragment of elongation factor SelB [74684]
  duplication: tandem repeat of four "winged helix" domains
  1. Moorella thermoacetica [TaxId: 1525] [74685] (21)
    1. 2v9v
      automatically matched to d1lvaa1
      complexed with cl, na
      1. region a:377-437 [152809]
    2. 2v9v
      automatically matched to d1lvaa2
      complexed with cl, na
      1. region a:438-510 [152810]
    3. 1lva
      complexed with mse, so4, y1
      1. region a:377-437 [74276]
      2. region a:438-510 [74277]
      3. region a:511-574 [74278]
      4. region a:575-634 [74279]
    4. 2uwm
      automatically matched to d1lvaa2
      1. region a:441-510 [139992]
    5. 2uwm
      automatically matched to d1lvaa3
      1. region a:511-574 [139993]
    6. 2uwm
      automatically matched to d1lvaa4
      1. region a:575-633 [139994]
    7. 2uwm
      automatically matched to d1lvaa2
      1. region b:441-510 [139995]
    8. 2uwm
      automatically matched to d1lvaa3
      1. region b:511-574 [139996]
    9. 2uwm
      automatically matched to d1lvaa4
      1. region b:575-633 [139997]
    10. 1wsu
      automatically matched to d1lvaa3
      1. region a:512-574 [121245]
    11. 1wsu
      automatically matched to d1lvaa4
      1. region a:575-634 [121246]
    12. 1wsu
      automatically matched to d1lvaa3
      1. region b:512-574 [121247]
    13. 1wsu
      automatically matched to d1lvaa4
      1. region b:575-632 [121248]
    14. 1wsu
      automatically matched to d1lvaa3
      1. region c:517-574 [121249]
    15. 1wsu
      automatically matched to d1lvaa4
      1. region c:575-632 [121250]
    16. 1wsu
      automatically matched to d1lvaa3
      1. region d:512-574 [121251]
    17. 1wsu
      automatically matched to d1lvaa4
      1. region d:575-634 [121252]
    18. 2ply
      automatically matched to d1lvaa1
      complexed with ca, cl, mg, na; mutant
      1. region a:392-437 [149651]
    19. 2ply
      automatically matched to d1lvaa2
      complexed with ca, cl, mg, na; mutant
      1. region a:438-510 [149652]
    20. 2ply
      automatically matched to d1lvaa3
      complexed with ca, cl, mg, na; mutant
      1. region a:511-574 [149653]
    21. 2ply
      automatically matched to d1lvaa4
      complexed with ca, cl, mg, na; mutant
      1. region a:575-632 [149654]
Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1)
1. Restriction endonuclease FokI, N-terminal (recognition) domain [46825]
  duplication: consists of three elaborated "winged helix" domains
  1. Flavobacterium okeanokoites [TaxId: 244] [46826] (2)
    1. 2fok
      1. region a:5-143 [16131]
      2. region a:144-286 [16132]
      3. region a:287-386 [16133]
      4. region b:5-143 [16134]
      5. region b:144-286 [16135]
      6. region b:287-378 [16136]
    2. 1fok
      protein/DNA complex
      1. region a:4-143 [16137]
      2. region a:144-281 [16138]
      3. region a:287-386 [16139]
TnsA endonuclease, C-terminal domain [46782] (1)
1. TnsA endonuclease, C-terminal domain [46783]
  1. Escherichia coli [TaxId: 562] [46784] (2)
    SQ P13988
    1. 1t0f
      complexed with the transposition protein TnsC peptide (SQ P05846 505-553), chains C and D
      complexed with mg, mla, mpd
      1. region a:169-268 [112195]
      2. region b:169-268 [112197]
    2. 1f1z
      complexed with cl, mg
      1. region a:169-267 [16081]
      2. region b:169-267 [16082]
Plant O-methyltransferase, N-terminal domain [63475] (5)
unknown function
1. Chalcone O-methyltransferase [63476]
  1. Alfalfa (Medicago sativa) [TaxId: 3879] [63477] (2)
    1. 1fp1
      complexed with hcc, sah
      1. region d:19-128 [59939]
    2. 1fpq
      complexed with sam
      1. region a:20-128 [59947]
2. Isoflavone O-methyltransferase [63478]
  1. Alfalfa (Medicago sativa) [TaxId: 3879] [63479] (2)
    1. 1fp2
      complexed with hmo, sah
      1. region a:8-108 [59941]
    2. 1fpx
      complexed with sam
      1. region a:8-108 [59950]
3. Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase [74686]
  1. Alfalfa (Medicago sativa) [TaxId: 3879] [74687] (2)
    1. 1kyz
      complexed with fer, sah
      1. region a:13-119 [73312]
      2. region c:10-119 [73314]
      3. region e:5-119 [73316]
    2. 1kyw
      complexed with hfl, sah
      1. region a:13-119 [73296]
      2. region c:5-119 [73298]
      3. region f:5-119 [73300]
4. Aclacinomycin-10-hydroxylase RdmB [101035]
  evolved a different function; binds SAM and SAH
  1. Streptomyces purpurascens [TaxId: 1924] [101036] (4)
    SQ Q54527
    1. 1qzz
      complexed with act, sam
      1. region a:10-101 [96719]
    2. 1r00
      complexed with act, sah
      1. region a:10-101 [96721]
    3. 1xds
      complexed with dra, sam
      1. region a:10-101 [115174]
      2. region b:10-101 [115176]
    4. 1xdu
      complexed with act, sfg
      1. region a:10-101 [115178]
5. Carminomycin 4-O-methyltransferase [109667]
  1. Streptomyces peucetius [TaxId: 1950] [109668] (2)
    SQ Q06528
    1. 1tw3
      complexed with ert, sah
      1. region a:14-98 [107373]
      2. region b:14-98 [107375]
    2. 1tw2
      complexed with ert, sah
      1. region a:14-98 [107369]
      2. region b:14-98 [107371]
Linker histone H1/H5 [46827] (3)
1. Histone H5, globular domain [46828]
  1. Chicken (Gallus gallus) [TaxId: 9031] [46829] (1)
    1. 1hst
      1. chain a [16140]
      2. chain b [16141]
2. Histone H1, globular domain [46830]
  1. Chicken (Gallus gallus) [TaxId: 9031] [46831] (1)
    1. 1ghc
      1. chain a [16142]
3. Histone H1 homologue Hho1p [101037]
  duplication: contains two similar globular domains
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101038] (4)
    1. 1ust
      N-terminal globular domain, GI
      1. chain a [99884]
    2. 1uss
      C-terminal globular domain, GII
      1. chain a [99883]
    3. 1yqa
      mutant
      1. region a:171-257 [123875]
    4. 1uhm
      N-terminal globular domain, GI
      1. chain a [99398]
Forkhead DNA-binding domain [46832] (6)
1. Afx (Foxo4) [46833]
  1. Human (Homo sapiens) [TaxId: 9606] [46834] (2)
    1. 3bpy
      automatically matched to d1e17a_
      complexed with mg
      1. region a:93-177 [155490]
    2. 1e17
      1. chain a [16143]
2. Adipocyte-transcription factor FREAC-11 (s12, fkh-14) [46835]
  1. Human (Homo sapiens) [TaxId: 9606] [46836] (1)
    1. 1d5v
      1. chain a [16144]
3. Interleukin enhancer binding factor [88984]
  1. Human (Homo sapiens) [TaxId: 9606] [88985] (3)
    1. 2c6y
      automatically matched to d1jxsa_
      complexed with mg
      1. region a:1-98 [130011]
    2. 2c6y
      automatically matched to d1jxsa_
      complexed with mg
      1. region b:1-96 [130012]
    3. 1jxs
      1. chain a [84254]
4. Genesis [46837]
  1. Rat (Rattus norvegicus) [TaxId: 10116] [46838] (2)
    1. 2hfh
      1. chain a [16145]
    2. 2hdc
      1. chain a [16146]
5. HFH-1 (HNF-3 forkhead homolog-1) [46839]
  1. Rat (Rattus norvegicus) [TaxId: 10116] [46840] (1)
    1. 1kq8
      1. chain a [68797]
6. Forkhead box protein P2, FOXP2 [140265]
  1. Human (Homo sapiens) [TaxId: 9606] [140266] (8)
    SQ O15409 503-584
    1. 2a07
      complexed with mg; mutant
      1. region f:503-584 [125938]
    2. 2a07
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region g:506-584 [125939]
    3. 2a07
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region h:506-584 [125940]
    4. 2a07
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region i:503-583 [125941]
    5. 2a07
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region j:503-584 [125942]
    6. 2a07
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region k:503-584 [125943]
    7. 2as5
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region f:503-584 [127235]
    8. 2as5
      automatically matched to 2A07 F:503-584
      complexed with mg; mutant
      1. region g:503-584 [127236]
DNA-binding domain from rap30 [46841] (1)
1. DNA-binding domain from rap30 [46842]
  1. Human (Homo sapiens) [TaxId: 9606] [46843] (2)
    1. 2bby
      1. chain a [16148]
    2. 1bby
      1. chain a [16149]
C-terminal domain of the rap74 subunit of TFIIF [63480] (1)
1. C-terminal domain of the rap74 subunit of TFIIF [63481]
  peptide-recognition motif
  1. Human (Homo sapiens) [TaxId: 9606] [63482] (4)
    1. 1i27
      complexed with zn; mutant
      1. chain a [61555]
    2. 1j2x
      complexed with Fcp1 C-terminal peptide, chain B
      complexed with so4, zn
      1. chain a [77066]
    3. 1nha
      1. chain a [80509]
    4. 1onv
      complexed with Fcp1 C-terminal peptide, chain B
      1. chain a [87171]
C-terminal domain of RPA32 [46844] (1)
1. C-terminal domain of RPA32 [46845]
  peptide-recognition motif
  1. Human (Homo sapiens) [TaxId: 9606] [46846] (2)
    1. 1dpu
      complexed with the fragment 73-88 of uracil DNA glycosylase UNG2
      1. chain a [16150]
    2. 1z1d
      automatically matched to d1dpua_
      1. region a:202-270 [124351]
DEP domain [63483] (5)
membrane-binding domain
1. Segment polarity protein Dishevelled-1 [63484]
  1. Mouse (Mus musculus) [TaxId: 10090] [63485] (1)
    1. 1fsh
      1. chain a [60006]
2. Regulatory domain of epac2, domain 2 [81693]
  1. Mouse (Mus musculus) [TaxId: 10090] [81694] (1)
    1. 1o7f
      1. region a:180-321 [81131]
3. Pleckstrin [101039]
  1. Mouse (Mus musculus) [TaxId: 10090] [101040] (1)
    1. 1uhw
      1. chain a [99410]
  2. Human (Homo sapiens) [TaxId: 9606] [116790] (2)
    SQ P08567 125-219 # structure of the N-terminal PH domain (1-105) is also known (scop_sp 50741)
    1. 2cso
      1. region a:8-122 [130778]
    2. 1w4m
      1. chain a [114193]
4. Pleckstrin 2 [101041]
  1. Mouse (Mus musculus) [TaxId: 10090] [101042] (1)
    1. 1v3f
      1. chain a [100289]
Cell cycle transcription factor e2f-dp [46847] (2)
heterodimer of two homologous chains
1. Cell cycle transcription factor E2F-4 [88652]
  1. Human (Homo sapiens) [TaxId: 9606] [88653] (1)
    1. 1cf7
      1. chain a [16151]
2. Cell cycle transcription factor DP-2 [88654]
  1. Human (Homo sapiens) [TaxId: 9606] [88655] (1)
    1. 1cf7
      1. chain b [16152]
The central core domain of TFIIE beta [46850] (1)
1. The central core domain of TFIIE beta [46851]
  1. Human (Homo sapiens) [TaxId: 9606] [46852] (2)
    1. 1d8j
      1. chain a [16153]
    2. 1d8k
      1. chain a [16154]
Z-DNA binding domain [46853] (4)
Pfam 02295
1. Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 [46854]
  1. Human (Homo sapiens) [TaxId: 9606] [46855] (9)
    1. 1xmk
      2nd Z-alpha domain
      complexed with cd, cl, ni
      1. region a:294-366 [122165]
    2. 2gxb
      automatically matched to d1qbjc_
      complexed with du, na
      1. region a:140-198 [135830]
    3. 2gxb
      automatically matched to d1qbjc_
      complexed with du, na
      1. region b:140-199 [135831]
    4. 1qbj
      protein/DNA complex
      1. chain a [16155]
      2. chain b [16156]
      3. chain c [16157]
    5. 2acj
      automatically matched to d1qbjc_
      1. region a:140-199 [126555]
    6. 2acj
      automatically matched to d1qbjc_
      1. region b:140-199 [126556]
    7. 2acj
      automatically matched to d1qbjc_
      1. region c:140-199 [126557]
    8. 2acj
      automatically matched to d1qbjc_
      1. region d:140-199 [126558]
    9. 1qgp
      mutant
      1. chain a [16158]
2. Dlm-1 [63486]
  1. Mouse (Mus musculus) [TaxId: 10090] [63487] (1)
    1. 1j75
      1. chain a [62673]
3. dsRNA-binding protein E3 (E3L) [101043]
  1. Vaccinia virus [TaxId: 10245] [101044] (1)
    1. 1oyi
      1. chain a [93729]
4. 34L [109669]
  1. Yaba-like disease virus, YLDV [TaxId: 132475] [109670] (1)
    SQ Q9DHS8 1-75
    1. 1sfu
      1. chain a [105503]
      2. chain b [105504]
P4 origin-binding domain-like [46856] (2)
C-terminus passes through the first loop
1. Class II MHC transcription factor RFX1 [46857]
  1. Human (Homo sapiens) [TaxId: 9606] [46858] (1)
    1. 1dp7
      complexed with bro, edo, peg; mutant
      1. chain p [16159]
2. P4 origin-binding domain [74688]
  1. Bacteriophage P4 [TaxId: 10680] [74689] (1)
    1. 1ka8
      1. chain a [72241]
      2. chain b [72242]
      3. chain c [72243]
      4. chain d [72244]
      5. chain e [72245]
      6. chain f [72246]
ets domain [46859] (9)
1. Fli-1 [46860]
  1. Human (Homo sapiens) [TaxId: 9606] [46861] (1)
    1. 1fli
      protein/DNA complex
      1. chain a [16160]
2. ETS-1 transcription factor, residues 331-440 [46862]
  1. Mouse (Mus musculus) [TaxId: 10090] [46863] (6)
    SQ P27577 301-440
    1. 1md0
      1. chain a [79000]
      2. chain b [79001]
    2. 1k78
      1. chain b [68257]
      2. chain f [68260]
    3. 1k79
      1. chain a [68262]
      2. chain d [68263]
    4. 1k7a
      1. chain a [68264]
      2. chain d [68265]
    5. 1mdm
      1. chain b [79012]
    6. 1r36
      mutant
      1. chain a [111675]
  2. Human (Homo sapiens) [TaxId: 9606] [46864] (3)
    1. 1gvj
      1. chain a [90525]
      2. chain b [90526]
    2. 2stt
      protein/DNA complex
      1. chain a [16163]
    3. 2stw
      protein/DNA complex
      1. chain a [16164]
3. Transcription factor PU.1, residues 171-259 [46865]
  1. Mouse (Mus musculus) [TaxId: 10090] [46866] (1)
    1. 1pue
      protein/DNA complex
      1. chain e [16165]
      2. chain f [16166]
4. GA binding protein (GABP) alpha [46867]
  1. Mouse (Mus musculus) [TaxId: 10090] [46868] (1)
    1. 1awc
      protein/DNA complex; complexed with bro
      1. chain a [16167]
5. Serum response factor accessory protein 1a, SAP-1 [46869]
  1. Human (Homo sapiens) [TaxId: 9606] [46870] (4)
    1. 1bc8
      protein/DNA complex; complexed with zn
      1. chain c [16168]
    2. 1bc7
      protein/DNA complex
      1. chain c [16169]
    3. 1k6o
      1. chain a [68226]
    4. 1hbx
      1. chain g [60934]
      2. chain h [60935]
6. Elk-1 [46871]
  1. Human (Homo sapiens) [TaxId: 9606] [46872] (1)
    1. 1dux
      1. chain c [16170]
      2. chain f [16171]
7. Sam pointed domain containing ets transcription SPDEF [140267]
  1. Human (Homo sapiens) [TaxId: 9606] [140268] (1)
    SQ O95238 247-334
    1. 1yo5
      1. region c:247-334 [123768]
8. E74-like factor 5 ese-2b [140269]
  1. Human (Homo sapiens) [TaxId: 9606] [140270] (1)
    SQ Q9UKW6 173-265
    1. 1wwx
      1. region a:8-101 [121379]
Heat-shock transcription factor [46873] (2)
1. Heat-shock transcription factor [46874]
  1. Drosophila melanogaster [TaxId: 7227] [46875] (2)
    1. 1hks
      1. chain a [16172]
    2. 1hkt
      1. chain a [16173]
  2. Milk yeast (Kluyveromyces lactis) [TaxId: 28985] [46876] (9)
    1. 2hts
      complexed with acy
      1. chain a [16174]
    2. 3hts
      protein/DNA complex; complexed with gol
      1. chain b [16175]
    3. 1fbu
      1. chain a [16176]
      2. chain b [16177]
    4. 1fbs
      mutant
      1. chain a [16180]
      2. chain b [16181]
    5. 1fbq
      mutant
      1. chain a [16178]
      2. chain b [16179]
    6. 1fym
      mutant
      1. chain a [65070]
      2. chain b [65071]
    7. 1fyl
      complexed with bro; mutant
      1. chain a [65068]
      2. chain b [65069]
    8. 1fyk
      mutant
      1. chain a [65067]
    9. 3hsf
      mutant
      1. chain a [16182]
Interferon regulatory factor [46877] (3)
Pfam 00605
1. Interferon regulatory factor 1 (IRF-1) [46878]
  1. Mouse (Mus musculus) [TaxId: 10090] [46879] (1)
    1. 1if1
      protein/DNA complex
      1. chain a [16183]
      2. chain b [16184]
2. Interferon regulatory factor-2, IRF-2 [46880]
  1. Mouse (Mus musculus) [TaxId: 10090] [46881] (3)
    1. 2irf
      complexed with ido, k
      1. chain g [16185]
      2. chain h [16186]
      3. chain i [16187]
      4. chain j [16188]
      5. chain k [16189]
      6. chain l [16190]
    2. 1irg
      1. chain a [16191]
    3. 1irf
      1. chain a [16192]
3. Interferon regulatory factor 3, IRF-3 [116791]
  1. Human (Homo sapiens) [TaxId: 9606] [116792] (9)
    SQ Q14653 3-112
    1. 2pi0
      automatically matched to d1t2ka_
      1. region a:5-110 [149489]
    2. 2pi0
      automatically matched to d1t2ka_
      1. region b:3-112 [149490]
    3. 2pi0
      automatically matched to d1t2ka_
      1. region c:4-110 [149491]
    4. 2pi0
      automatically matched to d1t2ka_
      1. region d:3-111 [149492]
    5. 2o6g
      automatically matched to d1t2ka_
      1. region e:3-112 [148628]
    6. 2o6g
      automatically matched to d1t2ka_
      1. region f:4-111 [148629]
    7. 2o6g
      automatically matched to d1t2ka_
      1. region g:3-112 [148630]
    8. 2o6g
      automatically matched to d1t2ka_
      1. region h:4-111 [148631]
    9. 1t2k
      mutant
      1. chain a [112220]
      2. chain b [112221]
39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1)
1. 39 kda initiator binding protein, IBP39, N-terminal domain [101046]
  1. Trichomonas vaginalis [TaxId: 5722] [101047] (2)
    1. 1pp7
      complexed with zn
      1. chain u [94973]
    2. 1pp8
      complexed with so4
      1. chain f [94974]
      2. chain m [94975]
      3. chain o [94976]
      4. chain p [94977]
      5. chain u [94978]
      6. chain v [94979]
Iron-dependent repressor protein [46882] (3)
1. Diphtheria toxin repressor (DtxR) [46883]
  1. Corynebacterium diphtheriae [TaxId: 1717] [46884] (17)
    SQ P33120
    1. 1g3w
      complexed with cd, so4; mutant
      1. region a:4-64 [65133]
    2. 2dtr
      complexed with co, so4
      1. region a:4-64 [16193]
    3. 1g3s
      mutant
      1. region a:4-64 [65124]
    4. 1bi1
      1. region a:4-64 [16196]
    5. 1xcv
      automatically matched to d1p92a1
      complexed with ni; mutant
      1. region a:1-64 [121862]
    6. 1bi0
      complexed with so4, zn
      1. region a:4-64 [16202]
    7. 1fwz
      complexed with so4, zn; mutant
      1. region a:4-64 [60077]
    8. 1p92
      complexed with bme; mutant
      1. region a:1-64 [104085]
    9. 1bi3
      complexed with so4, zn
      1. region a:4-64 [16199]
      2. region b:4-64 [16200]
    10. 1g3t
      mutant
      1. region a:3-64 [65127]
      2. region b:1003-1064 [65130]
    11. 1bi2
      1. region a:3-64 [16197]
      2. region b:3-64 [16198]
    12. 1g3y
      complexed with zn; mutant
      1. region a:3-64 [65136]
    13. 2tdx
      complexed with ni; mutant
      1. region a:1-64 [16201]
    14. 1f5t
      protein/DNA complex; complexed with ni; mutant
      1. region a:1002-1064 [16203]
      2. region b:2002-2064 [16204]
      3. region c:3002-3064 [16205]
      4. region d:4002-4064 [16206]
    15. 1ddn
      protein/DNA complex; complexed with ni; mutant
      1. region a:3-64 [16207]
      2. region b:3-64 [16208]
      3. region c:3-64 [16209]
      4. region d:3-64 [16210]
    16. 1dpr
      1. region a:3-64 [16194]
      2. region b:3-64 [16195]
    17. 1c0w
      protein/DNA complex; complexed with co
      1. region a:2-64 [16211]
      2. region b:2-64 [16212]
      3. region c:2-64 [16213]
      4. region d:2-64 [16214]
2. Iron-dependent regulator IdeR [46885]
  1. Mycobacterium tuberculosis [TaxId: 1773] [46886] (13)
    SQ Q50495
    1. 2isy
      automatically matched to d1b1ba1
      complexed with ni, po4
      1. region a:2-64 [137612]
    2. 2isy
      automatically matched to d1b1ba1
      complexed with ni, po4
      1. region b:2-64 [137614]
    3. 1fx7
      complexed with co, so4
      1. region a:1-64 [60088]
      2. region b:1-64 [60091]
      3. region c:1-64 [60094]
      4. region d:1-64 [60097]
    4. 2isz
      automatically matched to d1b1ba1
      complexed with na, ni
      1. region a:2-64 [137616]
    5. 2isz
      automatically matched to d1b1ba1
      complexed with na, ni
      1. region b:2-64 [137618]
    6. 2isz
      automatically matched to d1b1ba1
      complexed with na, ni
      1. region c:2-64 [137620]
    7. 2isz
      automatically matched to d1b1ba1
      complexed with na, ni
      1. region d:2-64 [137622]
    8. 2it0
      automatically matched to d1b1ba1
      complexed with act, ni
      1. region a:3-64 [137624]
    9. 2it0
      automatically matched to d1b1ba1
      complexed with act, ni
      1. region b:3-64 [137626]
    10. 2it0
      automatically matched to d1b1ba1
      complexed with act, ni
      1. region c:3-64 [137628]
    11. 2it0
      automatically matched to d1b1ba1
      complexed with act, ni
      1. region d:3-64 [137630]
    12. 1u8r
      complexed with co, na
      1. region a:1-64 [113168]
      2. region b:1-64 [113171]
      3. region c:1-64 [113174]
      4. region d:1-64 [113177]
      5. region g:1-64 [113180]
      6. region h:1-64 [113183]
      7. region i:1-64 [113186]
      8. region j:1-64 [113189]
    13. 1b1b
      1. region a:1-64 [16215]
3. Manganese transport regulator MntR [88986]
  1. Bacillus subtilis [TaxId: 1423] [88987] (20)
    1. 2ev0
      automatically matched to d1on1a1
      complexed with cd
      1. region a:2-62 [132413]
    2. 2ev0
      automatically matched to d1on1a1
      complexed with cd
      1. region b:2-62 [132415]
    3. 1on2
      complexed with mn; mutant
      1. region a:2-62 [87103]
      2. region b:2-62 [87105]
    4. 2ev6
      automatically matched to d1on1a1
      complexed with flc, gol, zn
      1. region a:4-62 [132421]
    5. 2ev6
      automatically matched to d1on1a1
      complexed with flc, gol, zn
      1. region b:4-62 [132423]
    6. 1on1
      complexed with mn
      1. region a:2-62 [87099]
      2. region b:2-62 [87101]
    7. 2f5d
      automatically matched to d1on1a1
      complexed with mn
      1. region a:3-62 [132979]
    8. 2f5d
      automatically matched to d1on1a1
      complexed with mn
      1. region b:2-62 [132981]
    9. 2ev5
      automatically matched to d1on1a1
      complexed with ca
      1. region a:3-62 [132417]
    10. 2ev5
      automatically matched to d1on1a1
      complexed with ca
      1. region b:4-62 [132419]
    11. 2f5e
      automatically matched to d1on1a1
      complexed with mn
      1. region a:2-62 [132983]
    12. 2f5e
      automatically matched to d1on1a1
      complexed with mn
      1. region b:2-62 [132985]
    13. 2f5f
      automatically matched to d1on1a1
      complexed with mn
      1. region a:4-62 [132987]
    14. 2f5f
      automatically matched to d1on1a1
      complexed with mn
      1. region b:2-62 [132989]
    15. 2f5c
      automatically matched to d1on1a1
      complexed with mn, so4
      1. region a:3-62 [132977]
    16. 2hyf
      automatically matched to d1on1a1
      complexed with epe, so4
      1. region a:3-62 [136880]
    17. 2hyf
      automatically matched to d1on1a1
      complexed with epe, so4
      1. region b:3-62 [136882]
    18. 2hyf
      automatically matched to d1on1a1
      complexed with epe, so4
      1. region c:3-62 [136884]
    19. 2hyf
      automatically matched to d1on1a1
      complexed with epe, so4
      1. region d:3-62 [136886]
    20. 2hyg
      automatically matched to d1on1a1
      1. region d:3-62 [136888]
Dissimilatory sulfite reductase DsvD [101048] (1)
1. Dissimilatory sulfite reductase DsvD [101049]
  1. Desulfovibrio vulgaris [TaxId: 881] [101050] (3)
    1. 1ucr
      complexed with so4
      1. chain a [99188]
      2. chain b [99189]
    2. 1wq2
      automatically matched to d1ucrb_
      complexed with so4
      1. region a:1-70 [121161]
    3. 1wq2
      automatically matched to d1ucrb_
      complexed with so4
      1. region b:1-68 [121162]
La domain [101051] (3)
Pfam 05383; RNA-binding domain
1. Lupus La autoantigen N-terminal domain [101052]
  1. Human (Homo sapiens) [TaxId: 9606] [101053] (12)
    1. 1zh5
      automatically matched to d1s7aa_
      complexed with so4
      1. region a:5-103 [125073]
    2. 1zh5
      automatically matched to d1s7aa_
      complexed with so4
      1. region b:6-103 [125075]
    3. 2voo
      automatically matched to d1s7aa_
      1. region a:10-103 [153373]
    4. 2voo
      automatically matched to d1s7aa_
      1. region b:9-103 [153375]
    5. 2vod
      automatically matched to d1s7aa_
      1. region a:6-103 [153365]
    6. 2vod
      automatically matched to d1s7aa_
      1. region b:6-103 [153367]
    7. 2von
      automatically matched to d1s7aa_
      1. region a:6-103 [153369]
    8. 2von
      automatically matched to d1s7aa_
      1. region b:7-103 [153371]
    9. 1yty
      automatically matched to d1s7aa_
      1. region a:6-103 [124018]
    10. 1yty
      automatically matched to d1s7aa_
      1. region b:7-103 [124020]
    11. 2vop
      automatically matched to d1s7aa_
      complexed with so4
      1. region a:8-103 [153377]
    12. 1s7a
      1. chain a [98633]
  2. Trypanosoma brucei [TaxId: 5691] [101054] (1)
    1. 1s29
      1. chain a [98373]
2. La-related protein 4 LARP4 [140271]
  C-mpl binding protein
  1. Human (Homo sapiens) [TaxId: 9606] [140272] (1)
    SQ Q71RC2 112-199
    1. 2cqk
      1. region a:43-130 [130725]
Methionine aminopeptidase, insert domain [46887] (2)
circularly permuted version of the "winged helix" fold
1. Methionine aminopeptidase, insert domain [46888]
  1. Archaeon Pyrococcus furiosus [TaxId: 2261] [46889] (4)
    1. 1xgs
      complexed with co
      1. region a:195-271 [16216]
      2. region b:195-271 [16217]
    2. 1xgn
      complexed with co
      1. region a:195-271 [16218]
      2. region b:195-271 [16219]
    3. 1xgm
      complexed with co
      1. region a:195-271 [16220]
      2. region b:195-271 [16221]
    4. 1xgo
      1. region a:195-271 [16222]
  2. Human (Homo sapiens) [TaxId: 9606] [46890] (18)
    SQ P50579 110-478
    1. 1b6a
      1. region a:375-448 [16223]
    2. 1qzy
      complexed with co, tbu, tde
      1. region a:375-448 [96717]
    3. 1bn5
      complexed with co, tbu
      1. region a:375-448 [16224]
    4. 1b59
      1. region a:375-448 [16225]
    5. 1yw9
      automatically matched to d1b59a1
      complexed with a84, mn
      1. region a:375-448 [124138]
    6. 1boa
      complexed with co, fum
      1. region a:375-448 [16226]
    7. 1kq9
      complexed with met, tbu, zn
      1. region a:375-448 [91021]
    8. 1kq0
      complexed with med, tbu, zn
      1. region a:375-448 [91018]
    9. 1yw7
      automatically matched to d1b59a1
      complexed with a41, mn
      1. region a:375-448 [124134]
    10. 1r58
      complexed with ao5, mn
      1. region a:375-448 [111695]
    11. 2ga2
      automatically matched to d1b59a1
      complexed with a19, mn
      1. region a:375-448 [134852]
    12. 1r5g
      complexed with ao1, mn
      1. region a:375-448 [111702]
    13. 2oaz
      automatically matched to d1b59a1
      complexed with co, i96
      1. region a:375-448 [138999]
    14. 1r5h
      complexed with ao2, mn
      1. region a:375-448 [111704]
    15. 2adu
      automatically matched to d1b59a1
      complexed with co, r20; mutant
      1. region a:375-448 [126595]
    16. 2ea2
      automatically matched to d1b59a1
      complexed with f77, mn
      1. region a:375-448 [146757]
    17. 2ea4
      automatically matched to d1b59a1
      complexed with f79, mn
      1. region a:375-448 [146759]
    18. 1yw8
      automatically matched to d1b59a1
      complexed with a75, mn
      1. region a:375-448 [124136]
PCI domain (PINT motif) [109671] (2)
Pfam 01399
1. COP9 signalosome complex subunit 4, GSN4 [109672]
  1. Mouse (Mus musculus) [TaxId: 10090] [109673] (1)
    SQ O88544 296-366
    1. 1ufm
      Structural genomics target
      1. chain a [107816]
2. Hypothetical protein C20orf116 homolog [116793]
  1. Mouse (Mus musculus) [TaxId: 10090] [116794] (1)
    SQ Q80WW9 216-274
    1. 1wi9
      Structural genomics target
      1. chain a [114663]
F93-like [109674] (3)
contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
1. Hypothetical protein F93 [109675]
  1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [109676] (1)
    SQ P20222
    1. 1tbx
      1. chain a [106748]
      2. chain b [106749]
2. Uncharacterized protein APE0880.1 [158290]
  1. Aeropyrum pernix [TaxId: 56636] [158291] (2)
    SQ Q9YDN4 1-92
    1. 2pg4
      complexed with cit, cl, edo, peg
      1. region a:1-92 [149455]
    2. 2pg4
      automatically matched to 2PG4 A:1-92
      complexed with cit, cl, edo, peg
      1. region b:3-92 [149456]
3. STIV F93 [158292]
  different dimerization mode than SSV1 F93
  1. Sulfolobus turreted icosahedral virus [TaxId: 269145] [158293] (2)
    SQ Q6Q0J9 5-93
    1. 2co5
      1. region a:5-93 [146418]
    2. 2co5
      automatically matched to 2CO5 A:5-93
      1. region b:5-93 [146419]
Archaeal DNA-binding protein [109677] (1)
contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
1. Sso10a (SSO10449) [109678]
  1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [109679] (3)
    SQ Q5W1E8
    1. 1r7j
      1. chain a [104836]
    2. 1xsx
      automatically matched to d1r7ja_
      1. region a:3-92 [122289]
    3. 1xsx
      automatically matched to d1r7ja_
      1. region b:3-92 [122290]
TrmB-like [109680] (2)
The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
1. Hypothetical protein AF2008 [109681]
  1. Archaeoglobus fulgidus [TaxId: 2234] [109682] (1)
    SQ O28271
    1. 1sfx
      Structural genomics target
      complexed with cl, edo
      1. chain a [105505]
      2. chain b [105506]
2. Hypothetical transcriptional regulator ST1889 [140273]
  1. Sulfolobus tokodaii [TaxId: 111955] [140274] (2)
    SQ Q96ZE4 1-109
    1. 2d1h
      1. region a:1-109 [131125]
    2. 2d1h
      automatically matched to 2D1H A:1-109
      1. region b:1-109 [131126]
Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1)
similar domain organization to the transcriptional regulator IclR
1. Heat-inducible transcription repressor HrcA, N-terminal domain [109684]
  1. Thermotoga maritima [TaxId: 2336] [109685] (1)
    SQ Q9WZV5
    1. 1stz
      Structural genomics target
      1. region a:14-100 [106009]
      2. region b:11-95 [106011]
      3. region c:11-95 [106013]
DNA replication factor Cdt1 [109686] (1)
1. DNA replication factor Cdt1 [109687]
  1. Mouse (Mus musculus) [TaxId: 10090] [109688] (1)
    SQ Q8R4E9 179-365
    1. 1wlq
      1. chain c [109400]
      2. chain f [109403]
Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1)
C-terminal part of Pfam 06272
1. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109690]
  1. Human (Homo sapiens) [TaxId: 9606] [109691] (1)
    SQ Q9UBQ5
    1. 1rz4
      complexed with so4
      1. region a:132-216 [105131]
Vacuolar sorting protein domain [109692] (3)
duplication: tandem repeat of two "winged-helix" domains
1. Vacuolar sorting protein SNF8 [109693]
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109694] (2)
    SQ Q12483 20-232
    1. 1u5t
      1. region a:20-164 [107684]
      2. region a:165-232 [107685]
    2. 1w7p
      1. region a:20-164 [114319]
      2. region a:165-232 [114320]
2. Vacuolar protein sorting-associated protein VPS36 [109695]
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109696] (2)
    SQ Q06696 396-566
    1. 1u5t
      1. region b:396-489 [107686]
      2. region b:490-564 [107687]
    2. 1w7p
      1. region d:396-449 [114325]
      2. region d:450-566 [114326]
3. Vacuolar protein sorting-associated protein VPS25 [109697]
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109698] (10)
    SQ P47142
    1. 1xb4
      automatically matched to d1u5tc1
      1. region a:2-125 [121832]
    2. 1xb4
      automatically matched to d1u5tc2
      1. region a:126-199 [121833]
    3. 1xb4
      automatically matched to d1u5tc1
      1. region b:2-125 [121834]
    4. 1xb4
      automatically matched to d1u5tc2
      1. region b:126-199 [121835]
    5. 1xb4
      automatically matched to d1u5tc1
      1. region c:3-125 [121836]
    6. 1xb4
      automatically matched to d1u5tc2
      1. region c:126-199 [121837]
    7. 1xb4
      automatically matched to d1u5tc1
      1. region d:2-125 [121838]
    8. 1xb4
      automatically matched to d1u5tc2
      1. region d:126-199 [121839]
    9. 1u5t
      1. region c:2-125 [107688]
      2. region c:126-199 [107689]
      3. region d:2-125 [107690]
      4. region d:126-199 [107691]
    10. 1w7p
      1. region b:1-125 [114321]
      2. region b:126-199 [114322]
      3. region c:1-125 [114323]
      4. region c:126-199 [114324]
Transcriptional regulator Rrf2 [109699] (2)
Pfam 02082
1. Hypothetical protein ywnA [109700]
  1. Bacillus subtilis [TaxId: 1423] [109701] (1)
    SQ P71036 4-130
    1. 1xd7
      complexed with so4
      1. chain a [109566]
2. Hypothetical protein BC1842 [140275]
  1. Bacillus cereus [TaxId: 1396] [140276] (3)
    SQ Q81EX1 5-142
    1. 1ylf
      complexed with cl
      1. region a:5-142 [123648]
    2. 1ylf
      automatically matched to 1YLF A:5-142
      complexed with cl
      1. region b:7-140 [123649]
    3. 1ylf
      automatically matched to 1YLF A:5-142
      complexed with cl
      1. region c:6-142 [123650]
Rio2 serine protein kinase N-terminal domain [109702] (1)
1. Rio2 serine protein kinase N-terminal domain [109703]
  1. Archaeoglobus fulgidus [TaxId: 2234] [109704] (5)
    SQ O30245 # AF2426
    1. 1zar
      automatically matched to d1tqia1
      complexed with adp, edo, mn
      1. region a:2-90 [124843]
    2. 1zao
      automatically matched to d1tqia1
      complexed with atp, edo, mn, po4
      1. region a:1-90 [124841]
    3. 1tqi
      complexed with edo
      1. region a:1-90 [107226]
    4. 1tqm
      complexed with anp
      1. region a:1-90 [107236]
    5. 1tqp
      complexed with atp
      1. region a:1-90 [107240]
Rad21/Rec8-like [116795] (1)
Pfam 04824
1. Sister chromatid cohesion protein 1 (SCC1), C-terminal domain [116796]
  1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116797] (1)
    SQ Q12158 483-561
    1. 1w1w
      complexed with atg, mg
      1. chain e [114084]
      2. chain f [114085]
      3. chain g [114086]
      4. chain h [114087]
Hypothetical protein PH1932 [116798] (1)
contains new dimerisation all-alpha C-terminal subdomain
1. Hypothetical protein PH1932 [116799]
  1. Pyrococcus horikoshii [TaxId: 53953] [116800] (2)
    SQ O59595
    1. 1uly
      1. chain a [113297]
    2. 2cwe
      1. region a:2-192 [130921]
An Obfc1 domain [116801] (1)
helix-loop insertion in the HTH motif
1. OB fold-containing protein 1, Obfc1 [116802]
  1. Mouse (Mus musculus) [TaxId: 10090] [116803] (1)
    SQ Q8K2X3 198-304
    1. 1wj5
      Structural genomics target
      1. chain a [114692]
ScpB/YpuH-like [116804] (1)
Pfam 04079
duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
1. Segregation and condensation protein B, ScpB [116805]
  1. Chlorobium tepidum [TaxId: 1097] [116806] (1)
    SQ Q8KF54 1-162
    1. 1t6s
      Structural genomics target
      complexed with no3
      1. region a:1-85 [112271]
      2. region a:86-162 [112272]
      3. region b:1-85 [112273]
      4. region b:86-162 [112274]
PadR-like [116807] (3)
Pfam 03551; related to the MarR-like family (Pfam 01047)
1. Predicted transcriptional regulator [116808]
  monomeric
  1. Clostridium thermocellum [TaxId: 1515] [116809] (1)
    SQ Q4CEJ8 4-106
    1. 1xma
      complexed with hg, unx
      1. chain a [115477]
      2. chain b [115478]
2. Hypothetical protein AphA [116810]
  contains extra C-terminal dimerisation domain
  1. Vibrio cholerae [TaxId: 666] [116811] (1)
    SQ Q9X399 # "winged helix" domain: 1-87, dimerisation domain: 91-179
    1. 1yg2
      Structural genomics target
      1. chain a [116681]
3. Hypothetical protein TM0937 [140277]
  1. Thermotoga maritima [TaxId: 2336] [140278] (1)
    SQ Q9X035 4-117
    1. 2esh
      complexed with ca
      1. region a:4-117 [132325]
Hypothetical protein YhgG [116812] (1)
1. Hypothetical protein YhgG [116813]
  1. Escherichia coli [TaxId: 562] [116814] (1)
    SQ P64638
    1. 1xn7
      Structural genomics target
      1. chain a [115576]
ROK associated domain [140279] (3)
found N-terminal to ROK domain in some proteins
1. Mlc protein N-terminal domain [140280]
  1. Escherichia coli [TaxId: 562] [140281] (6)
    SQ P50456 12-81
    1. 1z6r
      complexed with zn; mutant
      1. region a:12-81 [124557]
    2. 1z6r
      automatically matched to 1Z6R A:12-81
      complexed with zn; mutant
      1. region b:12-81 [124560]
    3. 1z6r
      automatically matched to 1Z6R A:12-81
      complexed with zn; mutant
      1. region c:12-81 [124563]
    4. 1z6r
      automatically matched to 1Z6R A:12-81
      complexed with zn; mutant
      1. region d:12-81 [124566]
    5. 3bp8
      automatically matched to d1z6ra1
      complexed with act, zn
      1. region a:12-81 [155463]
    6. 3bp8
      automatically matched to d1z6ra1
      complexed with act, zn
      1. region b:12-81 [155466]
2. N-acetylglucosamine kinase [140282]
  Transcriptional regulator, XylR-related
  1. Thermotoga maritima [TaxId: 2336] [140283] (1)
    SQ Q9X0V1 10-71
    1. 2hoe
      complexed with gol, k
      1. region a:10-71 [136639]
3. Transcriptional regulator VC2007 N-terminal domain [140284]
  1. Vibrio cholerae [TaxId: 666] [140285] (1)
    SQ Q9KQJ1 10-80
    1. 1z05
      complexed with bme, gol, so4, zn
      1. region a:10-80 [124298]
PF1790-like [140286] (1)
sequence similarity to PH1932 in the N-terminal domain; the C-terminal domain provides new dimerisation interface made of a beta-hairpin and a coiled coil
1. Transcriptional regulatory protein PF1790 [140287]
  1. Pyrococcus furiosus [TaxId: 2261] [140288] (2)
    SQ Q8U030 1-194
    1. 2p4w
      automatically matched to 1XNP A:1-194
      complexed with so4
      1. region a:1-194 [139495]
    2. 2p4w
      automatically matched to 1XNP A:1-194
      complexed with so4
      1. region b:1-194 [139496]
MukF N-terminal domain-like [140289] (1)
N-terminal part of Pfam 03882
1. Chromosome partition protein MukF (KicB), N-terminal domain [140290]
  1. Escherichia coli [TaxId: 562] [140291] (2)
    SQ P60293 8-118
    1. 1t98
      1. region a:8-118 [119196]
    2. 1t98
      automatically matched to 1T98 A:8-118
      1. region b:8-118 [119198]
CodY HTH domain [140292] (1)
Pfam 08222
1. GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain [140293]
  1. Bacillus subtilis [TaxId: 1423] [140294] (3)
    SQ P39779 167-257
    1. 2b0l
      1. region a:167-257 [127641]
    2. 2b0l
      automatically matched to 2B0L A:167-257
      1. region b:167-257 [127642]
    3. 2b0l
      automatically matched to 2B0L A:167-257
      1. region c:167-256 [127643]
FtsK C-terminal domain-like [140295] (2)
PfamB 000224
1. DNA translocase FtsK [140296]
  1. Escherichia coli [TaxId: 562] [140297] (1)
    SQ P46889 1261-1329
    1. 2j5p
      1. region a:1261-1329 [138050]
  2. Pseudomonas aeruginosa [TaxId: 287] [140298] (15)
    SQ Q9I0M3 742-811
    1. 2ve8
      automatically matched to d2j5oa1
      1. region a:745-811 [153008]
    2. 2ve8
      automatically matched to d2j5oa1
      1. region b:745-809 [153009]
    3. 2ve8
      automatically matched to d2j5oa1
      1. region c:746-810 [153010]
    4. 2ve8
      automatically matched to d2j5oa1
      1. region d:745-811 [153011]
    5. 2ve8
      automatically matched to d2j5oa1
      1. region e:745-810 [153012]
    6. 2ve8
      automatically matched to d2j5oa1
      1. region f:745-809 [153013]
    7. 2ve8
      automatically matched to d2j5oa1
      1. region g:747-807 [153014]
    8. 2ve8
      automatically matched to d2j5oa1
      1. region h:747-809 [153015]
    9. 2ve9
      automatically matched to d2j5oa1
      complexed with mg
      1. region a:746-808 [153016]
    10. 2ve9
      automatically matched to d2j5oa1
      complexed with mg
      1. region b:747-808 [153017]
    11. 2ve9
      automatically matched to d2j5oa1
      complexed with mg
      1. region c:746-808 [153018]
    12. 2ve9
      automatically matched to d2j5oa1
      complexed with mg
      1. region d:747-809 [153019]
    13. 2ve9
      automatically matched to d2j5oa1
      complexed with mg
      1. region e:747-809 [153020]
    14. 2ve9
      automatically matched to d2j5oa1
      complexed with mg
      1. region f:745-808 [153021]
    15. 2j5o
      1. region a:742-811 [138049]
Nudix-associated domain [140299] (2)
PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
1. Hypothetical protein BT0354, C-terminal domain [140300]
  1. Bacteroides thetaiotaomicron [TaxId: 818] [140301] (4)
    SQ Q8AAV8 150-225
    1. 2fb1
      complexed with po4
      1. region a:150-225 [133225]
    2. 2fb1
      automatically matched to 2FB1 A:150-225
      complexed with po4
      1. region b:150-225 [133227]
    3. 2fb1
      automatically matched to 2FB1 A:150-225
      complexed with po4
      1. region c:150-225 [133229]
    4. 2fb1
      automatically matched to 2FB1 A:150-225
      complexed with po4
      1. region d:150-225 [133231]
2. Hypothetical protein EF2700, C-terminal domain [140302]
  1. Enterococcus faecalis [TaxId: 1351] [140303] (2)
    SQ Q830S2 205-268
    1. 2fml
      complexed with gol
      1. region a:205-268 [133778]
    2. 2fml
      automatically matched to 2FML A:205-268
      complexed with gol
      1. region b:205-268 [133780]
HxlR-like [140304] (5)
Pfam 01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (scop_fa 46801)
1. Hypothetical protein PG0823 [140305]
  1. Porphyromonas gingivalis [TaxId: 837] [140306] (2)
    SQ Q7M7B7 3-104
    1. 2fsw
      1. region a:3-104 [134042]
    2. 2fsw
      automatically matched to 2FSW A:3-104
      1. region b:3-104 [134043]
2. Hypothetical protein PA1607 [140307]
  includes extra C-terminal SH3-like subdomain, which is segment-swapped in the dimer
  1. Pseudomonas aeruginosa [TaxId: 287] [140308] (2)
    SQ Q9I3B4 5-146
    1. 2f2e
      complexed with glc, so4
      1. region a:5-146 [132808]
    2. 2f2e
      automatically matched to 2F2E A:5-146
      complexed with glc, so4
      1. region b:6-145 [132809]
3. Hypothetical protein EF0647 [140309]
  1. Enterococcus faecalis [TaxId: 1351] [140310] (2)
    SQ Q838C3 1-108
    1. 1z7u
      complexed with fmt
      1. region a:1-108 [124672]
    2. 1z7u
      automatically matched to 1Z7U A:1-108
      complexed with fmt
      1. region b:1-107 [124673]
4. Putative transcriptional regulator YtfH [140311]
  1. Salmonella typhimurium [TaxId: 90371] [140312] (2)
    SQ Q7CP90 9-122
    1. 1yyv
      complexed with cl, mly
      1. region a:9-122 [124254]
    2. 1yyv
      automatically matched to 1YYV A:9-122
      complexed with cl, mly
      1. region b:12-122 [124255]
5. Putative transcriptional regulator YtcD [158294]
  1. Bacillus subtilis [TaxId: 1423] [158295] (4)
    SQ O34533 10-104
    1. 2hzt
      complexed with csu
      1. region a:4-98 [147462]
    2. 2hzt
      automatically matched to 2HZT A:4-98
      complexed with csu
      1. region b:4-98 [147463]
    3. 2hzt
      automatically matched to 2HZT A:4-98
      complexed with csu
      1. region c:4-98 [147464]
    4. 2hzt
      automatically matched to 2HZT A:4-98
      complexed with csu
      1. region d:4-98 [147465]
Marine metagenome family WH1 [158296] (1)
1. Hypothetical protein GOS_3836187 [158297]
  1. Environmental samples [158298] (1)
    marine metagenome
    1. 2od5
      complexed with 1pe, cl, edo, imd
      1. region a:6-96 [148736]
ReutB4095-like [158299] (1)
probable biological unit is a homohexamer
1. Putative DNA-binding protein ReutB4095 [158300]
  1. Ralstonia eutropha [TaxId: 106590] [158301] (2)
    SQ Q46TT3 12-92
    1. 2obp
      complexed with cl, no3
      1. region a:12-92 [148718]
    2. 2obp
      automatically matched to 2OBP A:12-92
      complexed with cl, no3
      1. region b:12-92 [148719]
PH0730 N-terminal domain-like [158302] (1)
1. Hypothetical protein PH0730 [158303]
  1. Pyrococcus horikoshii [TaxId: 53953] [158304] (1)
    SQ O58461 28-96
    1. 2p8t
      mutant
      1. region a:14-82 [149315]
FaeA-like [158305] (1)
Pfam 04703
1. P fimbrial regulatory protein PapI [158306]
  KS71A
  1. Escherichia coli [TaxId: 562] [158307] (1)
    SQ P62584 5-77
    1. 2htj
      1. region a:1-73 [147397]
STY4665 C-terminal domain-like [158308] (1)
Pfam 07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel
1. Hypothetical protein STY4665 [158309]
  1. Salmonella typhi [TaxId: 90370] [158310] (1)
    SQ Q8Z1C5 396-528
    1. 2ipq
      1. region x:396-528 [147770]
PSPTO2686-like [158311] (1)
Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
1. Hypothetical protein PSPTO2686 [158312]
  1. Pseudomonas syringae pv. tomato [TaxId: 323] [158313] (2)
    SQ Q882E2 13-96! SQ Q882E2 97-180
    1. 3bz6
      1. region a:13-96 [155739]
    2. 3bz6
      1. region a:97-180 [155740]
RHA1_ro06458-like [158314] (1)
1. Hypothetical protein RHA1_ro06458 [158315]
  1. Rhodococcus sp. RHA1 [TaxId: 101510] [158316] (1)
    SQ Q0S2K3 1-85
    1. 2ns0
      complexed with edo, gol
      1. region a:1-85 [148381]
YjcQ-like [158317] (1)
Pfam 09639
1. Uncharacterized protein YjcQ [158318]
  1. Bacillus subtilis [TaxId: 1423] [158319] (1)
    SQ O31639 5-82
    1. 2hgc
      1. region a:5-82 [147283]
F112-like [158320] (1)
1. F-112 [158321]
  1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [158322] (1)
    SQ P20220 4-73
    1. 2vqc
      1. region a:4-73 [153426]
MerB N-terminal domain-like [158323] (1)
1. Alkylmercury lyase MerB [158324]
  1. Escherichia coli [TaxId: 562] [158325] (1)
    SQ P77072 21-80
    1. 1s6l
      1. region a:21-80 [145773]
CED-4 C-terminal domain-like [158326] (1)
similar domain architecture to AAA+ helicases
1. Cell death protein 4, CED-4 [158327]
  1. Caenorhabditis elegans [TaxId: 6239] [158328] (1)
    SQ P30429 386-543
    1. 2a5y
      complexed with atp, mg; mutant
      1. region b:386-543 [144786]
ELL N2 domain-like [158329] (1)
PfamB 026212; includes recent PDB entry 2e5n
1. RNA polymerase II elongation factor ELL [158330]
  1. Human (Homo sapiens) [TaxId: 9606] [158331] (1)
    SQ P55199 197-297
    1. 2doa
      1. region a:8-98 [146548]
PF0610-like [158332] (1)
PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
1. Hypothetical protein PF0610 [158333]
  1. Pyrococcus furiosus [TaxId: 2261] [158334] (1)
    SQ Q8U362 1-105
    1. 2gmg
      1. region a:1-105 [147131]
Rv2827c N-terminal domain-like [158335] (1)
~80 N-terminal residues of Pfam 09407' DUF2005
1. Hypothetical protein Rv2827c [158336]
  1. Mycobacterium tuberculosis [TaxId: 1773] [158337] (2)
    SQ P71625 1-82
    1. 1zel
      complexed with act, fmt, mpd, na
      1. region a:1-82 [145994]
    2. 1zel
      automatically matched to 1ZEL A:1-82
      complexed with act, fmt, mpd, na
      1. region b:1-82 [145996]
Rps19E-like [158338] (1)
Pfam 01090; local sequence similarity to members of the GntR-like family
1. Ribosomal protein S19e [158339]
  1. Pyrococcus abyssi [TaxId: 29292] [158340] (1)
    SQ Q9V0G8 2-150
    1. 2v7f
      complexed with cl
      1. region a:2-150 [152721]
RPO3F domain-like [158341] (2)
middle region of Pfam 05158
1. DNA-directed RNA polymerase III subunit RPC6, RPO3F [158342]
  1. Mouse (Mus musculus) [TaxId: 10090] [158343] (1)
    SQ Q921X6 11-79
    1. 2dk8
      1. region a:8-75 [146535]
  2. Human (Homo sapiens) [TaxId: 9606] [158344] (1)
    SQ Q9H1D9 78-155
    1. 2dk5
      mutant
      1. region a:8-85 [146534]