Structural Classification of Proteins

Fold: Four-helical up-and-down bundle

: core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down

Lineage:

Root: scop
Class: All alpha proteins [46456]
Fold: Four-helical up-and-down bundle [47161]
core: 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down

Superfamilies:

Apolipoprotein [47162] (1)
uperfamily
1. Apolipoprotein [47163] (3)
  Can exist in a coiled-coil oligomeric form, see PDB entry 1AV1
  family may also include the five-helical bundle protein Apolipophorin-III
  1. Apolipoprotein E [88703]
    1. Human (Homo sapiens), E3 [TaxId: 9606] [47165] (7)
      1. 1h7i
        mutant
        
        chain a [60725]
      2. 1nfn
        
        chain a [16523]
      3. 1ea8
        mutant
        
        chain a [59400]
      4. 1lpe
        
        chain a [16524]
      5. 1bz4
        truncation mutant 165
        
        chain a [16521]
      6. 1or3
        truncation mutant 165
        
        chain a [16522]
      7. 1or2
        truncation mutant 165
        
        chain a [16525]
    2. Human (Homo sapiens), E2 [TaxId: 9606] [47167] (2)
      1. 1nfo
        mutant
        
        chain a [16526]
      2. 1le2
        mutant
        
        chain a [16527]
    3. Human (Homo sapiens), E4 [TaxId: 9606] [47169] (3)
      1. 1gs9
        mutant
        
        chain a [83313]
      2. 1b68
        
        chain a [59076]
      3. 1le4
        mutant
        
        chain a [16528]
Aspartate receptor, ligand-binding domain [47170] (1)
uperfamily
1. Aspartate receptor, ligand-binding domain [47171] (2)
  1. Aspartate receptor, ligand-binding domain [47172]
    1. Escherichia coli [TaxId: 562] [47173] (1)
      1. 2asr
        complexed with so4
        
        chain a [16529]
    2. Salmonella typhimurium [TaxId: 90371] [47174] (7)
      1. 2lig
        complexed with phn, so4; mutant
        
        chain a [16530]
        chain b [16531]
      2. 1vls
        
        chain a [16532]
      3. 1lih
        complexed with phn; mutant
        
        chain a [16535]
      4. 1vlt
        
        chain a [16533]
        chain b [16534]
      5. 1jmw
        mutant
        
        chain a [63181]
      6. 1was
        
        chain a [16536]
      7. 1wat
        
        chain a [16537]
        chain b [16538]
Cytochromes [47175] (2)
Heme-containing proteins
uperfamily
1. Cytochrome b562 [47176] (1)
  1. Cytochrome b562 [47177]
    1. Escherichia coli [TaxId: 562] [47178] (6)
      1. 256b
        complexed with hem, so4
        
        chain a [16539]
        chain b [16540]
      2. 1m6t
        b562ril, a redesigned four helix bundle
        complexed with so4; mutant
        
        chain a [78705]
      3. 1lm3
        complexed with hem, mg; mutant
        
        chain b [74027]
        chain d [74028]
      4. 1qq3
        complexed with heb; mutant
        
        chain a [16541]
      5. 1qpu
        complexed with hem
        
        chain a [16542]
      6. 1apc
        apo-form
        
        chain a [16543]
2. Cytochrome c'-like [47179] (9)
  1. Cytochrome c' [47180]
    1. Rhodospirillum molischianum [TaxId: 1083] [47181] (1)
      1. 2ccy
        complexed with hem
        
        chain a [16544]
        chain b [16545]
    2. Chromatium vinosum [TaxId: 1049] [47182] (1)
      1. 1bbh
        complexed with hem
        
        chain a [16546]
        chain b [16547]
    3. Alcaligenes denitrificans [TaxId: 32002] [47183] (1)
      1. 1cgn
        complexed with hem
        
        chain a [16548]
    4. Alcaligenes sp. [TaxId: 512] [47184] (5)
      1. 1e85
        complexed with hec, nmo
        
        chain a [16549]
      2. 1e84
        complexed with hec
        
        chain a [16552]
      3. 1cgo
        complexed with hem
        
        chain a [16550]
      4. 1e86
        complexed with cmo, hec
        
        chain a [16551]
      5. 1e83
        complexed with hec
        
        chain a [16553]
    5. Rhodocyclus gelatinosus [TaxId: 28068] [47185] (5)
      1. 2j8w
        automatically matched to d1jafa_
        complexed with hem
        
        region a:1-128 [147931]
      2. 2j8w
        automatically matched to d1jafa_
        complexed with hem
        
        region b:1-128 [147932]
      3. 2j9b
        automatically matched to d1jafa_
        complexed with hem
        
        region a:1-127 [147935]
      4. 2j9b
        automatically matched to d1jafa_
        complexed with hem
        
        region b:1-128 [147936]
      5. 1jaf
        complexed with hem
        
        chain a [16554]
        chain b [16555]
    6. Rhodobacter capsulatus [TaxId: 1061] [47186] (4)
      1. 1cpq
        complexed with hem
        
        chain a [16556]
      2. 1rcp
        complexed with hem
        
        chain a [16557]
        chain b [16558]
      3. 1cpr
        complexed with hem, zn
        
        chain a [16559]
      4. 1nbb
        complexed with hem, nbn
        
        chain a [16560]
        chain b [16561]
    7. Rhodobacter sphaeroides [TaxId: 1063] [81734] (1)
      1. 1gqa
        complexed with hec
        
        chain a [76275]
        chain d [76276]
    8. Rhodopseudomonas palustris [TaxId: 1076] [47187] (2)
      1. 1mqv
        complexed with hem; mutant
        
        chain a [79415]
        chain b [79416]
      2. 1a7v
        complexed with hem
        
        chain a [16562]
        chain b [16563]
  2. Cytochrome c-556 [101109]
    1. Rhodopseudomonas palustris [TaxId: 1076] [101110] (1)
      1. 1s05
        complexed with hem
        
        chain a [98254]
Hemerythrin-like [47188] (1)
uperfamily
1. Hemerythrin-like [47189] (3)
  Iron-binding proteins
  1. Hemerythrin [47190]
    1. Sipunculid worm (Themiste dyscritum) [TaxId: 6436] [47191] (4)
      1. 2hmz
        complexed with act, fea
        
        chain a [16564]
        chain b [16565]
        chain c [16566]
        chain d [16567]
      2. 2hmq
        complexed with act, feo
        
        chain a [16568]
        chain b [16569]
        chain c [16570]
        chain d [16571]
      3. 1hmd
        complexed with ace, feo
        
        chain a [16572]
        chain b [16573]
        chain c [16574]
        chain d [16575]
      4. 1hmo
        complexed with ace, feo, oxy
        
        chain a [16576]
        chain b [16577]
        chain c [16578]
        chain d [16579]
    2. Phascolopsis gouldii [TaxId: 6442] [47192] (4)
      1. 1i4y
        complexed with cl, feo
        
        chain a [61738]
        chain b [61739]
        chain c [61740]
        chain d [61741]
        chain e [61742]
        chain f [61743]
        chain g [61744]
        chain h [61745]
      2. 1i4z
        complexed with feo; mutant
        
        chain a [61746]
        chain b [61747]
        chain c [61748]
        chain d [61749]
        chain e [61750]
        chain f [61751]
        chain g [61752]
        chain h [61753]
      3. 1hrb
        complexed with fe
        
        chain a [16580]
      4. 1hrb
        duplicate of 1HRB
        complexed with fe
        
        chain b [118511]
  2. Myohemerythin [47193]
    1. Sipunculan worm (Themiste zostericola) [TaxId: 6437] [47194] (3)
      1. 2mhr
        complexed with azi, feo, so4
        
        chain a [16581]
      2. 1a7d
        complexed with cfo, cl
        
        chain a [16582]
      3. 1a7e
        complexed with cl, ofo; mutant
        
        chain a [16583]
TMV-like viral coat proteins [47195] (1)
uperfamily
1. TMV-like viral coat proteins [47196] (3)
  1. Tobacco mosaic virus coat protein [47197]
    1. Tobacco mosaic virus, vulgare strain [TaxId: 12242] [47198] (4)
      1. 1ei7
        
        chain a [16584]
        chain b [16585]
      2. 2tmv
        complexed with ca
        
        chain p [16586]
      3. 1vtm
        
        chain p [16587]
      4. 2om3
        automatically matched to d1ei7a_
        
        region a:1-154 [148865]
  2. Cucumber green mottle mosaic virus [47199]
    1. Cucumber green mottle mosaic virus, strain watermelon [TaxId: 12235] [47200] (1)
      1. 1cgm
        
        chain e [16588]
  3. Ribgrass mosaic virus [47201]
    1. Ribgrass mosaic virus [TaxId: 51680] [47202] (1)
      1. 1rmv
        protein/RNA complex; complexed with ace
        
        chain a [16589]
FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47212] (1)
uperfamily
1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47213] (1)
  1. FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) [47214]
    1. Human (Homo sapiens) [TaxId: 9606] [47215] (7)
      1. 3fap
        complexed with ard
        
        chain b [16612]
      2. 1nsg
        complexed with rpx
        
        chain b [16613]
      3. 2fap
        complexed with rad
        
        chain b [16614]
      4. 4fap
        complexed with ard
        
        chain b [16617]
      5. 1aue
        
        chain a [16615]
        chain b [16616]
      6. 1fap
        complexed with rap
        
        chain b [16618]
      7. 2gaq
        automatically matched to d1fapb_
        
        region a:4-98 [134893]
Proteasome activator [47216] (1)
uperfamily
1. Proteasome activator [47217] (2)
  1. Proteasome activator reg(alpha) [47218]
    The structure of the proteasome complex with this protein from (Trypanosoma brucei) is available (1fnt); however, PDB entry 1FNT designates protein chains by both upper case and lower case letters creating problems with its processing and presentation; the proteasome activator pa26 chains are designated by lower case letters (c;d;e;f;g;h;i;j;k;l;m;n;o;p)
    1. Human (Homo sapiens) [TaxId: 9606] [47219] (1)
      1. 1avo
        
        chain a,b [16619]
        chain c,d [16620]
        chain e,f [16621]
        chain g,h [16622]
        chain i,j [16623]
        chain k,l [16624]
        chain m,n [16625]
  2. Proteasome activator protein PA26 [158392]
    1. Trypanosoma brucei [TaxId: 5691] [158393] (21)
      SQ Q9U8G2 4-231
      1. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region o:4-231 [144615]
      2. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region p:4-231 [144616]
      3. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region q:4-231 [144617]
      4. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region r:4-231 [144618]
      5. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region s:4-231 [144619]
      6. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region t:4-231 [144620]
      7. 1yar
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region u:4-231 [144621]
      8. 1ya7
        complexed with gol, so4
        
        region o:4-231 [144608]
      9. 1ya7
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4
        
        region p:4-231 [144609]
      10. 1ya7
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4
        
        region q:4-231 [144610]
      11. 1ya7
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4
        
        region r:4-231 [144611]
      12. 1ya7
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4
        
        region s:4-231 [144612]
      13. 1ya7
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4
        
        region t:4-231 [144613]
      14. 1ya7
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4
        
        region u:4-231 [144614]
      15. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region o:4-231 [144622]
      16. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region p:4-231 [144623]
      17. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region q:4-231 [144624]
      18. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region r:4-231 [144625]
      19. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region s:4-231 [144626]
      20. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region t:4-231 [144627]
      21. 1yau
        automatically matched to 1YA7 O:4-231
        complexed with gol, so4; mutant
        
        region u:4-231 [144628]
alpha-catenin/vinculin-like [47220] (2)
uperfamily
1. alpha-catenin/vinculin [47221] (4)
  possible duplication: contains several domains of this fold
  The listed PDB entries contain different large fragments but not the whole proteins
  1. alpha-catenin [47222]
    1. Mouse (Mus musculus) [TaxId: 10090] [47223] (2)
      1. 1dov
        N-terminal, dimerization and beta-catenin binding domain
        
        chain a [16627]
      2. 1dow
        chimera of the N-terminal domain of alpha-catenin and beta-catenin fragment (chain B)
        
        chain a [16626]
    2. Human (Homo sapiens) [TaxId: 9606] [63511] (2)
      1. 1h6g
        middle domain; contains two domains of this fold
        complexed with ca, cl, mpd
        
        region a:377-507 [60669]
        region a:508-631 [60670]
        region b:392-507 [60671]
        region b:508-632 [60672]
      2. 1l7c
        CASP4
        complexed with mse
        
        region a:388-507 [73647]
        region a:508-631 [73648]
        region b:391-507 [73649]
        region b:508-631 [73650]
        region c:393-507 [73651]
        region c:508-631 [73652]
  2. Vinculin [47224]
    1. Chicken (Gallus gallus) [TaxId: 9031] [47225] (3)
      SQ P12003
      1. 1qkr
        tail domain
        complexed with so4
        
        chain a [16628]
        chain b [16629]
      2. 1t01
        complexed with Talin 1 fragment (SQ P26039 605-628), chain B
        
        region a:1-125 [106188]
        region a:126-252 [106189]
      3. 1st6
        full-length protein containing eight four-helix bundle domains
        
        region a:1-125 [106000]
        region a:126-252 [106001]
        region a:253-371 [106002]
        region a:372-488 [106003]
        region a:489-646 [106004]
        region a:647-718 [106005]
        region a:719-855 [106006]
        region a:875-1065 [106007]
    2. Human (Homo sapiens) [TaxId: 9606] [101111] (4)
      SQ P18206 1-257
      1. 1syq
        head domain; contains two domains of this fold; complexed with talin fragment, chain B (SQ Q9Y490 607-631)
        
        region a:1-128 [106124]
        region a:129-257 [106125]
      2. 1rke
        head domain; contains two domains of this fold; complexed with separate tail domain of the same or closely related protein
        
        region a:-3-128 [97608]
        region a:129-258 [97609]
      3. 1rke
        tail domain; complexed with separate head domain of the same or closely related protein
        
        chain b [97610]
      4. 1rkc
        head domain; contains two domains of this fold; complexed with talin fragment, chain B
        
        region a:1-128 [97606]
        region a:129-258 [97607]
2. VBS domain [140408] (1)
  Pfam 08913; Vinculin Binding Site
  1. Talin 1 [140409]
    1. Mouse (Mus musculus) [TaxId: 10090] [140410] (1)
      SQ P26039 1838-1973
      1. 2b0h
        3rd VBS
        
        region a:1838-1973 [127638]
FAT domain of focal adhesion kinase [68993] (1)
uperfamily
1. FAT domain of focal adhesion kinase [68994] (3)
  1. FAT domain of focal adhesion kinase [68995]
    1. Human (Homo sapiens) [TaxId: 9606] [68996] (9)
      1. 1k04
        swapped dimer
        complexed with cl
        
        chain a [67904]
      2. 2ra7
        automatically matched to d1k04a_
        complexed with act, c4c, zn
        
        region a:921-1048 [151820]
      3. 1ow6
        complexed with paxillin ld4 motif, chains D and F
        
        chain a [93631]
        chain b [93632]
        chain c [93633]
      4. 1ow7
        complexed with paxillin ld4 motif, chains D, E and F
        
        chain a [93634]
        chain b [93635]
        chain c [93636]
      5. 1k05
        
        chain a [67905]
        chain b [67906]
        chain c [67907]
      6. 1ow8
        complexed with paxillin ld2 motif, chains D and F
        
        chain a [93637]
        chain b [93638]
        chain c [93639]
      7. 3b71
        automatically matched to d1k04a_
        
        region a:916-1049 [154912]
      8. 3b71
        automatically matched to d1k04a_
        
        region b:916-1047 [154913]
      9. 3b71
        automatically matched to d1k04a_
        
        region c:916-1047 [154914]
    2. Mouse (Mus musculus) [TaxId: 10090] [68997] (1)
      1. 1k40
        
        chain a [68123]
    3. Chicken (Gallus gallus) [TaxId: 9031] [81735] (3)
      SQ Q00944 RE 920-1053
      1. 1qvx
        
        chain a [96448]
      2. 1pv3
        
        chain a [104321]
      3. 1ktm
        
        chain a [77541]
Oxygen-evolving enhancer protein 3, [101112] (1)
uperfamily
1. Oxygen-evolving enhancer protein 3, [101113] (1)
  1. Oxygen-evolving enhancer protein 3, [101114]
    PsbQ protein of photosystem II
    1. Spinach (Spinacia oleracea) [TaxId: 3562] [101115] (1)
      1. 1nze
        complexed with zn
        
        chain a [92374]
Histidine-containing phosphotransfer domain, HPT domain [47226] (6)
contains additional, fifth helix at the N-terminus
uperfamily
1. Aerobic respiration control sensor protein, ArcB [47227] (1)
  1. Aerobic respiration control sensor protein, ArcB [47228]
    1. Escherichia coli [TaxId: 562] [47229] (4)
      1. 2a0b
        complexed with zn
        
        chain a [16630]
      2. 1a0b
        complexed with zn
        
        chain a [16631]
      3. 1bdj
        complexed with so4
        
        chain b [16632]
      4. 1fr0
        
        chain a [59996]
2. Phosphorelay protein-like [47230] (3)
  1. Phosphorelay protein ypd1 [47231]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [47232] (6)
      1. 2r25
        automatically matched to d1c03a_
        complexed with bef, mg, na
        
        region a:2-167 [151529]
      2. 1c02
        
        chain a [16633]
        chain b [16634]
      3. 1oxk
        complexed with so4
        
        chain a [93690]
        chain c [93692]
        chain e [93694]
        chain g [93696]
        chain i [93698]
        chain k [93700]
      4. 1oxb
        complexed with so4
        
        chain a [93681]
      5. 1c03
        
        chain a [16635]
        chain b [16636]
        chain c [16637]
        chain d [16638]
      6. 1qsp
        
        chain a [16639]
        chain b [16640]
  2. Histidine-containing phosphotransfer protein HP2 [140411]
    1. Maize (Zea mays) [TaxId: 4577] [140412] (4)
      SQ Q9SLX1 9-139
      1. 1wn0
        
        region a:9-139 [121070]
      2. 1wn0
        automatically matched to 1WN0 A:9-139
        
        region b:11-138 [121071]
      3. 1wn0
        automatically matched to 1WN0 A:9-139
        
        region c:9-139 [121072]
      4. 1wn0
        automatically matched to 1WN0 A:9-139
        
        region d:9-139 [121073]
  3. Histidine-containing phosphotransfer protein HP1 [140413]
    1. Rice (Oryza sativa) [TaxId: 4530] [140414] (4)
      SQ Q6VAK4 2-143
      1. 1yvi
        
        region a:2-143 [124099]
      2. 1yvi
        automatically matched to 1YVI A:2-143
        
        region b:3-142 [124100]
      3. 2q4f
        automatically matched to 1YVI A:2-143
        
        region a:2-143 [139847]
      4. 2q4f
        automatically matched to 1YVI A:2-143
        
        region b:3-142 [139848]
3. Chemotaxis protein CheA P1 domain [63512] (2)
  1. Chemotaxis protein CheA P1 domain [63513]
    1. Salmonella typhimurium [TaxId: 90371] [63514] (1)
      1. 1i5n
        complexed with so4
        
        chain a [61805]
        chain b [61806]
        chain c [61807]
        chain d [61808]
    2. Thermotoga maritima [TaxId: 2336] [109765] (1)
      SQ Q56310 4-104
      1. 1tqg
        
        chain a [107224]
4. Sensor-like histidine kinase YojN, C-terminal domain [116868] (1)
  1. Sensor-like histidine kinase YojN, C-terminal domain [116869]
    1. Escherichia coli [TaxId: 562] [116870] (1)
      SQ P39838 775-890
      1. 1sr2
        
        chain a [112109]
5. Phosphorelay protein luxU [116871] (1)
  1. Phosphorelay protein luxU [116872]
    1. Vibrio harveyi [TaxId: 669] [116873] (1)
      SQ Q9ZBB6
      1. 1y6d
        
        chain a [116504]
6. SphA-like [158394] (1)
  1. Histidine phosphotransferase ShpA [158395]
    1. Caulobacter crescentus [TaxId: 155892] [158396] (2)
      SQ A0EJF9 8-111
      1. 2ooc
        complexed with gol, pg4
        
        region a:8-111 [148919]
      2. 2ooc
        automatically matched to 2OOC A:8-111
        complexed with gol, pg4
        
        region b:8-111 [148920]
Bacterial GAP domain [47233] (1)
contains extra helices in the loops at one end of the bundle
uperfamily
1. Bacterial GAP domain [47234] (3)
  1. ExoS toxin [47235]
    1. Pseudomonas aeruginosa [TaxId: 287] [47236] (2)
      1. 1he1
        complexed with af3, gdp, mg, ni
        
        chain a [16641]
        chain b [16642]
      2. 1he9
        
        chain a [60971]
  2. SptP tyrosine phosphatase [47237]
    1. Salmonella typhimurium [TaxId: 90371] [47238] (2)
      1. 1g4u
        complexed with af3, gdp, mg; mutant
        
        region s:167-296 [16643]
      2. 1g4w
        
        region r:171-290 [16644]
  3. YopE [68998]
    1. Yersinia pestis [TaxId: 632] [68999] (1)
      1. 1hy5
        
        chain a [65955]
        chain b [65956]
Outer surface protein C (OspC) [63515] (1)
uperfamily
1. Outer surface protein C (OspC) [63516] (1)
  1. Outer surface protein C (OspC) [63517]
    1. Lyme disease spirochete (Borrelia burgdorferi), different strains [TaxId: 139] [63518] (3)
      1. 1f1m
        complexed with zn; mutant
        
        chain a [59598]
        chain b [59599]
        chain c [59600]
        chain d [59601]
      2. 1g5z
        
        chain a [60298]
      3. 1ggq
        complexed with mg
        
        chain a [60486]
        chain b [60487]
        chain c [60488]
        chain d [60489]
Flagellar export chaperone FliS [101116] (1)
can form closed, open and helix-swapped bundles
uperfamily
1. Flagellar export chaperone FliS [101117] (2)
  1. Flagellar export chaperone FliS [101118]
    1. Aquifex aeolicus [TaxId: 63363] [101119] (2)
      1. 1orj
        
        chain a [93456]
        chain b [93457]
        chain c [93458]
        chain d [93459]
      2. 1ory
        complexed with a flagelin fragment, chain B
        complexed with po4; mutant
        
        chain a [93466]
    2. Bacillus subtilis [TaxId: 1423] [101120] (1)
      1. 1vh6
        structural genomics; swapped dimer
        
        chain a [100644]
        chain b [100645]
Domain of the SRP/SRP receptor G-proteins [47364] (1)
uperfamily
1. Domain of the SRP/SRP receptor G-proteins [47365] (7)
  1. Signal sequence recognition protein Ffh [47366]
    1. Thermus aquaticus [TaxId: 271] [47367] (25)
      1. 1ls1
        complexed with mo5, oxy
        
        region a:1-88 [78170]
      2. 2j45
        automatically matched to d2ffha1
        complexed with ca, edo, mes, mrd, na
        
        region a:1-88 [137983]
      3. 2j45
        automatically matched to d2ffha1
        complexed with ca, edo, mes, mrd, na
        
        region b:1-88 [137985]
      4. 2j46
        automatically matched to d2ffha1
        complexed with act, cl, mn, mrd
        
        region a:1-88 [137987]
      5. 2j46
        automatically matched to d2ffha1
        complexed with act, cl, mn, mrd
        
        region b:1-88 [137989]
      6. 2c04
        automatically matched to d2ffha1
        complexed with ca, gcp
        
        region a:1-88 [129570]
      7. 2c04
        automatically matched to d2ffha1
        complexed with ca, gcp
        
        region b:1-88 [129572]
      8. 2c03
        automatically matched to d2ffha1
        complexed with dio, edo, gdp
        
        region a:1-88 [129566]
      9. 2c03
        automatically matched to d2ffha1
        complexed with dio, edo, gdp
        
        region b:1-88 [129568]
      10. 1okk
        complexed with bzp, edo, gcp, mo3, so4
        
        region a:4-88 [93259]
      11. 1rj9
        complexed with gcp, mg
        
        region b:14-88 [97555]
      12. 1ffh
        complexed with mo5
        
        region a:2-88 [16960]
      13. 2j7p
        automatically matched to d2ffha1
        complexed with edo, gnp, iod, k, mg
        
        region a:3-88 [138119]
      14. 2j7p
        automatically matched to d2ffha1
        complexed with edo, gnp, iod, k, mg
        
        region b:4-88 [138121]
      15. 1jpn
        complexed with acy, gnp, oc3, oc4
        
        region a:1-88 [67039]
        region b:1-88 [67041]
      16. 1ng1
        complexed with acy, cd, edo, gdp, mo4, mo6
        
        region a:1-88 [16961]
      17. 1o87
        complexed with cl, fmt, gdp, mo4, mo5
        
        region a:1-88 [92640]
        region b:1-88 [92642]
      18. 2ng1
        complexed with dox, edo, gdp; mutant
        
        region a:2-88 [16962]
      19. 3ng1
        complexed with cd, edo, so4
        
        region a:1-88 [16963]
        region b:1-88 [16964]
      20. 2cnw
        automatically matched to d2ffha1
        complexed with 5gp, alf, gdp, mg
        
        region a:4-88 [130649]
      21. 2cnw
        automatically matched to d2ffha1
        complexed with 5gp, alf, gdp, mg
        
        region b:4-88 [130651]
      22. 2cnw
        automatically matched to d2ffha1
        complexed with 5gp, alf, gdp, mg
        
        region c:4-88 [130653]
      23. 1jpj
        complexed with gnp
        
        region a:1-88 [67024]
      24. 2ffh
        complexed with cd, so4; mutant
        
        region a:1-88 [16965]
        region b:1-88 [16966]
        region c:1-88 [16967]
      25. 2iy3
        automatically matched to d2ffha1
        
        region a:1-88 [137790]
    2. Archaeon Acidianus ambivalens [TaxId: 2283] [63538] (2)
      1. 1j8y
        mutant
        
        region f:3-86 [62747]
      2. 1j8m
        
        region f:3-86 [62742]
    3. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101121] (2)
      1. 1qzx
        
        region a:1-87 [96711]
        region b:1-87 [96714]
      2. 1qzw
        complexed with ccc, gtp
        
        region a:1-87 [96699]
        region c:1-87 [96702]
        region e:1-87 [96705]
        region g:1-87 [96708]
  2. Signal recognition particle receptor, FtsY [47368]
    1. Escherichia coli [TaxId: 562] [47369] (2)
      1. 2qy9
        automatically matched to d1ftsa1
        
        region a:201-284 [151469]
      2. 1fts
        
        region a:201-284 [16968]
    2. Thermus aquaticus [TaxId: 271] [101122] (8)
      1. 1okk
        complexed with bzp, edo, gcp, mo3, so4
        
        region d:21-78 [93261]
      2. 1rj9
        complexed with gcp, mg
        
        region a:27-95 [97553]
      3. 2j7p
        automatically matched to d1okkd1
        complexed with edo, gnp, iod, k, mg
        
        region d:22-78 [138123]
      4. 2j7p
        automatically matched to d1okkd1
        complexed with edo, gnp, iod, k, mg
        
        region e:27-78 [138125]
      5. 2iyl
        automatically matched to d1okkd1
        complexed with gdp, so4
        
        region d:21-78 [137801]
      6. 2cnw
        automatically matched to d1okkd1
        complexed with 5gp, alf, gdp, mg
        
        region d:21-78 [130655]
      7. 2cnw
        automatically matched to d1okkd1
        complexed with 5gp, alf, gdp, mg
        
        region e:23-78 [130657]
      8. 2cnw
        automatically matched to d1okkd1
        complexed with 5gp, alf, gdp, mg
        
        region f:26-78 [130659]
    3. Thermotoga maritima [TaxId: 2336] [109766] (1)
      SQ Q9WZ40
      1. 1vma
        Structural genomics target
        complexed with cit, mg
        
        region a:1-81 [108887]
        region b:1-81 [108889]
  3. Signal recognition particle 54 kDa protein, SRP54 [116874]
    1. Mouse (Mus musculus) [TaxId: 10090] [116875] (1)
      SQ P14576 4-85
      1. 1wgw
        Structural genomics target
        
        chain a [114625]
FAD-dependent thiol oxidase [69000] (1)
uperfamily
1. FAD-dependent thiol oxidase [69001] (2)
  1. Thiol oxidase Erv2p [69002]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69003] (2)
      1. 1jr8
        complexed with fad
        
        chain a [67115]
        chain b [67116]
      2. 1jra
        complexed with fad
        
        chain a [67117]
        chain b [67118]
        chain c [67119]
        chain d [67120]
  2. Augmenter of liver regeneration [89018]
    a mammalian FAD-dependent sulfhydryl oxidase
    1. Rat (Rattus norvegicus) [TaxId: 10116] [89019] (1)
      1. 1oqc
        complexed with fad
        
        chain a [87264]
        chain b [87265]
        chain c [87266]
        chain d [87267]
Group V grass pollen allergen [81736] (1)
uperfamily
1. Group V grass pollen allergen [81737] (2)
  1. Pollen allergen Phl P 6 [81738]
    1. Timothy grass (Phleum pratense) [TaxId: 15957] [81739] (1)
      1. 1nlx
        complexed with ars, zn
        
        chain a [80637]
        chain b [80638]
        chain c [80639]
        chain d [80640]
        chain e [80641]
        chain f [80642]
        chain g [80643]
        chain h [80644]
        chain i [80645]
        chain j [80646]
        chain k [80647]
        chain l [80648]
        chain m [80649]
        chain n [80650]
  2. Functional domain of pollen allergen Phl P 5b [89020]
    1. Timothy grass (Phleum pratense) [TaxId: 15957] [89021] (1)
      1. 1l3p
        complexed with mg, po4
        
        chain a [84520]
Nucleotidyltransferase substrate binding subunit/domain [81593] (4)
uperfamily
1. Family 1 bi-partite nucleotidyltransferase subunit [81740] (2)
  1. Hypothetical protein HI0074 [81741]
    function unknown; form complex with putative catalytic subunit HI0073 (see 1no5)
    1. Haemophilus influenzae [TaxId: 727] [81742] (1)
      1. 1jog
        structural genomics
        complexed with mse
        
        chain a [77142]
        chain b [77143]
        chain c [77144]
        chain d [77145]
  2. Probable nucleotidyltransferase subunit TTHA0048 [116876]
    1. Thermus thermophilus [TaxId: 274] [116877] (5)
      SQ Q5SM95
      Structural genomics target
      1. 1wty
        Structural genomics target
        
        chain a [114880]
        chain b [114881]
        chain c [114882]
        chain d [114883]
      2. 2ywa
        automatically matched to d1wtya_
        
        region a:2-116 [153807]
      3. 2ywa
        automatically matched to d1wtya_
        
        region b:2-116 [153808]
      4. 2ywa
        automatically matched to d1wtya_
        
        region c:3-116 [153809]
      5. 2ywa
        automatically matched to d1wtya_
        
        region d:2-116 [153810]
2. HEPN domain [89022] (2)
  1. Hypothetical protein TM0613 [89023]
    Family 5 probable bi-partite nucleotidyltransferase subunit; predicted partner is putative catalytic subunit TM0614
    1. Thermotoga maritima [TaxId: 2336] [89024] (1)
      1. 1o3u
        structural genomics
        complexed with mse
        
        chain a [86615]
  2. Hypothetical protein TT1696 [101123]
    1. Thermus thermophilus [TaxId: 274] [101124] (1)
      1. 1ufb
        structural genomics; dimeric structure is more similar to that of HI0074 (1jog) than more closely related TM0613 (1ou3)
        
        chain a [99331]
        chain b [99332]
        chain c [99333]
        chain d [99334]
3. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81592] (1)
  N-terminal catalytic domain is followed by an all-alpha domain
  1. Kanamycin nucleotidyltransferase (KNTase), C-terminal domain [81591]
    1. Staphylococcus aureus [TaxId: 1280] [81590] (2)
      1. 1kny
        complexed with apc, kan, mg; mutant
        
        region a:126-253 [75896]
        region b:126-253 [75898]
      2. 1kan
        CA-atoms only, mutant protein sequence
        
        region a:126-253 [75878]
        region b:126-253 [75880]
4. Glutamine synthase adenylyltransferase GlnE, domain 2 [109767] (1)
  1. Glutamine synthase adenylyltransferase GlnE, domain 2 [109768]
    1. Escherichia coli [TaxId: 562] [109769] (1)
      SQ P30870 1-437
      1. 1v4a
        
        region a:287-437 [108350]
RecG, N-terminal domain [69008] (1)
uperfamily
1. RecG, N-terminal domain [69009] (1)
  1. RecG, N-terminal domain [69010]
    1. Thermotoga maritima [TaxId: 2336] [69011] (1)
      1. 1gm5
        complexed with adp, mg
        
        region a:7-105 [65298]
Colicin D immunity protein [101125] (1)
uperfamily
1. Colicin D immunity protein [101126] (1)
  1. Colicin D immunity protein [101127]
    tRNA-mimic
    1. Escherichia coli [TaxId: 562] [101128] (3)
      1. 1v74
        complexed with 1pe
        
        chain b [100443]
      2. 1tfk
        automatically matched to d1v74b_
        complexed with mes
        
        region b:3-87 [119232]
      3. 1tfo
        automatically matched to d1v74b_
        
        region b:3-87 [119234]
Nickel-containing superoxide dismutase, NiSOD [109770] (1)
uperfamily
1. Nickel-containing superoxide dismutase, NiSOD [109771] (2)
  1. Nickel-containing superoxide dismutase, NiSOD [109772]
    1. Streptomyces seoulensis [TaxId: 73044] [109773] (5)
      SQ P80734
      1. 1q0g
        complexed with ni, so4
        
        chain a [104428]
        chain b [104429]
        chain c [104430]
        chain d [104431]
        chain e [104432]
        chain f [104433]
        chain g [104434]
        chain h [104435]
        chain i [104436]
        chain j [104437]
        chain k [104438]
        chain l [104439]
      2. 1q0m
        complexed with acy, ni, so4
        
        chain a [104458]
        chain b [104459]
        chain c [104460]
        chain d [104461]
        chain e [104462]
        chain f [104463]
      3. 1q0f
        complexed with 3ni, so4
        
        chain a [104416]
        chain b [104417]
        chain c [104418]
        chain d [104419]
        chain e [104420]
        chain f [104421]
        chain g [104422]
        chain h [104423]
        chain i [104424]
        chain j [104425]
        chain k [104426]
        chain l [104427]
      4. 1q0d
        complexed with 3ni, so4
        
        chain a [104404]
        chain b [104405]
        chain c [104406]
        chain d [104407]
        chain e [104408]
        chain f [104409]
        chain g [104410]
        chain h [104411]
        chain i [104412]
        chain j [104413]
        chain k [104414]
        chain l [104415]
      5. 1q0k
        complexed with ni, so4, thj
        
        chain a [104443]
        chain b [104444]
        chain c [104445]
        chain d [104446]
        chain e [104447]
        chain f [104448]
        chain g [104449]
        chain h [104450]
        chain i [104451]
        chain j [104452]
        chain k [104453]
        chain l [104454]
    2. Streptomyces coelicolor [TaxId: 1902] [109774] (3)
      SQ P80735
      1. 1t6u
        complexed with ni; mutant
        
        chain a [106584]
        chain b [106585]
        chain c [106586]
        chain d [106587]
        chain e [106588]
        chain f [106589]
        chain g [106590]
        chain h [106591]
        chain i [106592]
        chain j [106593]
        chain k [106594]
        chain l [106595]
      2. 1t6q
        mutant
        
        chain a [106579]
        chain b [106580]
        chain c [106581]
      3. 1t6i
        mutant
        
        chain a [106571]
        chain b [106572]
        chain c [106573]
Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109775] (1)
contains extra alpha+beta subdomain formed by the N- and C-termini.
uperfamily
1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109776] (1)
  1. Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain [109777]
    1. Mouse (Mus musculus) [TaxId: 10090] [109778] (1)
      SQ Q9DBG5 206-431
      1. 1szi
        
        chain a [106159]
Domain from hypothetical 2610208m17rik protein [109779] (1)
uperfamily
1. Domain from hypothetical 2610208m17rik protein [109780] (1)
  1. Domain from hypothetical 2610208m17rik protein [109781]
    1. Mouse (Mus musculus) [TaxId: 10090] [109782] (1)
      SQ Q8C4Q6 1-115
      1. 1ug7
        Structural genomics target
        
        chain a [107824]
TrmE connector domain [116878] (1)
uperfamily
1. TrmE connector domain [116879] (1)
  1. TrmE connector domain [116880]
    1. Thermotoga maritima [TaxId: 2336] [116881] (2)
      SQ Q9WYA4
      1. 1xzp
        complexed with so4
        
        region a:118-211,a:372-450 [116254]
      2. 1xzq
        complexed with fon
        
        region a:118-211,a:372-450 [116258]
YppE-like [140415] (1)
flattened bundle at one end with helices 2 and coming in contact and separating helices 1 and 3
uperfamily
1. YppE-like [140416] (3)
  Pfam 08807; DUF1798
  1. Hypothetical protein Lin2004 [140417]
    1. Listeria innocua [TaxId: 1642] [140418] (1)
      SQ Q92AB8 1-120
      1. 2huj
        
        region a:1-120 [136777]
  2. Hypothetical protein MW1337 [140419]
    SA1281 ortholog
    1. Staphylococcus aureus [TaxId: 1280] [140420] (1)
      SQ Q8NWP7 1-110
      1. 2ets
        complexed with cl, po4
        
        region a:1-110 [132371]
  3. Hypothetical protein YppE [140421]
    1. Bacillus subtilis [TaxId: 1423] [140422] (3)
      SQ P50833 1-123
      1. 2im8
        automatically matched to 2HFI A:1-123
        complexed with po4
        
        region a:1-123 [137506]
      2. 2im8
        automatically matched to 2HFI A:1-123
        complexed with po4
        
        region b:1-119 [137507]
      3. 2hfi
        
        region a:1-123 [136385]
MW0975(SA0943)-like [140423] (1)
open bundle; there is a long groove between helices 1 and 4
uperfamily
1. MW0975(SA0943)-like [140424] (1)
  1. Hypothetical protein MW0975 (SA0943) [140425]
    1. Staphylococcus aureus [TaxId: 1280] [140426] (1)
      SQ Q8NX77 21-205
      1. 2ap3
        
        region a:12-196 [127110]
VPS28 C-terminal domain-like [140427] (1)
uperfamily
1. VPS28 C-terminal domain-like [140428] (1)
  C-terminal part of Pfam 03997
  1. Vacuolar protein sorting-associated protein 28, VPS28 [140429]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140430] (10)
      SQ Q02767 148-241
      1. 2j9u
        automatically matched to 2G3K A:148-241
        complexed with zn
        
        region a:148-241 [138155]
      2. 2j9u
        automatically matched to 2G3K A:148-241
        complexed with zn
        
        region c:148-241 [138156]
      3. 2j9v
        automatically matched to 2G3K A:148-241
        
        region a:148-241 [138157]
      4. 2g3k
        
        region a:148-241 [134562]
      5. 2g3k
        automatically matched to 2G3K A:148-241
        
        region b:148-241 [134563]
      6. 2g3k
        automatically matched to 2G3K A:148-241
        
        region c:148-241 [134564]
      7. 2g3k
        automatically matched to 2G3K A:148-241
        
        region d:148-241 [134565]
      8. 2g3k
        automatically matched to 2G3K A:148-241
        
        region e:148-241 [134566]
      9. 2g3k
        automatically matched to 2G3K A:148-241
        
        region f:148-241 [134567]
      10. 2g3k
        automatically matched to 2G3K A:148-241
        
        region g:148-241 [134568]
TM1646-like [158397] (1)
1. TM1646-like [158398] (1)
  Pfam 03885; DUF327
  1. Hypothetical protein TM1646 [158399]
    1. Thermotoga maritima [TaxId: 2336] [158400] (1)
      SQ Q9X1X9 34-152
      1. 2p61
        
        region a:34-152 [149266]