Structural Classification of Proteins

Superfamily: HD-domain/PDEase-like

: uperfamily

Lineage:

Root: scop
Class: All alpha proteins [46456]
Fold: HD-domain/PDEase-like [109603]
multihelical; consists of two different alpha-helical bundles
Superfamily: HD-domain/PDEase-like [109604]
uperfamily

Families:

HD domain [101340] (13)
Pfam 01966; metal dependent phosphohydrolases
1. Stringent response-like protein RelA N-terminal domain [101341]
  1. Streptococcus equisimilis [TaxId: 119602] [101342] (1)
    1. 1vj7
      complexed with gdp, gpx, mn
      1. region a:5-196 [100801]
      2. region b:5-196 [100803]
2. 5'-nucleotidase YfbR [116969]
  1. Escherichia coli [TaxId: 562] [116970] (2)
    SQ P76491
    Structural genomics target
    1. 2paq
      automatically matched to d1wpha_
      1. region a:2-187 [139643]
    2. 2paq
      automatically matched to d1wpha_
      1. region b:2-187 [139644]
3. Oxetanocin-like protein PF0395 [116971]
  similar fold and oligomeric structure to 5'-nucleotidase YfbR
  1. Pyrococcus furiosus [TaxId: 2261] [116972] (1)
    SQ Q8U3R1
    1. 1xx7
      Structural genomics target
      complexed with ni, unx
      1. chain a [116143]
      2. chain b [116144]
      3. chain c [116145]
      4. chain d [116146]
      5. chain e [116147]
      6. chain f [116148]
4. Hypothetical protein AF1432 [140763]
  1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [140764] (4)
    SQ O28840 7-172! SQ O28840 7-173
    1. 1ynb
      1. region a:7-173 [123718]
    2. 1ynb
      automatically matched to 1YNB A:7-173
      1. region b:7-173 [123719]
    3. 1ynb
      automatically matched to 1YNB A:7-173
      1. region c:7-173 [123720]
    4. 1yoy
      1. region a:7-172 [123795]
5. Hypothetical protein aq_1910 [140765]
  elaborated with additional structures in C-terminal extension
  1. Aquifex aeolicus [TaxId: 63363] [140766] (2)
    SQ O67745 1-369
    1. 2hek
      complexed with br, cl, gdp, gol, po4, zn
      1. region a:1-369 [136354]
    2. 2hek
      automatically matched to 2HEK A:1-369
      complexed with br, cl, gdp, gol, po4, zn
      1. region b:1-369 [136355]
6. Hypothetical protein EF1143 [140767]
  Probable ortholog of aq_1910
  1. Enterococcus faecalis [TaxId: 1351] [140768] (2)
    SQ Q836G9 1-453
    1. 2o6i
      complexed with cl, hed, zn
      1. region a:1-453 [138920]
    2. 2o6i
      automatically matched to 2O6I A:1-453
      complexed with cl, hed, zn
      1. region b:1-453 [138921]
7. Predicted hydrolase mes0020 [158719]
  1. Uncultured thermotogales bacterium [TaxId: 221214] [158720] (1)
    SQ Q1EM40 1-217
    1. 2pq7
      complexed with cl, fe, mpd, po4
      1. region a:1-217 [149786]
8. Uncharacterized protein Lin1889 [158721]
  1. Listeria innocua [TaxId: 1642] [158722] (1)
    SQ Q92AN1 1-201
    1. 3b57
      complexed with mg
      1. region a:1-201 [154835]
9. Uncharacterized protein SE1688 [158723]
  1. Staphylococcus epidermidis [TaxId: 1282] [158724] (2)
    SQ Q8CRP0 1-216
    1. 2qgs
      complexed with zn
      1. region a:1-216 [150782]
    2. 2qgs
      automatically matched to 2QGS A:1-216
      complexed with zn
      1. region b:1-216 [150783]
10. Hypothetical protein Atu1052 [158725]
  1. Agrobacterium tumefaciens [TaxId: 358] [158726] (4)
    SQ Q8UGI5 6-205
    1. 2gz4
      1. region a:6-205 [147196]
    2. 2gz4
      automatically matched to 2GZ4 A:6-205
      1. region b:6-203 [147197]
    3. 2gz4
      automatically matched to 2GZ4 A:6-205
      1. region c:6-201 [147198]
    4. 2gz4
      automatically matched to 2GZ4 A:6-205
      1. region d:8-204 [147199]
11. Uncharacterized protein BH2835 [158727]
  1. Bacillus halodurans [TaxId: 86665] [158728] (4)
    SQ Q9K916 2-213
    1. 3dto
      1. region a:2-213 [157850]
    2. 3dto
      automatically matched to 3DTO A:2-213
      1. region b:2-213 [157851]
    3. 3dto
      automatically matched to 3DTO A:2-213
      1. region c:2-213 [157852]
    4. 3dto
      automatically matched to 3DTO A:2-213
      1. region d:2-213 [157853]
12. Uncharacterized protein LP2664 [158729]
  1. Lactobacillus plantarum [TaxId: 1590] [158730] (4)
    SQ Q88U62 1-215
    1. 2pjq
      1. region a:1-215 [149569]
    2. 2pjq
      automatically matched to 2PJQ A:1-215
      1. region b:1-215 [149570]
    3. 2pjq
      automatically matched to 2PJQ A:1-215
      1. region c:1-215 [149571]
    4. 2pjq
      automatically matched to 2PJQ A:1-215
      1. region d:1-215 [149572]
13. Uncharacterized protein BT9727_1981 [158731]
  1. Bacillus thuringiensis [TaxId: 1428] [158732] (2)
    SQ Q6HJG6 2-214
    1. 3djb
      complexed with mg; mutant
      1. region a:2-214 [157756]
    2. 3djb
      automatically matched to 3DJB A:2-214
      complexed with mg; mutant
      1. region b:2-214 [157757]
PDEase [48548] (6)
Pfam 00233; multihelical; can be divided into three subdomains
1. Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b [48549]
  1. Human (Homo sapiens) [TaxId: 9606] [48550] (14)
    SQ Q07343 324-667
    1. 1f0j
      complexed with ars, mg, zn; mutant
      1. chain a [19346]
      2. chain b [19347]
    2. 1xm6
      complexed with 5rm, mg, zn
      1. chain a [115471]
      2. chain b [115472]
    3. 1ror
      complexed with amp, zn; mutant
      1. chain a [111901]
      2. chain b [111902]
    4. 1ro6
      complexed with ars, mn, rol, zn; mutant
      1. chain a [111897]
      2. chain b [111898]
    5. 1xlz
      complexed with fil, mg, zn
      1. chain a [115459]
      2. chain b [115460]
    6. 1ro9
      complexed with 8br, zn; mutant
      1. chain a [111899]
      2. chain b [111900]
    7. 1xn0
      complexed with 4rr, 4sr, mg, zn
      1. chain a [115571]
      2. chain b [115572]
    8. 1xmu
      complexed with mg, rof, zn
      1. chain a [115562]
      2. chain b [115563]
    9. 1tb5
      complexed with amp, mg, zn
      1. chain a [106735]
      2. chain b [106736]
    10. 1xos
      complexed with mg, so4, via, zn
      1. chain a [115712]
    11. 1xm4
      complexed with mg, pil, zn
      1. chain a [115465]
      2. chain b [115466]
    12. 1xlx
      complexed with cio, mg, zn
      1. chain a [115455]
      2. chain b [115456]
    13. 1xot
      complexed with mg, vdn, zn
      1. chain a [115713]
      2. chain b [115714]
    14. 1xmy
      complexed with 4rr, mg, zn
      1. chain a [115569]
      2. chain b [115570]
2. Catalytic domain of cyclic nucleotide phosphodiesterase pde4d [89151]
  1. Human (Homo sapiens) [TaxId: 9606] [89152] (39)
    SQ Q08499 388-713
    1. 1y2k
      automatically matched to d1oyna_
      complexed with 7de, edo, mg, zn
      1. region a:86-411 [122571]
    2. 1y2k
      automatically matched to d1oyna_
      complexed with 7de, edo, mg, zn
      1. region b:86-411 [122572]
    3. 1y2b
      automatically matched to d1oyna_
      complexed with dee, edo, mg, zn
      1. region a:86-411 [122556]
    4. 1y2b
      automatically matched to d1oyna_
      complexed with dee, edo, mg, zn
      1. region b:86-411 [122557]
    5. 1xor
      complexed with mg, zar, zn
      1. chain a [115710]
      2. chain b [115711]
    6. 1xom
      complexed with cio, edo, mg, zn
      1. chain a [115704]
      2. chain b [115705]
    7. 1tb7
      complexed with amp, b3p, edo, mg, zn
      1. chain a [106739]
      2. chain b [106740]
    8. 1tbb
      complexed with edo, mg, rol, zn
      1. chain a [106741]
      2. chain b [106742]
    9. 1y2d
      automatically matched to d1oyna_
      complexed with 4de, b3p, edo, mg, zn
      1. region a:86-411 [122560]
    10. 1y2d
      automatically matched to d1oyna_
      complexed with 4de, b3p, edo, mg, zn
      1. region b:86-411 [122561]
    11. 1y2c
      automatically matched to d1oyna_
      complexed with 3de, edo, mg, zn
      1. region a:86-411 [122558]
    12. 1y2c
      automatically matched to d1oyna_
      complexed with 3de, edo, mg, zn
      1. region b:86-411 [122559]
    13. 1xon
      complexed with b3p, edo, mg, pil, zn
      1. chain a [115706]
      2. chain b [115707]
    14. 2qyn
      automatically matched to d1oyna_
      complexed with mg, npv, zn
      1. region a:86-411 [151475]
    15. 2qyn
      automatically matched to d1oyna_
      complexed with mg, npv, zn
      1. region b:88-411 [151476]
    16. 1xoq
      complexed with edo, mg, rof, zn
      1. chain a [115708]
      2. chain b [115709]
    17. 2qyl
      automatically matched to d1oyna_
      complexed with mg, npv, zn
      1. region a:153-485 [151474]
    18. 1y2e
      automatically matched to d1oyna_
      complexed with 5de, edo, mg, zn
      1. region a:86-411 [122562]
    19. 1y2e
      automatically matched to d1oyna_
      complexed with 5de, edo, mg, zn
      1. region b:88-411 [122563]
    20. 2fm0
      automatically matched to d1oyna_
      complexed with m98, mg, zn
      1. region a:79-412 [133752]
    21. 2fm0
      automatically matched to d1oyna_
      complexed with m98, mg, zn
      1. region b:86-412 [133753]
    22. 2fm0
      automatically matched to d1oyna_
      complexed with m98, mg, zn
      1. region c:86-412 [133754]
    23. 2fm0
      automatically matched to d1oyna_
      complexed with m98, mg, zn
      1. region d:79-412 [133755]
    24. 2fm5
      automatically matched to d1oyna_
      complexed with m99, mg, zn
      1. region a:79-412 [133761]
    25. 2fm5
      automatically matched to d1oyna_
      complexed with m99, mg, zn
      1. region b:86-412 [133762]
    26. 2fm5
      automatically matched to d1oyna_
      complexed with m99, mg, zn
      1. region c:86-412 [133763]
    27. 2fm5
      automatically matched to d1oyna_
      complexed with m99, mg, zn
      1. region d:79-412 [133764]
    28. 1oyn
      complexed with rol, zn
      1. chain a [87609]
      2. chain b [87610]
      3. chain c [87611]
      4. chain d [87612]
    29. 1zkn
      automatically matched to d1oyna_
      complexed with ibm, mg, zn
      1. region a:79-412 [125201]
    30. 1zkn
      automatically matched to d1oyna_
      complexed with ibm, mg, zn
      1. region b:86-412 [125202]
    31. 1zkn
      automatically matched to d1oyna_
      complexed with ibm, mg, zn
      1. region c:83-412 [125203]
    32. 1zkn
      automatically matched to d1oyna_
      complexed with ibm, mg, zn
      1. region d:79-412 [125204]
    33. 1q9m
      complexed with rol, zn
      1. chain a [96288]
      2. chain b [96289]
      3. chain c [96290]
      4. chain d [96291]
    34. 1ptw
      complexed with amp, zn
      1. chain a [95106]
      2. chain b [95107]
      3. chain c [95108]
      4. chain d [95109]
    35. 1y2h
      automatically matched to d1mkda_
      complexed with 6de, mg, zn
      1. region a:163-485 [122567]
    36. 1y2h
      automatically matched to d1mkda_
      complexed with 6de, mg, zn
      1. region b:163-485 [122568]
    37. 1mkd
      complexed with mg, zar, zn
      1. chain a [84982]
      2. chain b [84983]
      3. chain c [84984]
      4. chain d [84985]
      5. chain e [84986]
      6. chain f [84987]
      7. chain g [84988]
      8. chain h [84989]
      9. chain i [84990]
      10. chain j [84991]
      11. chain k [84992]
      12. chain l [84993]
    38. 1y2j
      automatically matched to d1mkda_
      complexed with 7de, mg, zn
      1. region a:163-485 [122569]
    39. 1y2j
      automatically matched to d1mkda_
      complexed with 7de, mg, zn
      1. region b:163-485 [122570]
3. cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx [101439]
  1. Human (Homo sapiens) [TaxId: 9606] [101440] (18)
    SQ O76074 534-860
    1. 1tbf
      complexed with gol, mg, via, zn
      1. chain a [106743]
    2. 1xoz
      complexed with cia, mg, zn
      1. chain a [115719]
    3. 2chm
      complexed with 3p4, mes, mg, zn
      1. region a:537-858 [130472]
    4. 1xp0
      complexed with mg, vdn, zn
      1. chain a [115720]
    5. 2h44
      automatically matched to d1t9ra_
      complexed with 7ca, mg, zn
      1. region a:535-860 [136069]
    6. 2h40
      automatically matched to d1t9ra_
      complexed with mg, zn
      1. region a:535-860 [136063]
    7. 1t9s
      complexed with 5gp, mg, zn
      1. chain a [106726]
      2. chain b [106727]
    8. 3bjc
      automatically matched to d1t9ra_
      complexed with mg, wan, zn
      1. region a:535-860 [155329]
    9. 3b2r
      automatically matched to d1t9ra_
      complexed with vdn
      1. region a:535-860 [154768]
    10. 3b2r
      automatically matched to d1t9ra_
      complexed with vdn
      1. region b:538-860 [154769]
    11. 1rkp
      complexed with ibm, mg, zn; mutant
      1. chain a [97620]
    12. 1t9r
      complexed with cit, po4, zn
      1. chain a [106725]
    13. 2h42
      automatically matched to d1t9ra_
      complexed with mg, via, zn
      1. region a:535-860 [136064]
    14. 2h42
      automatically matched to d1t9ra_
      complexed with mg, via, zn
      1. region b:535-860 [136065]
    15. 2h42
      automatically matched to d1t9ra_
      complexed with mg, via, zn
      1. region c:535-860 [136066]
    16. 1udt
      complexed with mg, via, zn
      1. chain a [99221]
    17. 1uho
      complexed with mg, vdn, zn
      1. chain a [107851]
    18. 1udu
      complexed with cia, mg, zn
      1. chain a [99222]
      2. chain b [99223]
4. cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b [101441]
  1. Human (Homo sapiens) [TaxId: 9606] [101442] (2)
    1. 1so2
      complexed with 666, hg9, mg
      1. chain a [98936]
      2. chain b [98937]
      3. chain c [98938]
      4. chain d [98939]
    2. 1soj
      complexed with ibm, mg
      1. chain a [98942]
      2. chain b [98943]
      3. chain c [98944]
      4. chain d [98945]
      5. chain e [98946]
      6. chain f [98947]
      7. chain g [98948]
      8. chain h [98949]
      9. chain i [98950]
      10. chain j [98951]
      11. chain k [98952]
      12. chain l [98953]
5. High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A [109942]
  1. Human (Homo sapiens) [TaxId: 9606] [109943] (14)
    SQ O76083 241-566
    1. 3dy8
      automatically matched to d2hd1a1
      complexed with 5gp, fmt, ibm, mg, mn
      1. region a:182-505 [157937]
    2. 3dy8
      automatically matched to d2hd1a1
      complexed with 5gp, fmt, ibm, mg, mn
      1. region b:182-505 [157938]
    3. 3dyn
      automatically matched to d2hd1a1
      complexed with ibm, mg, pcg, zn
      1. region a:182-505 [157942]
    4. 3dyn
      automatically matched to d2hd1a1
      complexed with ibm, mg, pcg, zn
      1. region b:182-505 [157943]
    5. 3dys
      automatically matched to d2hd1a1
      complexed with 5gp, fmt, ibm, mg, mn
      1. region a:182-505 [157946]
    6. 3dys
      automatically matched to d2hd1a1
      complexed with 5gp, fmt, ibm, mg, mn
      1. region b:182-505 [157947]
    7. 2hd1
      automatically matched to d1tbma_
      complexed with ibm, mg, zn
      1. region a:181-506 [136338]
    8. 2hd1
      automatically matched to d1tbma_
      complexed with ibm, mg, zn
      1. region b:181-506 [136339]
    9. 3dyq
      automatically matched to d2hd1a1
      complexed with ibm, na, pcg
      1. region a:182-505 [157944]
    10. 3dyq
      automatically matched to d2hd1a1
      complexed with ibm, na, pcg
      1. region b:182-505 [157945]
    11. 3dyl
      automatically matched to d2hd1a1
      complexed with fmt, ibm, mg, mn, pcg
      1. region a:182-505 [157940]
    12. 3dyl
      automatically matched to d2hd1a1
      complexed with fmt, ibm, mg, mn, pcg
      1. region b:182-505 [157941]
    13. 2yy2
      automatically matched to d2hd1a1
      complexed with ibm, mg, zn
      1. region a:181-506 [153829]
    14. 2yy2
      automatically matched to d2hd1a1
      complexed with ibm, mg, zn
      1. region b:181-504 [153830]
6. Catalytic domain of cyclic nucleotide phosphodiesterase 1b, PDE1B [109944]
  1. Human (Homo sapiens) [TaxId: 9606] [109945] (1)
    SQ Q01064 126-482
    1. 1taz
      complexed with mg, zn
      1. chain a [106734]
modified HD domain [116973] (1)
retains the superfamily core fold but lacks the conserved metal-binding site
1. Hypothetical protein Cj0248 [116974]
  1. Campylobacter jejuni [TaxId: 197] [116975] (1)
    SQ Q9PIP7
    1. 1vqr
      Structural genomics target
      1. chain a [114015]
      2. chain b [114016]
      3. chain c [114017]
      4. chain d [114018]
MioX-like [140769] (2)
Pfam 05153; DUF706
1. Myo-inositol oxygenase MioX [140770]
  1. Human (Homo sapiens) [TaxId: 9606] [140771] (2)
    SQ Q9UGB7 37-285
    1. 2ibn
      complexed with cys, fe, i1n, so4
      1. region a:37-285 [137195]
    2. 2ibn
      automatically matched to 2IBN A:37-285
      complexed with cys, fe, i1n, so4
      1. region b:37-285 [137196]
  2. Mouse (Mus musculus) [TaxId: 10090] [140772] (2)
    SQ Q9QXN5 28-285
    1. 3bxd
      automatically matched to d2huoa1
      complexed with fe, fmt, ins, oh
      1. region a:28-285 [155707]
    2. 2huo
      complexed with fe, fmt, ins, oh
      1. region a:28-285 [136778]
Ppx associated domain [140773] (1)
this domain is C-terminal to Ppx domain in some Exopolyphosphatases
1. Exopolyphosphatase Ppx C-terminal domain [140774]
  1. Escherichia coli [TaxId: 562] [140775] (6)
    SQ P0AFL6 312-508
    1. 1u6z
      complexed with so4
      1. region a:313-509 [119608]
    2. 1u6z
      automatically matched to 1U6Z A:313-509
      complexed with so4
      1. region b:313-509 [119611]
    3. 2flo
      automatically matched to 1U6Z A:313-509
      1. region a:313-506 [133733]
    4. 2flo
      automatically matched to 1U6Z A:313-509
      1. region b:313-506 [133736]
    5. 2flo
      automatically matched to 1U6Z A:313-509
      1. region c:313-506 [133739]
    6. 2flo
      automatically matched to 1U6Z A:313-509
      1. region d:313-506 [133742]