SCOP 1.75: Protein: Ubiquitin

Lineage for Protein: Ubiquitin

Root: SCOP 1.75
Class d: Alpha and beta proteins (a+b) [53931] (376 folds)
Fold d.15: beta-Grasp (ubiquitin-like) [54235] (14 superfamilies)
core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
Superfamily d.15.1: Ubiquitin-like [54236] (8 families)
Family d.15.1.1: Ubiquitin-related [54237] (38 proteins)
Pfam PF00240
Protein Ubiquitin [54238] (3 species)

Species:

Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId:4932] [89830] (6 PDB entries)
1. Domain for 1otr:
  - Domain d1otrb_: 1otr B: [87414]
    Other proteins in same PDB: d1otra_
2. Domain for 1q0w:
  - Domain d1q0wb_: 1q0w B: [95516]
    Other proteins in same PDB: d1q0wa_
3. Domain for 1wr1:
  - Domain d1wr1a1: 1wr1 A:1-76 [121184]
    Other proteins in same PDB: d1wr1b1
    automatically matched to d1otrb_
4. Domain for 2g3q:
  - Domain d2g3qb1: 2g3q B:1-76 [134569]
    Other proteins in same PDB: d2g3qa1
    automatically matched to d1otrb_
5. Domain for 2jt4:
  - Domain d2jt4b1: 2jt4 B:1-76 [148198]
    automatically matched to d1otrb_
6. Domains for 3cmm:
  1. Domain d3cmmb1: 3cmm B:1-76 [156833]
    automatically matched to d1otrb_
    complexed with pro
  2. Domain d3cmmd1: 3cmm D:1-76 [156834]
    automatically matched to d1otrb_
    complexed with pro
Human (Homo sapiens) [TaxId:9606] [54239] (63 PDB entries)
Uniprot P62988
identical sequence in many other species
1. Domains for 1aar:
  1. Domain d1aara_: 1aar A: [37586]
    di-ubiquitin
  2. Domain d1aarb_: 1aar B: [37587]
    di-ubiquitin
2. Domain for 1c3t:
  - Domain d1c3ta_: 1c3t A: [37594]
    designed hydrophobic core mutant
3. Domain for 1d3z:
  - Domain d1d3za_: 1d3z A: [37592]
4. Domains for 1f9j:
  1. Domain d1f9ja_: 1f9j A: [37590]
    a new crystal form of tetraubiquitin
  2. Domain d1f9jb_: 1f9j B: [37591]
    a new crystal form of tetraubiquitin
5. Domain for 1fxt:
  - Domain d1fxtb_: 1fxt B: [65056]
    Other proteins in same PDB: d1fxta_
6. Domain for 1g6j:
  - Domain d1g6ja_: 1g6j A: [60319]
    Structure in aot reverse micelles
7. Domains for 1gjz:
  1. Domain d1gjza_: 1gjz A: [65223]
  2. Domain d1gjzb_: 1gjz B: [65224]
8. Domains for 1nbf:
  1. Domain d1nbfc_: 1nbf C: [80389]
    Other proteins in same PDB: d1nbfa_, d1nbfb_, d1nbfe_
    complex with USP7
  2. Domain d1nbfd_: 1nbf D: [80390]
    Other proteins in same PDB: d1nbfa_, d1nbfb_, d1nbfe_
    complex with USP7
    complexed with glz
9. Domain for 1ogw:
  - Domain d1ogwa_: 1ogw A: [87001]
    synthetic protein with fluoro-Leu at 50 and 67
    complexed with lef
10. Domains for 1p3q:
  1. Domain d1p3qu_: 1p3q U: [87750]
    Other proteins in same PDB: d1p3qq_, d1p3qr_
    annotated as bovine in PDB, identical to human sequence
  2. Domain d1p3qv_: 1p3q V: [87751]
    Other proteins in same PDB: d1p3qq_, d1p3qr_
    annotated as bovine in PDB, identical to human sequence
    complexed with mse; mutant
11. Domain for 1q5w:
  - Domain d1q5wb_: 1q5w B: [95946]
    Other proteins in same PDB: d1q5wa_
    complexed with zn
12. Domains for 1s1q:
  1. Domain d1s1qb_: 1s1q B: [98352]
    Other proteins in same PDB: d1s1qa_, d1s1qc_
  2. Domain d1s1qd_: 1s1q D: [98354]
    Other proteins in same PDB: d1s1qa_, d1s1qc_
    complexed with acy, cu, so4
13. Domain for 1sif:
  - Domain d1sifa_: 1sif A: [105574]
    a multiple hydrophobic core mutant
14. Domains for 1tbe:
  1. Domain d1tbea_: 1tbe A: [37588]
    tetra-ubiquitin
  2. Domain d1tbeb_: 1tbe B: [37589]
    tetra-ubiquitin
15. Domain for 1ubi:
  - Domain d1ubia_: 1ubi A: [37584]
16. Domain for 1ubq:
  - Domain d1ubqa_: 1ubq A: [37585]
17. Domain for 1ud7:
  - Domain d1ud7a_: 1ud7 A: [37593]
    designed hydrophobic core mutant
18. Domain for 1uzx:
  - Domain d1uzxb_: 1uzx B: [100239]
    Other proteins in same PDB: d1uzxa_
    annotated as bovine in PDB, identical to human sequence
    complexed with mes, mso, so4
19. Domain for 1v80:
  - Domain d1v80a1: 1v80 A:1-76 [119867]
    automatically matched to d1aara_
20. Domain for 1v81:
  - Domain d1v81a1: 1v81 A:1-76 [119868]
    automatically matched to d1aara_
21. Domains for 1wr6:
  1. Domain d1wr6e1: 1wr6 E:1-72 [121186]
    Other proteins in same PDB: d1wr6a1, d1wr6b1, d1wr6c1, d1wr6d1
    automatically matched to d1aara_
  2. Domain d1wr6f1: 1wr6 F:1-73 [121187]
    Other proteins in same PDB: d1wr6a1, d1wr6b1, d1wr6c1, d1wr6d1
    automatically matched to d1aara_
  3. Domain d1wr6g1: 1wr6 G:1-72 [121188]
    Other proteins in same PDB: d1wr6a1, d1wr6b1, d1wr6c1, d1wr6d1
    automatically matched to d1aara_
  4. Domain d1wr6h1: 1wr6 H:1-74 [121189]
    Other proteins in same PDB: d1wr6a1, d1wr6b1, d1wr6c1, d1wr6d1
    automatically matched to d1aara_
22. Domain for 1wrd:
  - Domain d1wrdb1: 1wrd B:1-76 [121194]
    Other proteins in same PDB: d1wrda1
    automatically matched to d1aara_
23. Domains for 1xd3:
  1. Domain d1xd3b_: 1xd3 B: [115146]
    Other proteins in same PDB: d1xd3a_, d1xd3c_
  2. Domain d1xd3d_: 1xd3 D: [115148]
    Other proteins in same PDB: d1xd3a_, d1xd3c_
    complexed with gve, mg
24. Domain for 1xqq:
  - Domain d1xqqa1: 1xqq A:1-76 [122240]
    automatically matched to d1aara_
25. Domains for 1yd8:
  1. Domain d1yd8u1: 1yd8 U:1-73 [122974]
    Other proteins in same PDB: d1yd8g1, d1yd8h1
    automatically matched to d1aara_
  2. Domain d1yd8v1: 1yd8 V:1-73 [122975]
    Other proteins in same PDB: d1yd8g1, d1yd8h1
    automatically matched to d1aara_
26. Domain for 1yx5:
  - Domain d1yx5b1: 1yx5 B:1-76 [124172]
    automatically matched to d1aara_
27. Domain for 1yx6:
  - Domain d1yx6b1: 1yx6 B:1-76 [124173]
    automatically matched to d1aara_
28. Domain for 1zgu:
  - Domain d1zgub1: 1zgu B:1-76 [125062]
    Other proteins in same PDB: d1zgua1
    mutant
29. Domain for 2ayo:
  - Domain d2ayob1: 2ayo B:1-76 [127567]
    Other proteins in same PDB: d2ayoa1
    automatically matched to d1aara_
30. Domains for 2bgf:
  1. Domain d2bgfa1: 2bgf A:1-76 [128476]
    automatically matched to d1aara_
  2. Domain d2bgfb1: 2bgf B:1-76 [128477]
    automatically matched to d1aara_
31. Domain for 2c7m:
  - Domain d2c7mb1: 2c7m B:1-74 [130068]
    Other proteins in same PDB: d2c7ma1
    automatically matched to d1aara_
    complexed with zn
32. Domains for 2c7n:
  1. Domain d2c7nb1: 2c7n B:1-74 [130070]
    Other proteins in same PDB: d2c7na1, d2c7nc1, d2c7ng1, d2c7ni1
    automatically matched to d1aara_
    complexed with zn
  2. Domain d2c7nd1: 2c7n D:1-74 [130072]
    Other proteins in same PDB: d2c7na1, d2c7nc1, d2c7ng1, d2c7ni1
    automatically matched to d1aara_
    complexed with zn
  3. Domain d2c7nf1: 2c7n F:1-74 [130073]
    Other proteins in same PDB: d2c7na1, d2c7nc1, d2c7ng1, d2c7ni1
    automatically matched to d1aara_
    complexed with zn
  4. Domain d2c7nh1: 2c7n H:1-73 [130075]
    Other proteins in same PDB: d2c7na1, d2c7nc1, d2c7ng1, d2c7ni1
    automatically matched to d1aara_
    complexed with zn
  5. Domain d2c7nj1: 2c7n J:1-72 [130077]
    Other proteins in same PDB: d2c7na1, d2c7nc1, d2c7ng1, d2c7ni1
    automatically matched to d1aara_
    complexed with zn
  6. Domain d2c7nl1: 2c7n L:1-74 [130078]
    Other proteins in same PDB: d2c7na1, d2c7nc1, d2c7ng1, d2c7ni1
    automatically matched to d1aara_
    complexed with zn
33. Domains for 2d3g:
  1. Domain d2d3ga1: 2d3g A:1-72 [131206]
    automatically matched to d1aara_
  2. Domain d2d3gb1: 2d3g B:1-72 [131207]
    automatically matched to d1aara_
34. Domain for 2den:
  - Domain d2denb1: 2den B:1-76 [131432]
    automatically matched to d1aara_
    mutant
35. Domain for 2dx5:
  - Domain d2dx5b1: 2dx5 B:1-73 [131867]
    Other proteins in same PDB: d2dx5a1
    automatically matched to d1aara_
36. Domain for 2fid:
  - Domain d2fida1: 2fid A:1-73 [133516]
    Other proteins in same PDB: d2fidb1
    automatically matched to d1aara_
    complexed with zn
37. Domains for 2fif:
  1. Domain d2fifa1: 2fif A:1-73 [133518]
    Other proteins in same PDB: d2fifb1, d2fifd1, d2fiff1
    automatically matched to d1aara_
    complexed with so4, zn
  2. Domain d2fifc1: 2fif C:1-73 [133520]
    Other proteins in same PDB: d2fifb1, d2fifd1, d2fiff1
    automatically matched to d1aara_
    complexed with so4, zn
  3. Domain d2fife1: 2fif E:1-73 [133522]
    Other proteins in same PDB: d2fifb1, d2fifd1, d2fiff1
    automatically matched to d1aara_
    complexed with so4, zn
38. Domain for 2fuh:
  - Domain d2fuhb1: 2fuh B:1-76 [134174]
    Other proteins in same PDB: d2fuha1
    automatically matched to d1aara_
39. Domains for 2g45:
  1. Domain d2g45b1: 2g45 B:1-76 [134578]
    Other proteins in same PDB: d2g45a1, d2g45d1
    automatically matched to d1aara_
    complexed with cl, zn
  2. Domain d2g45e1: 2g45 E:1-76 [134579]
    Other proteins in same PDB: d2g45a1, d2g45d1
    automatically matched to d1aara_
    complexed with cl, zn
40. Domain for 2gmi:
  - Domain d2gmic1: 2gmi C:501-576 [135382]
    Other proteins in same PDB: d2gmia1, d2gmib1
    automatically matched to d1aara_
    mutant
41. Domain for 2hd5:
  - Domain d2hd5b1: 2hd5 B:1-76 [136341]
    Other proteins in same PDB: d2hd5a1
    automatically matched to d1aara_
    complexed with zn
42. Domain for 2hth:
  - Domain d2htha1: 2hth A:1-73 [136742]
    Other proteins in same PDB: d2hthb1
    automatically matched to d1aara_
43. Domain for 2ibi:
  - Domain d2ibib1: 2ibi B:1-75 [137194]
    Other proteins in same PDB: d2ibia1
    automatically matched to d1aara_
    complexed with neh, zn; mutant
44. Domains for 2j7q:
  1. Domain d2j7qb1: 2j7q B:1-75 [138127]
    Other proteins in same PDB: d2j7qa1, d2j7qc1
    automatically matched to d1aara_
    complexed with gol, gve, mg, pg4
  2. Domain d2j7qd1: 2j7q D:1-75 [138128]
    Other proteins in same PDB: d2j7qa1, d2j7qc1
    automatically matched to d1aara_
    complexed with gol, gve, mg, pg4
45. Domains for 2jf5:
  1. Domain d2jf5a1: 2jf5 A:1-73 [148030]
    automatically matched to d1aara_
    complexed with cd, cl, co, mg
  2. Domain d2jf5b1: 2jf5 B:1-73 [148031]
    automatically matched to d1aara_
    complexed with cd, cl, co, mg
46. Domains for 2jri:
  1. Domain d2jrib1: 2jri B:183-255 [148185]
    automatically matched to d1aara_
  2. Domain d2jric1: 2jri C:259-331 [148186]
    automatically matched to d1aara_
47. Domain for 2jy6:
  - Domain d2jy6a1: 2jy6 A:1-73 [148238]
    automatically matched to d1aara_
48. Domain for 2jzz:
  - Domain d2jzza1: 2jzz A:1-73 [148251]
    automatically matched to d1aara_
49. Domain for 2k39:
  - Domain d2k39a1: 2k39 A:1-73 [148263]
    automatically matched to d1aara_
50. Domain for 2k6d:
  - Domain d2k6db1: 2k6d B:1-73 [148276]
    automatically matched to d1aara_
51. Domain for 2nr2:
  - Domain d2nr2a1: 2nr2 A:1-76 [138518]
    automatically matched to d1aara_
52. Domains for 2o6v:
  1. Domain d2o6va1: 2o6v A:1-75 [138922]
    automatically matched to d1aara_
    complexed with mes, slz, so4; mutant
  2. Domain d2o6vb1: 2o6v B:101-151 [138923]
    automatically matched to d1gjza_
    complexed with mes, slz, so4; mutant
  3. Domain d2o6vc1: 2o6v C:201-276 [138924]
    automatically matched to d1aara_
    complexed with mes, slz, so4; mutant
  4. Domain d2o6vd1: 2o6v D:301-376 [145715]
    complexed with mes, slz, so4; mutant
  5. Domain d2o6ve1: 2o6v E:401-475 [138925]
    automatically matched to d1aara_
    complexed with mes, slz, so4; mutant
  6. Domain d2o6vf1: 2o6v F:501-551 [138926]
    automatically matched to d1gjza_
    complexed with mes, slz, so4; mutant
  7. Domain d2o6vg1: 2o6v G:601-676 [138927]
    automatically matched to d1aara_
    complexed with mes, slz, so4; mutant
  8. Domain d2o6vh1: 2o6v H:702-776 [145716]
    automatically matched to 2O6V D:301-376
    complexed with mes, slz, so4; mutant
53. Domain for 2oob:
  - Domain d2oobb1: 2oob B:1-72 [139167]
    automatically matched to d1aara_
54. Domains for 2pe9:
  1. Domain d2pe9a1: 2pe9 A:1-72 [149399]
    automatically matched to d1aara_
  2. Domain d2pe9b1: 2pe9 B:1-72 [149400]
    automatically matched to d1aara_
55. Domains for 2pea:
  1. Domain d2peaa1: 2pea A:1-72 [149401]
    automatically matched to d1aara_
  2. Domain d2peab1: 2pea B:1-72 [149402]
    automatically matched to d1aara_
56. Domains for 2qho:
  1. Domain d2qhoa1: 2qho A:1-72 [150790]
    automatically matched to d1aara_
  2. Domain d2qhoc1: 2qho C:1-73 [150791]
    automatically matched to d1aara_
  3. Domain d2qhoe1: 2qho E:1-73 [150792]
    automatically matched to d1aara_
  4. Domain d2qhog1: 2qho G:1-72 [150793]
    automatically matched to d1aara_
57. Domain for 2z59:
  - Domain d2z59b1: 2z59 B:1-73 [154162]
    automatically matched to d1aara_
58. Domains for 2zcc:
  1. Domain d2zcca1: 2zcc A:1-70 [154337]
    automatically matched to d1aara_
    complexed with zn
  2. Domain d2zccb1: 2zcc B:1-70 [154338]
    automatically matched to d1aara_
    complexed with zn
  3. Domain d2zccc1: 2zcc C:1-71 [154339]
    automatically matched to d1aara_
    complexed with zn
59. Domains for 2znv:
  1. Domain d2znvb1: 2znv B:1-51 [154707]
    automatically matched to d1gjza_
    complexed with edo, zn; mutant
  2. Domain d2znvc1: 2znv C:1-73 [154708]
    automatically matched to d1aara_
    complexed with edo, zn; mutant
  3. Domain d2znve1: 2znv E:1-51 [154709]
    automatically matched to d1gjza_
    complexed with edo, zn; mutant
  4. Domain d2znvf1: 2znv F:1-70 [154710]
    automatically matched to d1aara_
    complexed with edo, zn; mutant
60. Domain for 3by4:
  - Domain d3by4b1: 3by4 B:1-73 [155720]
    automatically matched to d1aara_
    complexed with 3cn
61. Domains for 3c0r:
  1. Domain d3c0rb1: 3c0r B:1-73 [155839]
    automatically matched to d1aara_
    complexed with 3cn
  2. Domain d3c0rd1: 3c0r D:1-73 [155840]
    automatically matched to d1aara_
    complexed with 3cn
62. Domains for 3dvg:
  1. Domain d3dvgx1: 3dvg X:1-73 [157892]
    Other proteins in same PDB: d3dvga1, d3dvga2, d3dvgb1, d3dvgb2
    automatically matched to d1aara_
    mutant
  2. Domain d3dvgy1: 3dvg Y:1-51 [157893]
    Other proteins in same PDB: d3dvga1, d3dvga2, d3dvgb1, d3dvgb2
    automatically matched to d1gjza_
    mutant
63. Domains for 3dvn:
  1. Domain d3dvnu1: 3dvn U:1-73 [157902]
    Other proteins in same PDB: d3dvna1, d3dvna2, d3dvnb1, d3dvnb2, d3dvnh1, d3dvnh2, d3dvnl1, d3dvnl2
    automatically matched to d1aara_
    mutant
  2. Domain d3dvnv1: 3dvn V:1-51 [157903]
    Other proteins in same PDB: d3dvna1, d3dvna2, d3dvnb1, d3dvnb2, d3dvnh1, d3dvnh2, d3dvnl1, d3dvnl2
    automatically matched to d1gjza_
    mutant
  3. Domain d3dvnx1: 3dvn X:1-73 [157904]
    Other proteins in same PDB: d3dvna1, d3dvna2, d3dvnb1, d3dvnb2, d3dvnh1, d3dvnh2, d3dvnl1, d3dvnl2
    automatically matched to d1aara_
    mutant
  4. Domain d3dvny1: 3dvn Y:1-51 [157905]
    Other proteins in same PDB: d3dvna1, d3dvna2, d3dvnb1, d3dvnb2, d3dvnh1, d3dvnh2, d3dvnl1, d3dvnl2
    automatically matched to d1gjza_
    mutant
Synthetic, based on Saccharomyces cerevisiae sequence [54240] (1 PDB entry)
- Domains for 1cmx:
  1. Domain d1cmxb_: 1cmx B: [37595]
    Other proteins in same PDB: d1cmxa_, d1cmxc_
    nearly completely disordered chain D in the crystal structure
  2. Domain d1cmxd_: 1cmx D: [37596]
    Other proteins in same PDB: d1cmxa_, d1cmxc_
    nearly completely disordered chain D in the crystal structure

More info for Protein Ubiquitin from d.15.1.1: Ubiquitin-related

Timeline for Protein Ubiquitin from d.15.1.1: Ubiquitin-related:

Protein Ubiquitin from d.15.1.1: Ubiquitin-related first appeared (with stable ids) in SCOP 1.55
Protein Ubiquitin from d.15.1.1: Ubiquitin-related appears in SCOP 1.73
Protein Ubiquitin from d.15.1.1: Ubiquitin-related appears in SCOPe 2.01
Protein Ubiquitin from d.15.1.1: Ubiquitin-related appears in the current release, SCOPe 2.08