SCOPe 2.07: Protein: Photoactive yellow protein, PYP

Lineage for Protein: Photoactive yellow protein, PYP

Root: SCOPe 2.07
Class d: Alpha and beta proteins (a+b) [53931] (388 folds)
Fold d.110: Profilin-like [55769] (10 superfamilies)
core: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
Superfamily d.110.3: PYP-like sensor domain (PAS domain) [55785] (8 families)
alpha-beta(2)-alpha(2)-beta(3)
Family d.110.3.1: PYP-like [55786] (3 proteins)
Protein Photoactive yellow protein, PYP [55787] (1 species)

Species:

Methylophilus methylotrophus, strain w3a1 [TaxId:17] [55788] (82 PDB entries)
Uniprot P16113
1. Domain for 1d7e:
  - Domain d1d7ea_: 1d7e A: [40900]
    the p65 crystal form
    complexed with hc4
2. Domain for 1f98:
  - Domain d1f98a_: 1f98 A: [40899]
    complexed with hc4; mutant
3. Domain for 1f9i:
  - Domain d1f9ia_: 1f9i A: [40898]
    complexed with hc4; mutant
4. Domain for 1gsv:
  - Domain d1gsva_: 1gsv A: [65537]
    complexed with hc4; mutant
5. Domain for 1gsw:
  - Domain d1gswa_: 1gsw A: [65538]
    complexed with hc4; mutant
6. Domain for 1gsx:
  - Domain d1gsxa_: 1gsx A: [65539]
    complexed with hc4; mutant
7. Domain for 1kou:
  - Domain d1koua_: 1kou A: [72832]
    complexed with dhc, nbu
8. Domain for 1nwz:
  - Domain d1nwza_: 1nwz A: [86370]
    ultra-high resolution structure
    complexed with hc4
9. Domains for 1odv:
  1. Domain d1odva_: 1odv A: [86887]
    1-25 deletion mutant
    complexed with hc4; mutant
  2. Domain d1odvb_: 1odv B: [86888]
    1-25 deletion mutant
    complexed with hc4; mutant
10. Domain for 1ot6:
  - Domain d1ot6a_: 1ot6 A: [93504]
    complexed with hc4; mutant
11. Domain for 1ot9:
  - Domain d1ot9a_: 1ot9 A: [93510]
    complexed with hc4
12. Domain for 1ota:
  - Domain d1otaa_: 1ota A: [93511]
    complexed with hc4; mutant
13. Domain for 1otb:
  - Domain d1otba_: 1otb A: [93512]
    complexed with hc4
14. Domains for 1otd:
  1. Domain d1otda_: 1otd A: [93513]
    complexed with hc4
  2. Domain d1otdb_: 1otd B: [93514]
    complexed with hc4
15. Domain for 1ote:
  - Domain d1otea_: 1ote A: [93515]
    complexed with hc4; mutant
16. Domain for 1oti:
  - Domain d1otia_: 1oti A: [93516]
    complexed with hc4; mutant
17. Domain for 1s1y:
  - Domain d1s1ya_: 1s1y A: [105220]
    complexed with hc4; mutant
18. Domain for 1s1z:
  - Domain d1s1za_: 1s1z A: [105221]
    complexed with hc4; mutant
19. Domain for 1s4r:
  - Domain d1s4ra_: 1s4r A: [98508]
    complexed with hc4
20. Domain for 1s4s:
  - Domain d1s4sa_: 1s4s A: [98509]
    complexed with hc4
21. Domain for 1t18:
  - Domain d1t18a_: 1t18 A: [119102]
    automated match to d1ot6a_
    complexed with hc4; mutant
22. Domain for 1t19:
  - Domain d1t19a_: 1t19 A: [119103]
    automated match to d1ot6a_
    complexed with hc4; mutant
23. Domain for 1t1a:
  - Domain d1t1aa_: 1t1a A: [119104]
    automated match to d1ot6a_
    complexed with hc4; mutant
24. Domain for 1t1b:
  - Domain d1t1ba_: 1t1b A: [119105]
    automated match to d1ot6a_
    complexed with hc4; mutant
25. Domain for 1t1c:
  - Domain d1t1ca_: 1t1c A: [119106]
    automated match to d1ot6a_
    complexed with hc4; mutant
26. Domain for 1ts0:
  - Domain d1ts0a_: 1ts0 A: [119330]
    automated match to d1nwza_
    complexed with hc4
27. Domain for 1ts6:
  - Domain d1ts6a_: 1ts6 A: [119331]
    automated match to d1nwza_
    complexed with hc4
28. Domain for 1ts7:
  - Domain d1ts7a_: 1ts7 A: [119332]
    automated match to d1nwza_
    complexed with hc4
29. Domain for 1ts8:
  - Domain d1ts8a_: 1ts8 A: [119333]
    automated match to d1nwza_
    complexed with hc4
30. Domain for 1ugu:
  - Domain d1ugua_: 1ugu A: [107839]
    complexed with hc4; mutant
31. Domain for 1uwn:
  - Domain d1uwnx_: 1uwn X: [100127]
    complexed with hc4, so4
32. Domain for 1uwp:
  - Domain d1uwpx_: 1uwp X: [119764]
    automated match to d1nwza_
    complexed with hc4, so4
33. Domain for 2d01:
  - Domain d2d01a_: 2d01 A: [131059]
    automated match to d1nwza_
    complexed with hc4
34. Domain for 2d02:
  - Domain d2d02a_: 2d02 A: [163517]
    automated match to d1nwza_
    complexed with hc4; mutant
35. Domain for 2i9v:
  - Domain d2i9va_: 2i9v A: [165452]
    automated match to d1nwza_
    complexed with hc4
36. Domain for 2kx6:
  - Domain d2kx6a_: 2kx6 A: [242688]
    automated match to d1nwza_
    complexed with hc4
37. Domain for 2phy:
  - Domain d2phya_: 2phy A: [40901]
    complexed with hc4
38. Domain for 2pyp:
  - Domain d2pypa_: 2pyp A: [40902]
    photostationary state: 50% ground state, 50% bleached
    complexed with hc4
39. Domain for 2pyr:
  - Domain d2pyra_: 2pyr A: [40903]
    complexed with hc4
40. Domain for 2qj5:
  - Domain d2qj5a_: 2qj5 A: [150821]
    automated match to d1nwza_
    complexed with hc4
41. Domain for 2qj7:
  - Domain d2qj7a_: 2qj7 A: [150822]
    automated match to d1nwza_
    complexed with hc4
42. Domain for 2qws:
  - Domain d2qwsa_: 2qws A: [151438]
    automated match to d1nwza_
    complexed with dod, hc4
43. Domain for 2zoh:
  - Domain d2zoha_: 2zoh A: [171384]
    automated match to d1nwza_
    complexed with hc4
44. Domain for 2zoi:
  - Domain d2zoia_: 2zoi A: [171385]
    automated match to d1nwza_
    complexed with dod, hc4
45. Domain for 3phy:
  - Domain d3phya_: 3phy A: [40904]
    dark state (unbleached)
    complexed with hc4
46. Domain for 3pyp:
  - Domain d3pypa_: 3pyp A: [40897]
    cryotrapped early light cycle intermediate
    complexed with hc4
47. Domain for 3umd:
  - Domain d3umda_: 3umd A: [217444]
    automated match to d1nwza_
    complexed with hc4
48. Domain for 3ume:
  - Domain d3umea_: 3ume A: [217445]
    automated match to d1nwza_
    complexed with hc4
49. Domain for 3ve3:
  - Domain d3ve3a_: 3ve3 A: [217781]
    automated match to d1nwza_
    complexed with hc4
50. Domain for 3ve4:
  - Domain d3ve4a_: 3ve4 A: [217782]
    automated match to d1nwza_
    complexed with hc4
51. Domain for 4b9o:
  - Domain d4b9oa_: 4b9o A: [219374]
    automated match to d1nwza_
    complexed with hc4
52. Domain for 4bbt:
  - Domain d4bbta_: 4bbt A: [219408]
    automated match to d1nwza_
    complexed with hc4
53. Domain for 4bbu:
  - Domain d4bbua_: 4bbu A: [219409]
    automated match to d1nwza_
    complexed with hc4
54. Domain for 4bbv:
  - Domain d4bbva_: 4bbv A: [219410]
    automated match to d1nwza_
    complexed with hc4
55. Domain for 4hy8:
  - Domain d4hy8a_: 4hy8 A: [196679]
    automated match to d1nwza_
    complexed with hc4
56. Domain for 4i38:
  - Domain d4i38a_: 4i38 A: [222875]
    automated match to d1nwza_
    complexed with hc4
57. Domain for 4i39:
  - Domain d4i39a_: 4i39 A: [222876]
    automated match to d1nwza_
    complexed with hc4
58. Domain for 4i3a:
  - Domain d4i3aa_: 4i3a A: [222877]
    automated match to d1nwza_
    complexed with hc4
59. Domain for 4i3i:
  - Domain d4i3ia_: 4i3i A: [222878]
    automated match to d1ot6a_
    complexed with hc4
60. Domain for 4i3j:
  - Domain d4i3ja_: 4i3j A: [196680]
    automated match to d1ot6a_
    complexed with hc4
61. Domain for 4wl9:
  - Domain d4wl9a_: 4wl9 A: [262104]
    automated match to d1nwza_
    complexed with hc4
62. Domain for 4wla:
  - Domain d4wlaa_: 4wla A: [262115]
    automated match to d1nwza_
    complexed with hc4
63. Domain for 5gx9:
  - Domain d5gx9a_: 5gx9 A: [338480]
    automated match to d1ot6a_
    complexed with dod, hc4; mutant
64. Domain for 5hd3:
  - Domain d5hd3a_: 5hd3 A: [317510]
    automated match to d1nwza_
65. Domain for 5hd5:
  - Domain d5hd5a_: 5hd5 A: [317752]
    automated match to d1nwza_
66. Domain for 5hdc:
  - Domain d5hdca_: 5hdc A: [317777]
    automated match to d1nwza_
67. Domain for 5hdd:
  - Domain d5hdda_: 5hdd A: [317773]
    automated match to d1nwza_
68. Domain for 5hds:
  - Domain d5hdsa_: 5hds A: [317775]
    automated match to d1nwza_
69. Domain for 6mhi:
  - Domain d6mhia_: 6mhi A: [369372]
    automated match to d1nwza_
    complexed with yyz
70. Domain for 6mhn:
  - Domain d6mhna_: 6mhn A: [369369]
    automated match to d1nwza_
    complexed with yaz
71. Domain for 6mkt:
  - Domain d6mkta_: 6mkt A: [369373]
    automated match to d1nwza_
    complexed with 3ct, hc4
72. Domains for 6mmd:
  1. Domain d6mmda_: 6mmd A: [369354]
    automated match to d1nwza_
    complexed with 2lt, hc4
  2. Domain d6mmdb_: 6mmd B: [369363]
    automated match to d1nwza_
    complexed with 2lt, hc4
73. Domain for 6p4i:
  - Domain d6p4ia_: 6p4i A: [374308]
    automated match to d1nwza_
    complexed with 60f
74. Domain for 6p5d:
  - Domain d6p5da_: 6p5d A: [374325]
    automated match to d1nwza_
    complexed with 60f
75. Domain for 6p5e:
  - Domain d6p5ea_: 6p5e A: [374298]
    automated match to d1nwza_
    complexed with 60f
76. Domain for 6p5f:
  - Domain d6p5fa_: 6p5f A: [374292]
    automated match to d1nwza_
    complexed with 60f
77. Domain for 6p5g:
  - Domain d6p5ga_: 6p5g A: [374295]
    automated match to d1nwza_
    complexed with 60f
78. Domain for 6umy:
  - Domain d6umya1: 6umy A:1-125 [389462]
    Other proteins in same PDB: d6umya2
    automated match to d1nwza_
    complexed with hc4, phi
79. Domain for 6umz:
  - Domain d6umza1: 6umz A:1-125 [389464]
    Other proteins in same PDB: d6umza2
    automated match to d1nwza_
    complexed with qbv
80. Domain for 6un0:
  - Domain d6un0a1: 6un0 A:1-125 [389460]
    Other proteins in same PDB: d6un0a2
    automated match to d1nwza_
    complexed with phi, qbv
81. Domain for 6un2:
  - Domain d6un2a_: 6un2 A: [389423]
    automated match to d1nwza_
    complexed with hc4
82. Domain for 7av6:
  - Domain d7av6a1: 7av6 A:25-125 [404411]
    Other proteins in same PDB: d7av6a2
    automated match to d2i9va_
    complexed with fmt

More info for Protein Photoactive yellow protein, PYP from d.110.3.1: PYP-like

Timeline for Protein Photoactive yellow protein, PYP from d.110.3.1: PYP-like:

Protein Photoactive yellow protein, PYP from d.110.3.1: PYP-like first appeared (with stable ids) in SCOP 1.55, called Protein Photoactive yellow protein, PYP from d.110.3.1: Photoactive yellow protein, PYP
Protein Photoactive yellow protein, PYP from d.110.3.1: PYP-like appears in SCOPe 2.06
Protein Photoactive yellow protein, PYP from d.110.3.1: PYP-like appears in the current release, SCOPe 2.08