1. c.36.1 Thiamin diphosphate-binding fold (THDP-binding) there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules ! two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules !
Thiamin diphosphate-binding fold (THDP-binding) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
2r8o d2r8oa1 A:334-352,356-373,453-461,495-509,511-519
2r5n d2r5nb1 B:334-352,356-373,454-461,495-509,512-519
2r8p d2r8pb1 B:334-352,356-373,453-461,495-510,511-519
2r8o d2r8ob1 B:334-352,356-373,453-461,495-510,511-519
2r5n d2r5na1 A:334-352,356-373,453-461,495-510,511-519
1qgd d1qgda1 A:334-352,356-373,454-461,495-510,512-519
1qgd d1qgdb1 B:334-352,356-373,454-461,495-510,512-519
2r8p d2r8pa1 A:334-352,356-373,454-461,495-510,512-519
1umc d1umcc_ C:34-62,73-85,196-204,239-257,259-267
1umd d1umdc_ C:34-62,73-85,196-204,239-257,259-267
1umb d1umbc_ C:34-62,73-85,196-204,239-257,259-267
1umc d1umca_ A:34-62,73-85,196-204,239-257,259-267
1umb d1umba_ A:34-62,73-85,196-204,239-257,259-267
1umd d1umda_ A:34-62,73-85,196-204,239-257,259-267
1w88 d1w88a_ A:42-70,81-93,194-202,237-255,257-265
1um9 d1um9c_ C:34-62,73-85,196-205,239-257,259-268
2bp7 d2bp7g1 G:73-101,109-124,234-243,278-296,298-307
1um9 d1um9a_ A:34-62,73-85,196-205,239-257,259-268
1w88 d1w88g_ G:42-70,81-93,194-202,237-255,257-265
1w88 d1w88c_ C:42-70,81-93,194-202,237-255,257-265
2bp7 d2bp7a1 A:73-101,109-124,234-243,278-296,298-307
1qs0 d1qs0a_ A:73-101,109-124,234-243,278-296,298-307
2bp7 d2bp7e1 E:73-101,109-124,234-243,278-296,298-307
1w85 d1w85e_ E:42-70,81-92,194-202,237-255,257-265
1w85 d1w85a_ A:42-70,81-92,194-202,237-255,257-265
1w88 d1w88e_ E:42-70,81-93,194-202,237-255,257-265
1w85 d1w85g_ G:42-70,81-92,194-202,237-255,257-265
1w85 d1w85c_ C:42-70,81-92,194-202,237-255,257-265
1x7z d1x7za_ A:53-81,89-104,213-222,257-276,276-285
2bff d2bffa1 A:53-81,89-104,213-222,257-276,276-285
2bp7 d2bp7c1 C:73-101,109-124,234-243,278-296,298-307
2ozl d2ozla1 A:28-56,68-80,188-196,229-247,249-257
2bfb d2bfba1 A:53-81,92-104,212-222,257-276,276-285
1x7w d1x7wa_ A:53-81,92-104,213-222,257-276,276-285
1ni4 d1ni4a_ A:28-56,65-80,188-196,229-247,249-257
1x7y d1x7ya_ A:53-81,92-104,213-222,257-276,276-285
2ozl d2ozlc1 C:28-56,68-80,188-196,229-247,249-257
1x7x d1x7xa_ A:53-81,92-104,212-222,257-276,276-285
2bfc d2bfca1 A:53-81,92-104,212-222,257-276,276-285
1v11 d1v11a_ A:53-81,89-104,213-222,257-276,276-285
1ols d1olsa_ A:53-81,89-104,212-222,257-276,276-285
1ni4 d1ni4c_ C:28-56,68-80,188-196,229-247,249-257
1dtw d1dtwa_ A:53-81,89-104,213-223,257-276,276-286
1v1m d1v1ma_ A:53-81,89-104,212-222,257-276,276-285
2bfd d2bfda1 A:53-81,89-104,213-222,257-276,276-285
2bfe d2bfea1 A:53-81,92-104,212-222,257-276,276-285
1v16 d1v16a_ A:53-81,89-104,213-222,257-276,276-285
1v1r d1v1ra_ A:53-81,89-104,213-222,257-276,276-285
2beu d2beua1 A:53-81,89-104,213-223,257-276,276-286
1olu d1olua_ A:53-81,92-104,212-222,257-276,276-285
1wci d1wcia1 A:53-81,89-104,213-223,257-276,276-286
1olx d1olxa_ A:53-81,89-104,213-222,257-276,276-285
2bev d2beva1 A:53-81,89-104,213-223,257-276,276-286
1u5b d1u5ba_ A:53-81,92-104,213-223,257-276,276-286
1x80 d1x80a_ A:53-81,89-104,213-222,257-276,276-285
2bew d2bewa1 A:53-81,89-104,213-223,257-276,276-286
2. c.37.1 P-loop containing nucleoside triphosphate hydrolases division into families based on beta-sheet topologies !
P-loop containing nucleoside triphosphate hydrolases 3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
1w36 d1w36g2 G:364-377,377-389,393-398,562-573,575-581
1w36 d1w36d2 D:364-377,377-389,393-398,562-573,575-581
3. c.56.5 Zn-dependent exopeptidases core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest !
Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
1lfw d1lfwa1 A:12-27,42-60,80-89,119-138,171-176
4. c.22.1 Ribosomal protein L4
Ribosomal protein L4 3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
2hgj d2hgjf1 F:29-45,102-122,121-126,182-190,190-196
2hgq d2hgqf1 F:29-45,102-122,121-126,182-190,190-196
3dll d3dllc1 C:23-40,96-116,115-120,176-184,184-189
2hgu d2hguf1 F:29-45,102-122,121-126,182-190,190-195
1xbp d1xbpc1 C:23-40,96-115,116-120,176-184,184-189
5. c.46.1 Rhodanese/Cell cycle control phosphatase
Rhodanese/Cell cycle control phosphatase 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
1yt8 d1yt8a4 A:195-210,244-263,264-268,331-346,348-353
6. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
1nwy d1nwyc_ C:23-40,96-116,115-120,176-184,184-190
1pnu d1pnuc_ C:23-40,96-115,116-121,176-184,184-190
1pny d1pnyc_ C:23-40,96-115,116-121,176-184,184-190
1jzy d1jzyk_ K:23-40,96-115,116-120,176-184,184-190
1jzx d1jzxk_ K:23-40,96-115,116-120,176-184,184-190
1k01 d1k01k_ K:23-40,96-115,116-120,176-184,184-190
1j5a d1j5ak_ K:23-40,96-115,116-120,176-184,184-190
1jzz d1jzzk_ K:23-40,96-115,116-120,176-184,184-190
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1131 (enumeration index: query2645) of S5
3ahc A:18-42,64-86,206-215,255-285,290-298
2yic D:475-501,511-529,669-678,713-732,732-741
2yic C:475-501,511-529,670-678,713-732,733-741
2yic B:475-501,511-529,670-678,713-732,733-741
2yic A:475-501,511-529,670-678,713-732,733-741
3kiy F:29-45,102-121,122-126,182-190,190-195
2y11 F:29-46,102-121,122-126,182-190,190-195
3ahh A:18-42,64-86,206-215,255-285,290-298
3exg M:28-56,68-80,188-197,229-247,249-258
3exg Y:28-56,68-80,188-197,229-247,249-258
3exg 1:28-56,68-80,188-196,229-247,249-257
3exg 3:28-56,68-80,188-196,229-247,249-257
3exg A:28-56,68-80,188-196,229-247,249-257
3exg K:28-56,68-80,188-197,229-247,249-258
3exg U:28-56,68-80,188-197,229-247,249-258
3exg C:28-56,68-80,188-196,229-247,249-257
3exg W:28-56,68-80,188-196,229-247,249-257
3exg G:28-56,68-80,188-196,229-247,249-257
3exg Q:28-56,68-80,188-197,229-247,249-258
3exg E:28-56,68-80,188-197,229-247,249-258
3exg 5:28-56,65-80,188-196,229-247,249-257
3exg S:28-56,68-80,188-196,229-247,249-257
3exg I:28-56,68-80,188-196,229-247,249-257
3exg O:28-56,68-80,188-196,229-247,249-257
2y13 F:29-45,102-121,122-126,182-190,190-195
2o1x A:26-47,58-70,175-183,263-277,279-287
2o1x B:26-47,58-70,175-183,263-277,279-287
2o1x D:26-48,58-70,175-183,263-277,279-287
2o1x C:26-49,58-70,175-183,263-278,279-287
3pip C:23-40,96-116,115-121,176-184,184-189
3hux F:29-45,102-121,122-126,182-190,190-195
2wdi F:29-46,102-121,122-126,182-190,190-195
2x9u F:29-45,102-121,122-126,182-190,190-195
3zvp F:29-45,102-121,122-126,182-190,190-195
3kom A:334-352,356-373,454-463,496-511,512-520
3kom B:334-352,356-373,454-463,496-511,512-520
2y0p C:475-501,511-529,670-678,713-732,733-741
2y0p B:475-501,511-529,670-678,713-732,733-741
2y0p A:475-501,511-529,670-678,713-732,733-741
2y0p D:475-501,511-529,670-678,713-732,733-741
3k70 G:364-377,377-389,393-398,562-573,575-581
3k70 D:364-377,377-389,393-398,562-573,575-581
3ahe A:18-42,65-86,206-215,255-285,290-298
3ahj A:18-42,64-86,206-215,255-285,290-298
3ooy B:8-34,44-56,177-185,220-230,235-242
3ooy A:8-34,44-56,177-185,220-230,235-242
3mos A:8-34,44-56,177-185,220-231,235-242
2wh2 F:29-45,102-121,122-126,182-190,190-195
2jgd B:196-222,232-250,381-390,426-445,445-454
2jgd A:196-222,232-250,381-390,426-445,445-454
2xqe F:29-45,102-121,122-126,182-190,190-195
3kcr E:24-41,97-116,118-123,176-184,184-189
3ai7 C:18-42,64-86,206-215,255-285,290-298
3ai7 D:18-42,64-86,206-215,255-285,290-298
3ai7 G:18-42,64-86,206-215,255-285,290-298
3ai7 E:18-42,64-86,206-215,255-285,290-298
3ai7 A:18-42,64-86,206-215,255-285,290-298
3ai7 B:18-42,64-86,206-215,255-285,290-298
3ai7 F:18-42,67-86,206-215,255-285,290-298
3ai7 H:18-42,64-86,206-215,255-285,290-298
2wdn F:29-45,102-121,122-126,182-190,190-195
3exi A:28-56,68-80,188-197,229-247,249-258
3dv0 E:42-70,81-93,194-202,237-255,257-265
3dv0 A:42-70,81-93,194-202,237-255,257-265
3dv0 G:42-70,81-93,194-202,237-255,257-265
3dv0 C:42-70,81-93,194-202,237-255,257-265
3ki9 A:9-24,39-57,77-86,115-134,167-172
2j9f A:53-81,89-104,213-223,257-276,276-286
2j9f C:53-81,89-104,213-223,257-276,276-286
2xt6 A:475-501,511-529,669-678,713-732,732-741
2xt6 B:475-501,511-529,669-678,713-732,732-741
3kir F:29-45,102-121,122-126,182-190,190-195
3ahf A:18-42,64-86,206-215,255-285,290-298
3duf A:42-70,81-93,194-202,237-255,257-265
3duf C:42-70,81-93,194-202,237-255,257-265
3duf G:42-70,81-92,194-202,237-255,257-265
3duf E:42-70,81-93,194-202,237-255,257-265
2x9s F:29-45,102-121,122-126,182-190,190-195
3uk1 A:355-371,375-392,478-487,520-534,535-543
3uk1 B:355-371,375-392,478-487,520-534,535-543
2wdj F:29-46,102-121,122-126,182-190,190-195
2y17 F:29-45,102-121,122-126,182-190,190-195
3kiw F:29-45,102-121,122-126,182-190,190-195
3i9c F:29-45,102-121,122-126,182-190,190-195
3kno F:29-45,102-121,122-126,182-190,190-195
2xux F:29-45,102-121,122-126,182-190,190-195
2xt9 A:475-501,511-529,670-678,713-732,733-741
2xta A:475-501,511-529,669-678,713-732,732-741
2xta C:475-501,511-529,669-678,713-732,732-741
2xta D:475-501,511-529,669-678,713-732,732-741
2xta B:475-501,511-529,669-678,713-732,732-741
3exh A:28-56,68-80,188-196,229-247,249-257
3exh E:28-56,68-80,188-196,229-247,249-257
3exh G:28-56,68-80,188-196,229-247,249-257
3exh C:28-56,65-80,188-196,229-247,249-257
3m34 A:2-25,35-46,174-182,216-230,233-240
3ahg A:18-42,64-86,206-215,255-285,290-298
2yid C:475-501,511-529,670-678,713-732,733-741
2yid B:475-501,511-529,669-678,713-732,732-741
2yid D:475-501,511-529,669-678,713-732,732-741
2yid A:475-501,511-529,669-678,713-732,732-741
2y15 F:29-45,102-121,122-126,182-190,190-195
3dva E:42-70,81-93,194-202,237-255,257-265
3dva C:42-70,81-92,194-202,237-255,257-265
3dva G:42-70,81-93,194-202,237-255,257-265
3dva A:42-70,81-93,194-202,237-255,257-265
3kit F:29-45,102-121,122-126,182-190,190-195
2wdl F:29-45,102-121,122-126,182-190,190-195
3exe E:28-56,68-80,188-196,229-247,249-257
3exe C:28-56,68-80,188-196,229-247,249-257
3exe G:28-56,68-80,188-196,229-247,249-257
3exe A:28-56,65-79,188-196,229-247,249-257
2o1s C:24-44,56-68,173-181,258-272,274-282
2o1s B:24-40,53-68,173-181,258-272,274-282
2o1s D:24-41,53-68,173-181,258-273,274-282
2o1s A:24-43,56-68,173-181,258-272,274-282
2y19 F:29-46,102-121,122-126,182-190,190-195
2y0z F:29-45,102-121,122-126,182-190,190-195
3ahd A:18-42,64-86,206-215,255-285,290-298
3ahi A:18-42,64-86,206-215,255-285,290-298
2wh4 F:29-45,102-121,122-126,182-190,190-195
3exf A:28-56,68-80,188-196,229-247,249-257
3exf E:28-56,68-80,188-196,229-247,249-257
3exf C:28-56,65-80,188-196,229-247,249-257
3exf G:28-56,68-80,188-196,229-247,249-257