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
2ozl d2ozla1 A:28-56,90-99,101-111,125-129,130-136
1ni4 d1ni4a_ A:28-56,90-99,101-111,125-129,130-136
2ozl d2ozlc1 C:28-56,90-99,101-111,125-129,130-136
1ni4 d1ni4c_ C:28-56,91-99,101-111,125-129,130-136
1v1r d1v1ra_ A:53-81,112-123,125-135,150-154,155-160
2bfb d2bfba1 A:53-81,112-123,125-135,150-154,155-160
1olu d1olua_ A:53-81,112-123,125-135,150-154,155-160
1x80 d1x80a_ A:53-81,111-123,125-135,150-154,155-160
2bfc d2bfca1 A:53-81,111-123,125-135,150-154,155-160
1x7w d1x7wa_ A:53-81,111-123,125-135,150-154,155-160
1x7y d1x7ya_ A:53-81,111-123,125-135,150-154,155-160
1ols d1olsa_ A:53-81,111-123,125-135,150-154,155-160
1v16 d1v16a_ A:53-81,111-123,125-135,150-154,155-160
1v1m d1v1ma_ A:53-81,111-123,125-135,150-154,155-160
1v11 d1v11a_ A:53-81,111-123,125-135,150-154,155-160
1x7x d1x7xa_ A:53-81,111-123,125-135,150-154,155-160
1dtw d1dtwa_ A:53-81,115-123,125-135,150-154,155-160
2bev d2beva1 A:53-81,115-123,125-135,150-154,155-160
1wci d1wcia1 A:53-81,115-123,125-135,150-154,155-160
2bfe d2bfea1 A:53-81,115-123,125-135,150-154,155-160
2beu d2beua1 A:53-81,115-123,125-135,150-154,155-160
2bew d2bewa1 A:53-81,115-123,125-135,150-154,155-160
2bfd d2bfda1 A:53-81,115-123,125-135,150-154,155-160
1u5b d1u5ba_ A:53-81,115-123,125-135,150-154,155-160
2bff d2bffa1 A:53-81,115-123,125-135,150-154,155-160
1x7z d1x7za_ A:53-81,115-123,125-135,150-154,155-160
1umd d1umda_ A:34-62,97-105,107-117,132-136,137-142
1um9 d1um9a_ A:34-62,97-105,107-117,132-136,137-142
1umb d1umba_ A:34-62,97-105,107-117,132-136,137-142
1olx d1olxa_ A:53-81,115-123,125-135,150-154,155-160
1um9 d1um9c_ C:34-62,97-105,107-117,132-136,137-142
1umd d1umdc_ C:34-62,97-105,107-117,132-136,137-142
1umb d1umbc_ C:34-62,97-105,107-117,132-136,137-142
1umc d1umcc_ C:34-62,97-105,107-117,132-136,137-142
1umc d1umca_ A:34-62,97-105,107-117,132-136,137-142
2bp7 d2bp7c1 C:73-101,135-143,145-155,170-174,175-180
2bp7 d2bp7g1 G:73-101,135-143,145-155,170-174,175-180
1qs0 d1qs0a_ A:73-101,135-143,145-155,170-174,175-180
2bp7 d2bp7a1 A:73-101,135-143,145-155,170-174,175-180
2bp7 d2bp7e1 E:73-101,135-143,145-155,170-174,175-180
2. d.67.2 Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
RRF/tRNA synthetase additional domain-like core: alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
1f7v d1f7va3 A:18-26,30-48,50-59,67-72,108-115
1f7u d1f7ua3 A:18-25,30-48,50-59,68-73,108-115
3. d.51.1 Eukaryotic type KH-domain (KH-domain type I) Prokaryotic and eukaryotic domains share a KH-motif but have different topologies !
Eukaryotic type KH-domain (KH-domain type I) beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
1tua d1tuaa1 A:22-33,55-72,74-84,128-134,135-142
4. e.3.1 beta-lactamase/transpeptidase-like
beta-lactamase/transpeptidase-like contains a cluster of helices and an alpha+beta sandwich
3dwk d3dwkc2 C:396-414,471-483,504-518,519-523,543-547
3dwk d3dwkb2 B:396-414,471-483,504-518,519-523,543-547
3dwk d3dwka2 A:396-414,471-483,504-518,519-523,543-547
3dwk d3dwkd2 D:396-414,471-483,504-518,519-523,543-547
2olu d2olua2 A:396-414,471-483,504-518,519-523,543-547
2olv d2olvb2 B:396-414,471-483,504-518,519-523,543-547
2olv d2olva2 A:396-414,471-483,504-518,519-523,543-547
1u60 d1u60b_ B:64-81,131-148,201-215,216-220,221-225
2z2m d2z2mb1 B:335-351,408-420,457-471,472-476,497-502
1u60 d1u60a_ A:64-81,131-148,201-215,216-220,221-225
2zc3 d2zc3b1 B:336-351,408-420,457-471,472-476,497-502
2z2l d2z2lb1 B:336-351,408-420,457-471,472-476,497-502
1u60 d1u60c_ C:64-81,131-148,201-215,216-220,221-225
1u60 d1u60d_ D:64-81,131-148,201-215,216-220,221-225
5. e.8.1 DNA/RNA polymerases "palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain !
DNA/RNA polymerases divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
1s77 d1s77d_ D:100-110,110-130,133-159,745-749,753-757
1msw d1mswd_ D:100-110,110-130,133-158,744-750,752-758
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1165 (enumeration index: query2073) of S5
1zx4 A:206-221,223-235,248-274,276-281,289-297
2wae A:384-400,467-486,524-538,539-543,569-574
3exg K:28-56,90-99,101-111,125-129,130-136
3exg C:28-56,90-99,101-111,125-129,130-136
3exg Q:28-56,90-99,101-111,125-129,130-136
3exg S:28-56,90-99,101-111,125-129,130-136
3exg A:28-56,90-99,101-111,125-129,130-136
3exg W:28-56,90-99,101-111,125-129,130-136
3exg O:28-56,90-99,101-111,125-129,130-136
3exg I:28-56,90-99,101-111,125-129,130-134
3exg Y:28-56,90-99,101-111,125-129,130-136
3exg 1:28-56,90-99,101-111,125-129,130-136
3exg M:28-56,90-99,101-111,125-129,130-135
3exg U:28-56,90-99,101-111,125-129,130-136
3exg 5:28-56,90-99,101-111,125-129,130-136
3exg G:28-56,90-99,101-111,125-129,130-135
3exg E:28-56,90-99,101-111,125-129,130-136
3exg 3:28-56,90-99,101-111,125-129,130-136
2y0p A:475-501,541-551,553-563,579-588,593-602
2y0p D:475-501,541-551,553-563,579-588,593-602
2y0p C:475-501,541-551,553-563,579-588,593-602
2y0p B:475-501,541-551,553-563,579-588,593-602
2e3u A:53-64,86-103,105-115,160-166,167-174
3aev B:53-64,86-103,105-115,160-166,167-174
3exi A:28-56,90-99,101-111,125-129,130-136
2j9f C:53-81,115-123,125-135,150-154,155-160
2j9f A:53-81,115-123,125-135,150-154,155-160
2wad B:384-400,467-486,524-538,539-543,569-574
2wad A:384-400,467-486,524-538,539-543,569-574
3i4x A:9-19,33-45,47-63,87-95,406-415
3i4x B:9-19,33-45,47-63,87-95,406-415
3i4z B:9-19,33-45,47-63,87-95,406-415
3i4z A:9-19,33-45,47-63,87-95,406-415
3exh G:28-56,90-99,101-111,125-129,130-134
3exh A:28-56,90-99,101-111,125-129,130-136
3exh E:28-56,90-99,101-111,125-129,130-136
3exh C:28-56,91-99,101-111,125-129,130-136
2yid B:475-501,541-551,553-563,579-588,593-602
2yid A:475-501,541-551,553-563,579-588,593-602
2yid C:475-501,541-551,553-563,579-588,593-602
2yid D:475-501,541-551,553-563,579-588,593-602
3exe E:28-56,90-99,101-111,125-129,130-136
3exe C:28-56,90-99,101-111,125-129,130-136
3exe A:28-56,90-99,101-111,125-129,130-136
3iyl W:80-104,114-128,130-138,155-160,161-166
3o24 A:16-26,40-52,54-73,100-108,443-452
3czd A:284-301,350-367,423-437,438-442,443-447
3exf G:28-56,90-99,101-111,125-129,130-136
3exf A:28-56,90-99,101-111,125-129,130-136
3exf C:28-56,90-99,101-111,125-129,130-136
3exf E:28-56,90-99,101-111,124-129,130-135
2aga A:34-57,59-70,81-93,115-122,166-172