1. c.66.1 S-adenosyl-L-methionine-dependent methyltransferases
S-adenosyl-L-methionine-dependent methyltransferases core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
2py6 d2py6a1 A:169-180,182-199,371-387,390-397,401-408
2py6 d2py6a1 A:161-170,182-199,371-387,390-397,401-408
2. d.150.1 4'-phosphopantetheinyl transferase possibly related to the IspF (
4'-phosphopantetheinyl transferase beta-alpha(3)-beta(2) motif
1f80 d1f80c_ C:18-31,31-41,42-65,77-83,85-91
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:22-33,55-72,74-84,86-93,135-142
4. d.145.1 FAD-binding/transporter-associated domain-like
FAD-binding/transporter-associated domain-like consists of two alpha+beta subdomains
1jrp d1jrpc4 C:248-257,260-271,292-302,347-354,362-374
1jrp d1jrpe4 E:248-257,260-270,292-302,347-354,362-374
1jrp d1jrpa4 A:248-257,260-270,292-302,347-354,362-374
1jrp d1jrpg4 G:248-261,260-270,292-302,347-354,362-374
1jro d1jroe4 E:248-261,260-270,292-302,347-354,362-374
1jro d1jrog4 G:248-261,260-270,292-302,347-354,362-374
1jro d1jroc4 C:248-261,260-270,292-302,347-354,362-374
1jro d1jroa4 A:248-261,260-270,292-302,347-354,362-374
5. a.160.1 PAP/OAS1 substrate-binding domain this domain follows the catalytic nucleotidyltransferase domain !
PAP/OAS1 substrate-binding domain core: 5-helical bundle; up-and-down; right-handed twist
1tfy d1tfyd1 D:141-159,171-183,184-195,198-204,205-211
2dr5 d2dr5a1 A:141-159,171-183,184-195,198-204,205-211
2zh4 d2zh4a1 A:144-159,171-183,184-195,198-204,205-211
2zh2 d2zh2a1 A:144-159,171-183,184-195,198-204,205-211
1tfw d1tfwb1 B:141-159,171-183,184-195,198-204,205-211
2dra d2draa1 A:144-159,171-183,184-195,198-204,205-211
1tfw d1tfwc1 C:141-159,171-183,184-195,198-204,205-211
1ueu d1ueua1 A:144-159,171-183,184-195,198-204,205-211
2zh5 d2zh5a1 A:144-159,171-183,184-195,198-204,205-211
1tfy d1tfya1 A:141-159,171-183,184-195,198-204,205-211
1tfy d1tfyb1 B:141-159,171-183,184-195,198-204,205-211
2zh6 d2zh6a1 A:141-159,171-183,184-195,198-204,205-211
1uev d1ueva1 A:144-159,171-183,184-195,198-204,205-211
2zh3 d2zh3a1 A:144-159,171-183,184-195,198-204,205-211
1r8b d1r8ba1 A:141-159,171-183,184-195,198-204,205-211
2dr9 d2dr9a1 A:141-159,171-183,184-195,198-204,205-211
1r8a d1r8aa1 A:141-159,171-183,184-195,198-204,205-211
1r89 d1r89a1 A:141-159,171-183,184-195,198-204,205-211
2drb d2drba1 A:141-159,171-183,184-195,198-204,205-211
2dr7 d2dr7a1 A:144-159,171-183,184-195,198-204,205-211
2dr8 d2dr8a1 A:141-159,171-183,184-195,198-204,205-211
2dvi d2dvia1 A:141-159,171-183,184-195,198-204,205-211
1uet d1ueta1 A:144-159,171-183,184-195,198-204,205-211
1tfy d1tfyc1 C:141-159,171-183,184-195,198-204,205-211
2zh1 d2zh1a1 A:144-159,171-183,184-195,198-204,205-211
2zhb d2zhba1 A:144-159,171-183,184-195,198-204,205-211
2zh8 d2zh8a1 A:144-159,171-183,184-195,198-204,205-211
1sz1 d1sz1a1 A:141-159,171-183,184-195,198-204,205-211
1sz1 d1sz1b1 B:141-159,171-183,184-195,198-204,205-211
2zh9 d2zh9a1 A:141-159,171-183,184-195,198-204,205-211
1tfw d1tfwd1 D:141-159,171-183,184-195,198-203,206-211
6. e.50.1 AF1104-like
AF1104-like 2 domains; d1: [all-alpha; 3-helical bundle, similar to the immunoglobulin/albumin-binding domain-like fold (scop_cf 46996)]; d2: [alpha/beta; 3 layers, a/b/a; 6-stranded mixed beta-sheet, order: 321456, strand 6 is antiparallel to the rest]
2ffj d2ffja1 A:85-96,98-110,122-138,259-267,280-288
2ffj d2ffjb1 B:85-96,98-113,122-138,259-267,280-288
2g8l d2g8la1 A:69-93,96-110,117-132,255-263,276-283
7. c.7.1 PFL-like glycyl radical enzymes duplication: the N- and C-terminal halves have similar topologies !
PFL-like glycyl radical enzymes contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
1l1l d1l1lc_ C:8-20,47-63,71-92,93-97,420-425
1l1l d1l1lb_ B:8-20,47-63,71-92,93-97,420-425
8. 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:18-26,30-48,50-59,99-107,108-115
1f7u d1f7ua3 A:18-25,30-48,50-59,99-107,108-115
9. a.25.1 Ferritin-like contains bimetal-ion centre in the middle of the bundle !
Ferritin-like core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection
1yv1 d1yv1b1 B:28-58,59-89,135-163,170-176,177-183
1yv1 d1yv1a1 A:28-58,59-89,135-163,170-176,177-183
10. 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
1r6b d1r6bx3 X:654-677,683-696,699-723,728-738,739-749
1ksf d1ksfx3 X:654-677,683-696,699-723,728-738,739-749
1qvr d1qvra3 A:758-781,787-800,803-827,831-840,843-849
1qvr d1qvrb3 B:758-781,787-800,803-827,831-840,843-848
1qvr d1qvrc3 C:758-781,787-800,803-827,831-841,842-848
11. e.58.1 Viral ssDNA binding protein
Viral ssDNA binding protein 2 domains; d1: [large alpha+beta domain subdivided into the 'head', 'neck' and 'shoulders' regions; in the 'neck', there is an OB-fold interrupted by large insertions]; d2: [all-alpha, 6 helices; orthogonal array]
1urj d1urjb_ B:309-334,666-694,702-719,975-988,998-1004
1urj d1urja_ A:308-334,666-694,702-719,975-988,998-1004
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1164 (enumeration index: query2061) of S5
2xo5 C:124-136,168-184,185-203,204-208,463-469
2xo5 A:124-136,168-184,185-203,204-208,463-469
3pxi A:715-738,744-758,760-784,790-798,799-807
3pxi B:715-738,744-758,760-784,790-798,799-807
3pxi C:715-738,744-758,760-784,790-798,799-807
2w3r E:248-261,260-270,292-302,347-354,363-374
2w3r G:248-261,260-270,292-302,347-354,363-374
2w3r C:248-261,260-270,292-302,347-354,362-374
2w3r A:248-261,260-270,292-302,347-354,362-374
2e3u A:53-64,86-103,105-115,117-124,167-174
3o2k A:16-26,40-52,54-70,185-194,196-205
3o2k A:16-26,40-52,54-70,100-108,109-117
2wat E:1783-1791,1792-1802,1804-1824,1836-1842,1846-1852
2wat A:1783-1791,1792-1802,1804-1824,1836-1842,1846-1852
3qmn M:22-32,32-42,44-64,75-82,84-91
3qmn H:22-32,32-43,44-64,75-82,84-91
3qmn D:22-32,32-42,44-64,75-82,84-91
3aev B:53-64,86-103,105-115,117-123,167-174
2w55 C:248-261,260-271,292-302,347-354,362-374
2w55 A:248-261,260-270,292-302,347-354,362-374
2w55 G:248-261,260-270,292-302,347-354,363-374
2w55 E:248-261,260-271,292-302,347-354,362-374
2xaw A:124-136,168-182,185-203,204-208,463-469
2cvt A:127-136,166-180,182-196,197-201,444-450
3ouy B:141-159,171-183,184-195,198-204,205-211
3ouy A:141-159,171-183,184-195,198-204,205-211
3ov7 B:141-159,171-183,184-195,198-204,205-211
3ov7 A:141-159,171-183,184-195,198-204,205-211
2w54 G:248-261,260-270,292-302,347-354,362-374
2w54 E:248-261,260-271,292-302,347-354,362-374
2w54 C:248-261,260-271,292-302,347-354,362-374
2w54 A:248-261,260-271,292-302,347-354,362-374
2w3s G:248-261,260-270,292-302,347-354,362-374
2w3s C:248-261,260-271,292-302,347-354,362-374
2w3s A:248-261,260-270,292-302,347-354,362-374
2w3s E:248-261,260-271,292-302,347-354,362-374
3ova A:144-159,171-183,184-195,198-204,205-211
2was F:1783-1792,1792-1802,1804-1823,1836-1842,1846-1852
3i4x B:9-19,33-45,47-63,87-95,96-104
3i4x A:9-19,33-45,47-63,172-181,182-191
3i4x A:9-19,33-45,47-63,87-95,96-104
3i4x B:9-19,33-45,47-63,172-181,182-191
3i4z A:9-19,33-45,47-63,172-181,182-191
3i4z A:9-19,33-45,47-63,87-95,96-104
3i4z B:9-19,33-45,47-63,172-181,182-191
3i4z B:9-19,33-45,47-63,87-95,96-104
3hrq A:1335-1343,1354-1374,1538-1556,1572-1577,1611-1626
3hrq B:1335-1343,1354-1375,1538-1556,1572-1577,1611-1626
3hrq A:1335-1343,1354-1374,1538-1556,1564-1573,1611-1626
3hrq B:1335-1343,1354-1375,1538-1556,1564-1573,1611-1626
3hmj B:1783-1791,1792-1802,1804-1824,1836-1842,1846-1852
3hmj C:1783-1791,1792-1802,1804-1824,1836-1842,1846-1852
3hmj A:1783-1791,1792-1802,1804-1824,1836-1842,1846-1852
3ovb B:141-159,171-183,184-195,198-204,205-211
3ovb A:141-159,171-183,184-195,198-204,205-211
3ovs B:144-159,171-183,184-195,198-204,205-211
3ovs A:141-159,171-183,184-195,198-204,205-211
3o24 A:16-26,40-52,54-73,185-194,196-205
3o24 A:16-26,40-52,54-73,100-108,109-117
3hrr A:1335-1343,1354-1374,1538-1556,1572-1577,1611-1626
3hrr B:1335-1343,1354-1374,1538-1556,1572-1577,1611-1626
3hrr B:1335-1343,1354-1374,1538-1556,1564-1573,1611-1626
3hrr A:1335-1343,1354-1374,1538-1556,1564-1573,1611-1626
3iuz A:14-26,40-61,60-74,78-88,235-242
2ff4 B:32-46,51-61,156-185,306-312,327-336
2ff4 A:32-46,51-61,156-185,306-312,327-336
2fez A:32-46,51-61,156-185,306-312,327-336