1. 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]
2q40 d2q40a1 A:134-146,147-165,221-241,334-343,356-365
1xfi d1xfia_ A:134-146,147-165,221-241,334-343,356-365
2. a.289.1 Sec63 N-terminal domain-like
Sec63 N-terminal domain-like multihelical; consists of two helical subdomains
2q0z d2q0zx1 X:34-45,111-127,128-145,255-265,266-276
3. d.153.1 N-terminal nucleophile aminohydrolases (Ntn hydrolases) N-terminal residue provides two catalytic groups, nucleophile and proton donor !
Ntn hydrolase-like 4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
2nlz d2nlzc1 C:271-287,293-315,440-459,470-474,477-482
2nlz d2nlza1 A:271-287,293-315,440-459,470-474,477-482
2nlz d2nlzb1 B:271-287,293-315,440-459,470-474,477-482
2nlz d2nlzd1 D:271-287,293-315,440-459,470-474,477-482
4. d.213.1 VSV matrix protein
VSV matrix protein beta-alpha(2)-beta(4)-alpha-beta(2); two layers: alpha/beta; bifurcated coiled beta-sheet: order of the first 5 strands: 23154
1lg7 d1lg7a_ A:80-93,101-116,198-209,209-215,219-226
5. d.3.1 Cysteine proteinases the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet !
Cysteine proteinases consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
2im9 d2im9a1 A:49-70,75-88,117-132,300-309,312-318
2im9 d2im9a1 A:49-70,75-88,117-132,266-274,288-299
2im9 d2im9a1 A:49-70,75-88,117-132,173-177,332-341
6. a.118.8 TPR-like
alpha-alpha superhelix multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
1ya0 d1ya0a1 A:357-375,386-401,447-471,474-480,481-487
1ya0 d1ya0b1 B:357-375,386-401,447-471,474-480,481-487
7. d.14.1 Ribosomal protein S5 domain 2-like
Ribosomal protein S5 domain 2-like core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
1k47 d1k47e1 E:105-123,127-143,148-157,158-165,188-194
1k47 d1k47c1 C:105-123,127-143,148-157,158-165,188-194
1k47 d1k47d1 D:105-123,127-143,148-157,158-165,188-194
1k47 d1k47f1 F:105-123,127-143,148-157,158-165,188-194
1k47 d1k47b1 B:105-123,127-143,148-157,158-165,188-194
1uek d1ueka1 A:58-72,114-123,123-132,134-139,142-147
8. d.334.1 IlvD/EDD N-terminal domain-like
IlvD/EDD N-terminal domain-like contains a large cluster of helices and a mixed beta-sheet of 4 strands; order 2134, strands 3 and 4 are parallel
2gp4 d2gp4b2 B:283-298,300-315,319-331,419-426,427-434
2gp4 d2gp4a2 A:283-298,300-315,319-331,419-426,427-434
9. e.13.1 DNA primase core
DNA primase core 2 domains: (1) alpha+beta; (2) toprim alpha/beta
1eqn d1eqnb_ B:115-134,164-176,175-186,187-192,194-199
1eqn d1eqnc_ C:115-134,164-176,175-186,187-192,194-199
1dd9 d1dd9a_ A:115-133,166-176,175-186,187-191,195-199
10. c.94.1 Periplasmic binding protein-like II Similar in architecture to the superfamily I but partly differs in topology !
Periplasmic binding protein-like II consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication ! mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
2ons d2onsa1 A:133-140,153-171,172-184,188-192,193-200
2onr d2onra1 A:133-140,153-171,172-184,188-192,193-199
2onk d2onke1 E:130-141,153-171,172-180,188-192,193-200
2onk d2onkj1 J:130-141,153-171,172-180,188-192,193-200
11. a.7.3 Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
Spectrin repeat-like 3 helices; bundle, closed, left-handed twist; up-and-down
1l0v d1l0vm1 M:447-464,468-489,499-526,549-557,559-567
1kf6 d1kf6m1 M:447-464,468-489,499-526,549-557,559-567
1kfy d1kfym1 M:447-464,468-489,499-526,549-557,559-567
3cir d3cira1 A:447-464,468-489,499-526,549-557,559-567
1kfy d1kfya1 A:447-464,468-489,499-526,549-557,559-567
1l0v d1l0va1 A:447-464,468-489,499-526,549-557,559-567
1kf6 d1kf6a1 A:447-464,468-489,499-526,549-557,559-567
3cir d3cirm1 M:447-464,468-490,499-526,549-557,559-567
2b76 d2b76a1 A:447-464,468-489,499-526,548-557,559-568
12. d.278.1 Ligand-binding domain in the NO signalling and Golgi transport
Ligand-binding domain in the NO signalling and Golgi transport an N-terminal helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomain enclose a ligand-binding cavity
1wc8 d1wc8a_ A:36-64,70-88,128-143,143-154,160-171
2pwn d2pwna1 A:36-64,70-88,128-143,143-154,160-171
13. 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
1nij d1nija1 A:134-143,142-152,215-223,223-232,294-303
14. a.7.12 PhoU-like duplication: consists of two sequence each repeats adopting this fold !
Spectrin repeat-like 3 helices; bundle, closed, left-handed twist; up-and-down
1sum d1sumb_ B:116-140,141-174,173-210,212-217,218-223
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1163 (enumeration index: query1999) of S5
3ae2 A:465-482,486-507,517-544,582-591,592-601
2gq2 D:86-97,188-201,205-224,230-236,238-244
2gq2 C:86-97,188-201,205-224,230-236,238-244
2gq2 A:86-97,188-201,205-224,230-236,238-244
2gq2 B:86-97,188-201,205-224,230-236,238-244
1zoy A:465-482,486-507,517-544,582-591,592-601
3aea A:465-482,486-507,517-544,582-591,592-601
2j3r A:36-64,70-87,128-143,144-152,160-170
2j3r B:61-75,81-99,136-155,157-165,167-175
2cfh A:36-64,70-88,128-143,143-154,160-171
2cfh B:36-64,70-88,128-143,143-154,160-171
3p4r A:447-464,468-489,499-526,549-557,559-567
3p4r M:447-464,468-489,499-526,549-557,559-567
1zp0 A:465-482,486-507,517-544,582-591,592-601
3kxc A:36-64,70-88,128-143,144-154,160-170
3sfe A:465-482,486-507,517-544,582-591,592-601
2af6 C:86-97,188-201,205-224,230-236,238-244
2af6 B:86-97,188-201,205-224,230-236,238-244
2af6 H:86-97,188-201,205-224,230-236,238-244
2af6 F:86-97,188-201,205-224,230-236,238-244
2af6 G:86-97,188-201,205-224,230-236,238-244
2af6 D:86-97,188-201,205-224,230-236,238-244
2af6 A:86-97,188-201,205-224,230-236,238-244
2af6 E:86-97,188-201,205-224,230-236,238-244
3k6x A:141-149,161-179,180-193,193-200,202-209
3k6x B:141-149,161-179,180-192,194-200,202-209
3ae5 A:465-482,486-507,517-544,582-591,592-601
3dtk A:126-138,140-152,154-167,169-178,254-262
3ae7 A:465-482,486-507,517-544,582-591,592-601
2qsf A:164-176,191-215,261-277,324-332,336-340
3jz3 A:282-298,349-368,417-430,431-439,441-449
3jz3 B:276-298,349-368,419-430,431-439,441-449
3cg3 A:135-142,155-173,175-186,187-191,192-197
3otn A:383-400,426-443,445-456,456-462,463-469
3otn B:383-400,426-443,445-456,456-462,463-469
3fnn A:86-97,188-201,205-224,230-236,238-244
3aef A:465-482,486-507,517-544,582-591,592-601
2h89 A:464-481,485-506,516-543,581-590,591-600
2qsg A:164-176,191-215,261-277,324-333,335-340
3b39 B:109-133,166-174,175-186,187-192,194-199
2h88 A:464-481,485-506,516-543,581-590,591-600
2h88 N:464-481,485-506,516-543,581-590,591-600
3k85 B:113-131,135-152,156-166,167-175,177-185
3k85 A:113-131,135-152,156-166,167-175,177-185
1sz7 A:36-63,70-88,128-143,144-154,160-170
3ae3 A:465-482,486-507,517-544,582-591,592-601
3sfd A:465-482,486-507,517-544,582-591,592-601
3im1 A:1875-1886,1953-1969,1970-1986,2097-2107,2108-2118
3p4q M:447-464,468-490,499-526,549-557,559-567
3p4q A:447-464,468-489,499-526,549-557,559-567
3ae4 A:465-482,486-507,517-544,582-591,592-601
3aeb A:465-482,486-507,517-544,582-591,592-601
2ovi D:5-13,17-26,28-37,116-127,129-138
3aed A:465-482,486-507,517-544,582-591,592-601
3im2 A:1875-1886,1953-1969,1970-1986,2097-2107,2108-2118
3k6w A:141-149,161-179,180-192,193-200,202-209
1yq3 A:464-481,485-506,516-543,581-590,591-600
3cfz A:138-146,158-176,177-189,191-197,198-206
2fbw A:464-481,485-506,516-543,581-590,591-600
2fbw N:464-481,485-506,516-543,581-590,591-600
3k6u A:141-149,161-179,180-192,193-200,202-209
3k17 D:120-139,142-159,163-172,173-181,203-210
3k17 B:120-139,142-159,163-172,173-181,203-210
3k17 A:120-139,142-159,163-172,173-181,203-210
3k17 C:120-139,142-159,163-172,173-181,203-210
3cij A:133-140,153-171,172-184,188-192,193-200
3cij B:133-141,153-171,172-184,188-192,193-200
3re2 A:59-78,88-103,127-143,164-170,181-185
3dge A:284-318,366-385,442-457,458-465,469-478
3dge B:284-318,366-385,442-457,458-465,469-477
3ae9 A:465-482,486-507,517-544,582-591,592-601
3lml B:19-31,351-380,386-408,418-424,428-437
3lml A:17-31,351-380,386-408,418-424,428-437
3lml E:21-31,351-380,386-408,418-424,429-437
3lml C:17-31,351-380,386-408,418-424,428-437
3lml D:20-31,351-380,386-408,418-424,429-437
3lml F:20-31,351-380,386-408,418-424,428-437
3fvy A:499-522,531-557,566-583,586-595,597-606
3cg1 A:140-147,160-178,180-190,192-196,197-203
3cg1 B:140-147,160-178,180-191,192-196,197-203
3aec A:465-482,486-507,517-544,582-591,592-601
3ae6 A:465-482,486-507,517-544,582-591,592-601
3pt1 A:144-159,174-191,255-274,414-422,459-467
3csk A:508-530,541-567,576-593,598-604,609-615
3hzg C:86-97,188-201,205-224,230-236,238-244
3hzg B:86-97,188-201,205-224,230-236,238-244
3hzg A:86-97,188-201,205-224,230-236,238-244
3hzg D:86-97,188-201,205-224,230-236,238-244
2w2r A:80-93,98-116,200-209,209-214,220-226
2vs7 A:84-101,102-118,131-146,148-157,158-166
3d36 A:235-262,310-330,379-393,394-401,402-413
3aee A:465-482,486-507,517-544,582-591,592-601
3p4p M:447-464,468-489,499-526,549-557,559-567
3p4p A:447-464,468-489,499-526,549-557,559-567
3p4s A:447-464,468-489,499-526,549-557,559-567
3p4s M:447-464,468-489,499-526,549-557,559-567
3lpz A:156-175,175-194,195-215,218-223,228-233
3aeg A:465-482,486-507,517-544,582-591,592-601
3gwc E:86-97,188-201,205-224,230-236,238-244
3gwc B:86-97,188-201,205-224,230-236,238-244
3gwc D:86-97,188-201,205-224,230-236,238-244
3gwc H:86-97,188-201,205-224,230-236,238-244
3gwc A:86-97,188-201,205-224,230-236,238-244
3gwc C:86-97,188-201,205-224,230-236,238-244
3gwc G:86-97,188-201,205-224,230-236,238-244
3gwc F:86-97,188-201,205-224,230-236,238-244
3cfx B:141-149,161-179,180-192,194-200,202-209
3cfx A:141-149,161-179,180-192,193-200,202-209
3abv A:465-482,486-507,517-544,582-591,592-601
3k6v A:141-149,161-179,180-192,193-200,202-209
1yq4 A:464-481,485-506,516-543,581-590,591-600
3lc6 A:263-276,279-288,289-308,332-339,411-418
3ge9 A:86-97,188-203,205-224,230-236,238-244
3dte A:126-138,140-152,154-166,169-178,254-262
3dti A:126-138,140-152,154-166,169-177,254-262
2c0j A:36-64,70-88,128-143,143-154,160-171
3ae8 A:465-482,486-507,517-544,582-591,592-601
3hib A:1875-1886,1953-1969,1970-1986,2097-2107,2108-2118
2wqy A:464-481,485-506,516-543,581-590,591-600
2wqy N:464-481,485-506,516-543,581-590,591-600
2wtx B:159-167,168-179,186-202,203-207,209-214
3ae1 A:465-482,486-507,517-544,582-591,592-601
2qsh A:164-176,191-215,261-277,324-333,335-340
2gs8 A:105-123,127-140,139-148,149-156,157-163
2j3w E:36-64,70-87,128-143,143-154,160-171