1. 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:102-122,152-159,182-190,196-210
2hgu d2hguf1 F:102-122,152-159,182-190,196-210
2v49 d2v49f1 F:102-121,153-158,182-190,196-207
2v47 d2v47f1 F:102-121,153-158,182-190,196-207
2j01 d2j01f1 F:102-121,153-158,182-190,196-207
2j03 d2j03f1 F:102-121,153-158,182-190,196-207
2qov d2qove1 E:97-116,145-151,176-183,190-201
2qox d2qoxe1 E:97-116,145-151,176-183,190-201
2qbe d2qbee1 E:97-116,145-151,176-183,190-201
2qbg d2qbge1 E:97-116,145-151,176-183,190-201
2i2t d2i2te1 E:97-116,145-151,176-184,190-201
2i2v d2i2ve1 E:97-116,145-151,176-184,190-201
2qbi d2qbie1 E:97-116,145-151,176-184,190-201
2qbk d2qbke1 E:97-116,145-151,176-184,190-201
2qao d2qaoe1 E:97-116,145-151,176-183,190-201
2qbc d2qbce1 E:97-116,145-151,176-184,190-201
2qba d2qbae1 E:97-116,145-151,176-184,190-201
2qoz d2qoze1 E:97-116,145-151,176-183,190-201
2qam d2qame1 E:97-116,145-151,176-183,190-201
2qp1 d2qp1e1 E:97-116,145-151,176-183,190-201
3df2 d3df2e1 E:97-116,145-151,176-183,190-201
3df4 d3df4e1 E:97-116,145-151,176-183,190-201
2z4l d2z4le1 E:97-116,145-151,176-183,190-201
2z4n d2z4ne1 E:97-116,145-151,176-183,190-201
2hgu d2hguf1 F:102-122,172-178,182-190,196-210
1dmg d1dmga_ A:96-121,152-159,201-209,214-226
2hgq d2hgqf1 F:102-122,172-178,182-190,196-210
1dmg d1dmga_ A:96-121,176-183,201-209,214-226
2z4n d2z4ne1 E:97-116,166-172,176-183,190-201
2z4l d2z4le1 E:97-116,166-172,176-183,190-201
2qox d2qoxe1 E:97-116,166-172,176-183,190-201
2qov d2qove1 E:97-116,166-172,176-183,190-201
2i2v d2i2ve1 E:97-116,166-172,176-184,190-201
2qam d2qame1 E:97-116,166-172,176-183,190-201
2qao d2qaoe1 E:97-116,166-172,176-183,190-201
2qbe d2qbee1 E:97-116,166-172,176-183,190-201
2qbg d2qbge1 E:97-116,166-172,176-183,190-201
2qbi d2qbie1 E:97-116,166-172,176-184,190-201
2qoz d2qoze1 E:97-116,166-172,176-183,190-201
2qbk d2qbke1 E:97-116,166-172,176-184,190-201
2qp1 d2qp1e1 E:97-116,166-172,176-183,190-201
3df4 d3df4e1 E:97-116,166-172,176-183,190-201
2qba d2qbae1 E:97-116,166-172,176-184,190-201
2qbc d2qbce1 E:97-116,166-172,176-184,190-201
3df2 d3df2e1 E:97-116,166-172,176-183,190-201
2. c.30.1 PreATP-grasp domain precedes the ATP-grasp domain common to all superfamily members, can contain a substrate-binding function !
PreATP-grasp domain 3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands ! possible rudiment form of Rossmann-fold domain
1m0w d1m0wb1 B:1097-1114,1280-1286,1295-1309,1315-1323
1m0w d1m0wa1 A:97-114,280-286,295-309,315-323
1m0t d1m0tb1 B:1099-1114,1277-1286,1295-1309,1315-1323
2hgs d2hgsa1 A:97-114,262-267,276-289,296-304
1m0t d1m0ta1 A:100-114,276-286,295-309,315-323
3. 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
1rj9 d1rj9a2 A:63-78,250-256,263-274,293-303
1rj9 d1rj9b2 B:69-87,240-248,253-264,283-293
2j7p d2j7pa2 A:69-87,240-248,253-264,283-293
2j7p d2j7pb2 B:69-87,240-248,253-264,283-293
2cnw d2cnwc2 C:69-87,240-247,253-264,283-293
1okk d1okka2 A:69-87,240-247,253-264,283-293
2cnw d2cnwa2 A:69-87,240-246,253-264,283-293
2cnw d2cnwb2 B:69-87,240-246,253-264,283-293
1p72 d1p72b_ B:37-47,54-59,311-326,332-351
1p72 d1p72a_ A:37-48,54-59,311-326,332-351
1p6x d1p6xb_ B:37-47,54-59,311-326,332-351
1p6x d1p6xa_ A:37-48,54-59,311-326,332-351
1p73 d1p73c_ C:37-47,54-59,311-326,332-351
1p75 d1p75a_ A:37-48,54-59,311-326,332-351
2iy3 d2iy3a2 A:69-87,240-247,253-264,283-294
4. a.269.1 FtsH protease domain-like contains zincin-like (
FtsH protease domain-like array of 6 helices and a 2-stranded beta-ribbon
2cea d2ceac1 C:413-435,441-445,452-459,575-590
5. a.26.1 4-helical cytokines there are two different topoisomers of this fold with different entanglements of the two crossover connections !
4-helical cytokines core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections
2z3r d2z3ri1 I:0-20,24-28,32-55,95-114
1csg d1csga_ A:12-29,39-44,54-66,102-117
2gmf d2gmfb_ B:12-29,39-44,54-66,102-117
2gmf d2gmfa_ A:12-29,39-44,54-66,102-117
1hmc d1hmca_ A:12-26,32-39,45-66,109-132
1hmc d1hmcb_ B:12-26,32-39,45-66,109-132
6. d.165.1 Ribosome inactivating proteins (RIP)
Ribosome inactivating proteins (RIP) contains mixed beta-sheet
1rzo d1rzoc_ C:1017-1034,1134-1139,1139-1156,1180-1194
1ift d1ifta_ A:17-34,135-140,140-157,181-195
2pjo d2pjoa1 A:17-34,135-140,140-157,181-195
7. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
1ml5 d1ml5f_ F:103-120,211-215,219-230,237-246
1giy d1giyf_ F:103-120,211-215,219-230,237-246
8. d.68.2 EPT/RTPC-like
IF3-like beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
1rf4 d1rf4d_ D:232-246,375-380,383-397,406-415
1rf6 d1rf6b_ B:232-247,375-380,383-396,406-415
1rf6 d1rf6a_ A:232-247,375-380,383-398,406-415
1rf4 d1rf4b_ B:232-247,375-380,383-398,406-415
1rf4 d1rf4a_ A:232-247,375-380,383-398,406-415
9. d.223.1 Polo-box domain Serine/threonine protein kinase-associated motif embedded in two distinct folds !
Polo-box domain beta(6)-alpha; antiparallel beta-sheet, meander
1umw d1umwa2 A:373-388,558-563,564-571,573-594
1q4o d1q4ob2 B:372-388,557-563,564-571,573-592
10. c.55.3 Ribonuclease H-like consists of one domain of this fold !
Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
2hbj d2hbja2 A:181-190,233-243,270-284,293-305
2hbk d2hbka2 A:181-190,233-243,270-284,293-305
2hbl d2hbla2 A:181-190,233-243,270-284,293-305
2hbm d2hbma2 A:181-190,233-243,270-284,293-305
11. 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
1x3z d1x3za1 A:11-34,264-270,285-302,305-326
1x3w d1x3wa1 A:68-80,168-179,179-187,190-206
1x3z d1x3za1 A:68-80,168-179,179-187,190-206
1x3z d1x3za1 A:101-121,168-179,179-187,190-206
1x3w d1x3wa1 A:101-122,168-179,179-187,190-206
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 205 (enumeration index: query112) of S4
3fik E:97-116,145-150,176-184,190-201
3fin F:102-121,153-158,182-190,196-207
2wrr F:102-121,153-159,182-190,196-207
2wrr F:102-121,172-178,182-190,196-207
3ofq E:97-116,166-172,176-184,189-201
3ofq E:97-116,145-151,176-184,189-201
3i1p E:97-116,145-151,176-184,190-201
3kak B:125-142,290-296,305-319,325-333
3kak A:125-142,290-296,305-319,325-333
1vt2 E:97-116,145-151,176-184,190-201
1vt2 E:97-116,166-172,176-184,190-201
3ofc E:97-116,145-151,176-184,190-201
3kaj B:125-142,290-296,305-319,325-333
3kaj A:125-142,290-296,305-319,325-333
3bjg A:17-34,135-140,140-157,181-195
4a27 A:81-90,98-105,319-328,358-372
3ofr E:97-116,145-151,176-184,190-201
3ofr E:97-116,166-172,176-184,190-201
3og0 E:97-116,166-172,176-184,190-201
3og0 E:97-116,145-151,176-184,190-201
3kal A:125-142,290-296,305-319,325-333
3kal B:125-142,290-296,305-319,325-333
3ofz E:97-116,145-151,176-184,190-201
3izu F:97-116,166-172,176-183,190-201
3izu F:97-116,145-151,176-183,190-201
2y19 F:102-121,172-178,182-190,196-207
2y19 F:102-121,153-159,182-190,196-207
3r8s E:97-116,145-151,176-184,190-201
3r8s E:97-116,166-172,176-184,190-201
3ofd E:97-116,145-151,176-184,190-201
2xxa D:68-88,246-253,259-270,289-299
2xxa B:68-88,246-253,259-270,289-299
2xxa C:69-88,243-249,256-267,286-296
2xxa A:69-88,243-249,256-267,286-296
2xqb A:1-17,24-28,32-55,95-113
2y0x F:102-121,172-178,182-190,196-207
3i1t E:97-116,166-172,176-184,190-201
3i1t E:97-116,145-151,176-184,190-201
3izt F:97-116,166-172,176-183,190-201
3r8t E:97-116,145-151,176-184,190-201
3r8t E:97-116,166-172,176-184,190-201
3knk F:102-121,172-178,182-190,196-207
3hio A:17-34,135-140,140-157,181-195
3zvp F:102-121,172-178,182-190,196-207
3knm F:102-121,153-158,182-190,196-207
3dup A:2-12,146-152,233-244,248-263
3dup B:2-12,146-152,233-244,248-263
3q1t A:123-132,132-138,196-214,215-234
3q1t B:123-132,132-138,196-214,215-234
3q1t D:123-132,132-138,196-214,215-234
3q1t E:123-132,132-138,196-214,215-234
3q1t C:123-132,132-138,196-214,215-234
2y0v F:102-121,172-178,182-190,196-207
3i1n E:97-116,145-151,176-184,190-201
2px3 A:147-164,312-318,324-335,356-366
3i9c F:102-121,153-158,182-190,196-207
3oas E:97-116,145-151,176-184,190-201
2wwq E:97-116,166-172,176-184,189-201
2wwq E:97-116,145-149,176-184,189-201
3oat E:97-116,145-151,176-184,190-201
3orb E:97-116,145-151,176-184,190-201
2xkv A:69-87,240-247,253-264,283-293
3ejj A:12-26,31-39,53-66,109-132
3ejj B:12-26,32-39,45-66,109-132
2y11 F:102-121,172-178,182-190,196-207
2y11 F:102-121,153-159,182-190,196-207
3u1n D:232-249,404-408,408-416,415-423
3u1n A:232-249,404-408,408-416,415-423
3u1n B:232-249,404-408,408-416,415-423
3u1n C:232-249,404-408,408-416,415-423
3huz F:102-121,153-158,182-190,196-207
3esw A:102-122,168-179,179-187,189-206
3esw A:68-80,168-179,179-187,189-206
3j01 E:97-116,166-172,176-184,190-201
3j01 E:97-116,145-151,176-184,190-201
3i20 E:97-116,145-151,176-184,190-201
2wyo B:89-107,316-325,334-348,354-363
2wyo A:89-107,315-325,334-348,354-363
2wyo C:89-107,315-325,334-348,354-363
2wyo D:89-107,315-325,334-348,354-363
3i1r E:97-116,145-151,176-184,190-201
3i22 E:97-116,145-151,176-184,190-201
2xux F:102-121,153-158,182-190,195-207
2xux F:102-121,172-178,182-190,195-207
3bbo G:153-172,206-211,235-243,248-261
3d5b F:102-121,153-158,182-190,196-207
3d5d F:102-121,153-158,182-190,196-207