1. a.118.8 TPR-like
alpha-alpha superhelix multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
2axz d2axza2 A:73-89,91-103,106-124,294-299,301-306
2axz d2axzd2 D:73-89,91-103,106-124,295-299,301-305
2axz d2axzb2 B:73-89,91-103,106-124,295-299,301-305
2. c.1.8 (Trans)glycosidases
TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
1jda d1jdaa2 A:311-325,332-340,340-356,403-409,412-417
1p6w d1p6wa2 A:305-316,323-331,331-347,391-397,398-404
3bsg d3bsga2 A:305-316,323-331,331-347,391-397,398-404
3. a.102.2 Seven-hairpin glycosidases
alpha/alpha toroid multihelical; up to seven alpha-hairpins are arranged in closed circular array; there may be sequence similarities between different superfamilies
1fo3 d1fo3a_ A:394-413,414-431,462-477,683-688,690-695
1fo2 d1fo2a_ A:327-347,348-368,394-413,683-688,690-695
1hcu d1hcub_ B:174-193,194-211,244-259,480-485,487-492
1fmi d1fmia_ A:327-347,348-368,394-413,683-688,690-695
1fo3 d1fo3a_ A:327-347,348-368,394-413,683-688,690-695
2ri9 d2ri9b1 B:2195-2214,2215-2232,2266-2281,2496-2501,2503-2508
1x9d d1x9da1 A:327-347,348-368,401-413,683-688,690-695
1hcu d1hcua_ A:174-193,194-211,241-259,480-485,487-492
1dl2 d1dl2a_ A:204-223,224-243,269-289,520-525,527-532
1g6i d1g6ia_ A:204-223,224-243,269-289,520-525,527-532
1hcu d1hcuc_ C:174-193,194-211,241-259,480-485,487-492
1hcu d1hcud_ D:174-193,194-211,241-259,480-485,487-492
1g6i d1g6ia_ A:269-289,290-309,336-352,520-525,527-532
1krf d1krfa_ A:195-214,215-232,263-281,496-501,503-508
1kre d1krea_ A:195-214,215-232,263-281,496-501,503-508
1fmi d1fmia_ A:394-413,414-431,457-477,683-688,690-695
1kre d1kreb_ B:195-214,215-232,263-281,496-501,503-508
1kkt d1kkta_ A:195-214,215-232,263-281,496-501,503-508
1dl2 d1dl2a_ A:269-289,290-309,336-352,520-525,527-532
1kkt d1kktb_ B:195-214,215-232,263-281,496-501,503-508
1fmi d1fmia_ A:457-477,480-499,523-540,683-688,690-695
1fo2 d1fo2a_ A:457-477,480-499,523-540,683-688,690-695
1hcu d1hcuc_ C:97-121,126-150,174-193,480-485,487-492
1hcu d1hcua_ A:97-121,126-150,174-193,480-485,487-492
2ri9 d2ri9a1 A:1119-1143,1148-1172,1195-1214,1496-1501,1503-1508
1kre d1krea_ A:119-143,148-172,195-214,496-501,503-508
1krf d1krfa_ A:119-143,148-172,195-214,496-501,503-508
1hcu d1hcud_ D:97-121,126-150,174-193,480-485,487-492
1x9d d1x9da1 A:457-477,480-499,523-540,683-688,690-695
1x9d d1x9da1 A:401-413,414-431,457-477,683-688,690-695
1hcu d1hcub_ B:97-121,126-150,174-193,480-485,487-492
1kkt d1kkta_ A:119-143,148-172,195-214,496-501,503-508
1krf d1krfb_ B:119-143,148-172,195-214,496-501,503-508
1kkt d1kktb_ B:119-143,148-172,195-214,496-501,503-508
1kre d1kreb_ B:119-143,148-172,195-214,496-501,503-508
2ri9 d2ri9b1 B:2119-2143,2148-2172,2195-2214,2496-2501,2503-2508
1dl2 d1dl2a_ A:129-152,155-178,204-223,520-525,527-532
1g6i d1g6ia_ A:129-152,155-178,204-223,520-525,527-532
1kre d1krea_ A:263-281,284-303,328-346,496-501,503-508
1kkt d1kkta_ A:263-281,284-303,328-346,496-501,503-508
2ri8 d2ri8b1 B:2263-2281,2284-2303,2328-2346,2496-2501,2503-2508
1nxc d1nxca_ A:414-429,432-451,474-491,630-635,637-642
4. d.110.2 GAF domain-like alpha(2)-beta(3)-alpha-beta(3)-alpha; antiparallel beta-sheet: order 321654 !
Profilin-like core: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
1mkm d1mkma2 A:133-143,144-155,167-182,183-188,193-204
1mkm d1mkmb2 B:133-143,144-155,167-182,183-188,193-204
1td5 d1td5d_ D:65-76,76-88,99-114,115-120,125-136
2o9a d2o9ad1 D:65-76,76-88,99-114,115-120,125-136
2o9a d2o9ac1 C:65-75,76-88,99-114,115-120,125-136
1tf1 d1tf1d_ D:69-80,80-92,103-118,119-124,129-140
2o99 d2o99d1 D:65-76,76-88,99-114,115-120,125-136
2o9a d2o9aa1 A:65-76,76-88,99-114,115-120,125-136
2o99 d2o99c1 C:65-75,76-88,99-114,115-120,125-136
1tf1 d1tf1c_ C:69-79,80-92,103-118,119-124,129-140
2o99 d2o99b1 B:65-76,76-88,99-114,115-120,125-136
1tf1 d1tf1a_ A:69-79,80-92,103-118,119-124,129-140
1td5 d1td5a_ A:65-75,76-88,99-114,115-120,125-136
2o9a d2o9ab1 B:65-75,76-88,99-114,115-120,125-136
1td5 d1td5c_ C:65-76,76-88,99-114,115-120,125-136
1td5 d1td5b_ B:65-76,76-88,99-114,115-120,125-136
1tf1 d1tf1b_ B:69-79,80-92,103-118,119-124,129-140
5. a.93.1 Heme-dependent peroxidases
Heme-dependent peroxidases multihelical; consists of two all-alpha domains
1lyk d1lykb_ B:19-38,95-110,112-127,135-139,289-293
1arx d1arxa_ A:20-39,96-111,113-130,136-140,290-294
1lyc d1lyca_ A:19-38,95-110,112-129,135-139,289-293
1gzb d1gzba_ A:20-39,96-111,113-130,136-140,290-294
1h3j d1h3ja_ A:19-38,95-110,112-129,135-139,289-293
1lyc d1lycb_ B:19-38,95-110,112-129,135-139,289-293
2e3b d2e3ba1 A:20-39,96-111,113-130,136-140,290-294
1arv d1arva_ A:20-39,96-111,113-130,136-140,290-294
1h3j d1h3jb_ B:19-38,95-110,112-129,135-139,289-293
1arp d1arpa_ A:20-39,96-111,113-130,136-140,290-294
1aru d1arua_ A:20-39,96-111,113-130,136-140,290-294
1ly8 d1ly8a_ A:19-38,95-110,112-129,135-139,289-293
1gza d1gzaa_ A:20-39,96-111,113-130,136-140,290-294
1ck6 d1ck6a_ A:20-39,96-111,113-130,136-140,290-294
1ary d1arya_ A:20-39,96-111,113-130,136-140,290-294
1c8i d1c8ia_ A:20-39,96-111,113-130,136-140,290-294
1arw d1arwa_ A:20-39,96-111,113-130,136-140,290-294
2e3a d2e3aa1 A:20-39,96-111,113-130,136-140,290-294
1ly9 d1ly9b_ B:19-38,95-110,112-129,135-139,289-293
1hsr d1hsra_ A:20-39,96-111,113-130,136-140,290-294
2e39 d2e39a1 A:20-39,96-111,113-130,136-140,290-294
1ly8 d1ly8b_ B:19-38,95-110,112-129,135-139,289-293
1ly9 d1ly9a_ A:19-38,95-110,112-129,135-139,289-293
1lyk d1lyka_ A:19-38,95-110,112-129,135-139,289-293
6. 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
1msw d1mswd_ D:67-78,110-130,133-158,744-750,752-758
7. a.118.4 Lipovitellin-phosvitin complex, superhelical domain
alpha-alpha superhelix multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
1lsh d1lsha1 A:543-558,560-574,576-593,636-648,655-667
1lsh d1lsha1 A:322-340,340-352,354-369,814-837,854-874
8. d.129.3 Bet v1-like contains a single copy of this fold with a alpha-beta2 insertion after the first helix; there is a cavity between the beta-sheet and the long C-terminal helix !
TBP-like beta-alpha-beta(4)-alpha
2b1x d2b1xe2 E:170-183,269-281,281-291,291-299,301-312
2b1x d2b1xc2 C:170-183,269-281,281-291,292-299,301-312
2b1x d2b1xa2 A:170-183,269-281,281-291,291-299,301-312
9. a.123.1 Nuclear receptor ligand-binding domain
Nuclear receptor ligand-binding domain multihelical; 3 layers or orthogonally packed helices
1pk5 d1pk5b_ B:333-352,358-382,400-417,421-425,427-431
10. e.24.1 Ribosomal protein L1
Ribosomal protein L1 2 domains: (1) alpha+beta; (2) alpha/beta (interrupts domain 1)
1zho d1zhoa1 A:4-15,21-34,181-200,208-217,218-225
1zho d1zhog1 G:4-15,21-34,181-200,208-217,218-225
2hgj d2hgjc1 C:5-15,21-34,181-200,208-217,218-225
1zho d1zhoc1 C:4-15,21-34,181-200,208-217,218-224
2hw8 d2hw8a1 A:4-15,21-34,181-200,208-217,218-225
11. d.122.1 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 8-stranded mixed beta-sheet; 2 layers: alpha/beta
1ea6 d1ea6a2 A:176-196,222-232,232-240,267-274,320-327
1uyk d1uyka_ A:23-36,127-135,136-145,144-154,159-165
2uwd d2uwda1 A:23-36,127-135,136-145,144-154,159-165
2cct d2ccta1 A:23-36,127-135,136-145,144-154,159-165
2vw5 d2vw5b1 B:9-23,113-121,122-131,130-140,145-152
2bsm d2bsma1 A:23-36,127-135,136-145,144-154,159-165
1osf d1osfa_ A:23-36,127-135,136-145,144-154,159-165
2qfo d2qfoa1 A:23-36,127-135,136-145,144-154,159-165
2vci d2vcia1 A:23-36,127-135,136-145,144-154,159-165
2vw5 d2vw5a1 A:9-23,113-121,122-131,130-140,145-152
2vcj d2vcja1 A:23-36,127-135,136-145,144-154,159-165
1uyc d1uyca_ A:23-36,127-135,136-145,144-154,159-165
2h55 d2h55a1 A:23-36,127-135,136-145,144-154,159-165
2iws d2iwsa1 A:9-22,113-121,122-131,130-141,142-152
2iwx d2iwxa1 A:9-22,113-121,122-131,130-140,145-151
2vw5 d2vw5d1 D:9-24,113-121,122-131,130-141,142-152
2iwu d2iwua1 A:9-24,113-121,122-131,130-141,142-152
12. b.36.1 PDZ domain-like peptide-binding domain !
PDZ domain-like contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
2i4s d2i4sb1 B:-3-218,217-226,271-285,286-295,296-305
2i4s d2i4sa1 A:-3-218,217-226,271-282,286-295,296-305
13. d.309.1 AMMECR1-like
AMMECR1-like duplication; contains two beta(2)-alpha-beta(2) structural repeats, swapped with C-terminal strands; extra N-terminal helix and C-terminal strand
1wsc d1wsca1 A:13-33,38-47,83-99,112-126,192-204
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1161 (enumeration index: query1110) of S5
2g7u D:140-150,151-163,174-189,190-195,200-211
2g7u C:140-150,151-162,174-189,190-195,200-211
2g7u A:140-150,151-162,174-189,190-195,200-211
2g7u B:140-150,151-162,174-189,190-195,200-211
3b28 B:23-36,127-135,136-145,144-154,159-165
3b28 A:23-36,127-135,136-145,144-154,159-165
3kc6 A:540-557,574-585,585-607,634-639,644-649
2y11 C:4-15,21-34,181-200,208-217,221-225
2vy8 A:540-557,574-585,588-608,634-639,644-649
2cgf A:9-22,113-121,122-131,130-140,145-151
3owd A:23-36,127-135,136-145,144-154,159-165
3s8p B:73-89,160-170,171-190,228-234,258-267
3s8p A:73-89,160-170,171-190,228-234,258-267
2xab B:23-36,127-135,136-145,144-154,159-165
3f5c A:333-352,359-382,400-417,421-425,427-431
2xcm B:11-24,115-123,124-133,132-142,147-153
3cw4 A:6-34,40-51,51-73,100-107,108-115
2wi2 B:23-36,127-135,136-145,144-154,159-165
2ov7 A:4-15,21-33,181-200,208-217,218-225
2ov7 B:5-15,21-34,181-200,208-217,221-225
3l56 A:541-557,574-585,585-607,634-641,642-649
3l56 B:541-557,574-585,585-607,634-641,642-649
2wrr C:4-15,21-34,181-200,208-217,221-225
2xrn A:145-156,156-165,177-192,193-198,203-214
2xrn B:145-156,156-165,177-192,193-198,203-214
3d3o A:59-69,70-89,93-108,109-114,120-127
3d3o B:59-70,70-86,93-108,108-114,120-127
2y13 C:4-15,21-34,181-200,208-217,221-225
2ye8 A:23-36,127-135,136-145,144-154,159-165
3ias V:65-73,74-87,89-106,339-349,350-361
3ias D:65-73,74-87,89-106,339-349,350-361
3ias 4:65-73,74-87,89-106,339-349,350-361
3ias M:65-73,74-87,89-106,339-349,350-361
2wrl C:5-15,22-35,182-201,209-218,219-226
3rq4 A:7-23,72-79,82-101,138-145,169-177
1yuc A:314-334,340-363,381-398,402-406,408-412
3hne A:52-72,71-91,604-612,623-630,631-638
3hux C:6-16,22-35,182-201,209-219,221-225
2y0v C:4-15,21-34,181-200,208-217,221-225
2x9u C:5-16,22-35,182-201,209-218,219-226
2pff D:1447-1474,1478-1512,1747-1764,1867-1876,1877-1886
2pff G:1447-1474,1478-1512,1747-1764,1867-1876,1877-1886
2pff A:1447-1474,1478-1512,1747-1764,1867-1876,1877-1886
3hyz A:23-36,127-135,136-145,144-154,159-165
2wrj C:5-16,22-35,182-201,209-218,219-226
2wep A:9-22,113-121,122-131,130-140,145-151
3hnf A:52-72,71-90,604-612,623-630,631-638
2yeb A:23-36,127-135,136-145,144-154,159-165
2xro A:145-155,156-165,177-192,193-198,203-214
2xro E:145-155,156-165,177-192,193-198,203-214
2xro B:145-156,156-165,177-192,193-198,203-214
2xro F:145-156,156-165,177-192,193-198,203-214
3iam 4:65-73,74-87,89-106,339-349,350-361
3iam D:65-73,74-87,89-106,339-349,350-361
2ye6 A:23-36,127-135,136-145,144-154,159-165
1ysp A:59-69,70-81,93-108,109-114,119-130
2yec A:23-36,127-135,136-145,144-154,159-165
2vpl A:4-15,21-34,181-200,208-217,218-225
2vpl C:4-15,21-34,181-200,208-217,218-225
2ye3 A:23-36,127-135,136-145,144-154,159-165
2wi7 A:23-36,127-135,136-145,144-154,159-165
2xtg C:5-16,22-35,182-201,209-218,219-226
2vy7 A:540-557,574-585,585-608,634-639,644-649
2xqe C:4-15,21-34,181-200,208-217,218-225
3hek B:23-36,127-135,136-145,144-154,159-165
2y0x C:4-15,21-34,181-200,208-217,221-225
3q5k A:8-21,112-120,121-130,129-139,144-150
2yej A:23-36,127-135,136-145,144-154,159-165
3n54 B:102-109,110-120,175-186,186-197,200-212
1yok A:314-333,340-363,381-398,401-406,408-413
3o6o B:8-21,112-120,121-130,129-139,144-150
3o6o A:8-19,112-120,121-130,129-139,144-150
3f7d A:237-251,267-284,302-319,323-327,329-333
3mq0 A:158-169,169-178,191-206,207-212,217-228
3mq0 B:158-169,169-178,191-206,207-212,217-228
3kir C:5-16,22-35,182-201,209-218,219-226
3r4k C:135-145,146-157,168-183,184-189,194-205
3r4k D:135-145,146-157,168-183,184-189,194-205
3r4k A:135-145,146-157,168-183,184-189,194-205
3r4k B:135-145,146-157,168-183,184-189,194-205
1ysq A:65-76,76-88,101-116,117-122,128-135
2ybb 4:65-73,74-87,89-106,339-349,350-361
2xx5 A:9-22,113-121,122-131,130-141,142-152
2x9s C:5-16,22-35,182-201,209-218,219-226
2ia2 A:148-158,159-170,182-197,198-203,208-219
2ia2 D:148-159,159-170,182-197,198-203,208-219
2ia2 C:148-159,159-170,182-197,198-203,208-219
2ia2 B:148-158,159-170,182-197,198-203,208-219
3i9v 4:65-73,74-87,89-106,339-349,350-361
3i9v D:65-73,74-87,89-106,339-349,350-361
2y17 C:4-15,21-34,181-200,208-217,221-225
1zh7 A:333-353,359-382,400-417,421-425,427-431
1zh7 B:333-353,359-382,400-417,421-425,427-431
2o1w B:79-93,187-196,197-206,205-215,220-227
3opd B:8-22,112-120,121-130,129-139,144-150
1yow A:236-250,259-283,301-318,322-326,328-332
2o0y B:151-162,161-173,175-193,194-199,204-215
2o0y A:151-162,161-173,175-193,194-199,204-215
2wro C:4-15,21-34,181-200,208-217,221-225
2xx2 B:9-22,113-121,122-131,130-140,145-151
2xx2 C:9-22,113-121,122-131,130-140,145-151
3r2v A:541-557,574-585,585-607,634-641,642-649
3hmj A:1444-1478,1481-1512,1748-1764,1865-1875,1876-1886
3hmj C:1444-1478,1481-1512,1748-1764,1865-1875,1876-1886
3hmj B:1444-1478,1481-1512,1748-1764,1865-1875,1876-1886
3b24 B:23-36,127-135,136-145,144-154,159-165
2wi6 A:23-36,127-135,136-145,144-154,159-165
2y15 C:4-15,21-34,181-200,208-217,221-225
2yeh A:23-36,127-135,136-145,144-154,159-165
3b26 A:23-36,127-135,136-145,144-154,159-165
3kit C:5-16,22-35,182-201,209-218,219-226
2wi1 A:23-36,127-135,136-145,144-154,159-165
2yei A:23-36,127-135,136-145,144-154,159-165
3r4n B:23-36,127-135,136-145,144-154,159-165
3mnr P:23-36,127-135,136-145,144-154,159-165
3q5l B:8-21,112-120,121-130,129-139,144-150
3q5l D:8-21,112-120,121-130,129-139,144-150
2y19 C:4-15,21-34,181-200,208-217,221-225
2y0z C:4-15,21-34,181-200,208-217,218-225
3k99 A:23-37,127-135,136-145,144-154,159-165
3k99 D:23-37,127-135,136-145,144-154,159-165
3m9s 4:65-73,74-87,89-106,339-349,350-361
3m9s D:65-73,74-87,89-106,339-349,350-361
2yee A:23-36,127-135,136-145,144-154,159-165
3k60 A:9-22,113-121,122-131,130-140,145-151
2og6 A:17-35,41-55,56-70,74-80,274-282
3khw A:541-557,574-585,585-607,634-641,642-649
3khw B:541-557,574-585,585-607,634-640,643-649
3lm3 A:249-256,273-282,282-306,368-375,384-392
3q3u A:14-30,86-102,104-121,127-131,280-284
2vy6 A:541-557,574-585,585-607,634-641,642-649
1wsc B:13-33,38-47,83-99,113-126,192-204