1. c.124.1 NagB/RpiA/CoA transferase-like
NagB/RpiA/CoA transferase-like core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
1t9k d1t9kb_ B:13-19,49-68,72-89,91-109,113-145
1t9k d1t9ka_ A:13-19,49-68,72-89,91-109,113-145
1t9k d1t9kd_ D:13-19,49-68,72-89,91-109,113-145
1t9k d1t9kc_ C:13-19,49-68,72-89,91-109,113-145
1t5o d1t5oa_ A:11-16,46-66,69-89,91-109,110-145
1t5o d1t5od_ D:11-16,46-66,69-89,91-109,110-145
1t5o d1t5ob_ B:11-16,46-66,69-89,91-109,110-145
1t5o d1t5oc_ C:11-16,46-66,69-89,91-109,110-145
2a0u d2a0ub1 B:26-32,62-85,89-109,111-128,133-175
2a0u d2a0ua1 A:26-32,62-85,89-109,111-129,133-175
1w2w d1w2w.3 I:16-22,52-75,87-107,109-126,128-170
1w2w d1w2w.4 M:16-22,52-75,87-107,109-126,128-170
1w2w d1w2w.2 E:16-22,52-75,87-107,109-126,128-170
1w2w d1w2w.1 A:16-22,52-75,87-107,109-126,128-170
2. f.13.1 Family A G protein-coupled receptor-like
Family A G protein-coupled receptor-like core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane
1jgj d1jgja_ A:65-69,94-119,120-152,153-182,189-217
1s54 d1s54a_ A:74-80,104-128,130-164,164-193,200-227
1s54 d1s54b_ B:74-80,104-128,130-164,164-193,200-227
1q5i d1q5ib_ B:74-80,104-128,130-164,164-193,200-227
1q5j d1q5jb_ B:74-80,104-128,130-164,164-193,200-227
1q5i d1q5ia_ A:74-80,104-128,130-164,164-193,200-227
1q5j d1q5ja_ A:74-80,104-128,130-164,164-193,200-227
1kme d1kmea_ A:74-80,104-128,130-164,164-193,200-227
1at9 d1at9a_ A:73-80,104-129,130-161,164-193,200-227
1kme d1kmeb_ B:74-80,104-128,130-164,164-193,200-227
1tn5 d1tn5b_ B:74-80,104-128,130-164,164-193,200-227
1tn5 d1tn5a_ A:74-80,104-128,130-164,164-193,200-227
1m0m d1m0ma_ A:73-80,104-128,130-156,164-193,200-227
1c3w d1c3wa_ A:73-80,104-128,130-156,164-193,200-227
1c8r d1c8ra_ A:73-80,104-128,130-156,164-193,200-227
2ntu d2ntua1 A:73-80,104-128,130-156,164-193,200-227
2ntw d2ntwa1 A:73-80,104-128,130-156,164-193,200-227
1kg9 d1kg9a_ A:73-80,104-128,130-156,164-193,200-227
1kg8 d1kg8a_ A:73-80,104-128,130-155,167-193,200-227
1f50 d1f50a_ A:73-80,104-128,130-156,164-192,200-227
1o0a d1o0aa_ A:73-80,104-128,130-156,164-193,200-227
1kgb d1kgba_ A:73-80,104-128,130-156,164-193,200-227
1p8u d1p8ua_ A:73-80,104-128,130-156,164-192,200-227
1p8h d1p8ha_ A:73-80,104-128,130-156,164-192,200-227
1iw9 d1iw9a_ A:73-80,104-128,130-164,164-192,200-227
1r2n d1r2na_ A:73-80,104-128,130-164,164-192,200-227
1brr d1brrc_ C:73-80,104-128,130-164,164-192,200-227
1brr d1brrb_ B:73-80,104-128,130-164,164-193,200-227
1e0p d1e0pa_ A:73-80,104-128,130-164,164-193,200-227
2at9 d2at9a_ A:73-80,104-128,130-157,164-192,200-227
1r84 d1r84a_ A:73-80,104-128,130-164,164-192,200-227
1py6 d1py6b_ B:73-80,104-128,130-164,164-193,200-227
1brr d1brra_ A:73-80,104-128,130-164,164-192,200-227
1uaz d1uaza_ A:79-86,110-134,136-170,170-199,206-233
1py6 d1py6a_ A:73-80,104-128,130-164,164-193,200-227
1s53 d1s53b_ B:73-80,104-128,130-164,164-193,200-227
1s53 d1s53a_ A:73-80,104-128,130-164,164-193,200-227
1x0k d1x0k11 1:73-80,104-128,130-164,164-192,200-227
1pxr d1pxrb_ B:73-80,104-128,130-164,164-192,200-227
1pxr d1pxra_ A:73-80,104-128,130-164,164-192,200-227
1pxs d1pxsb_ B:73-80,104-128,130-164,164-193,200-227
1tn0 d1tn0b_ B:73-80,104-128,130-164,164-193,200-227
1pxs d1pxsa_ A:73-80,104-128,130-164,164-193,200-227
1s51 d1s51b_ B:73-80,104-128,130-164,164-193,200-227
1tn0 d1tn0a_ A:73-80,104-128,130-164,164-193,200-227
1ixf d1ixfa_ A:73-80,104-128,130-164,164-192,200-227
1s51 d1s51a_ A:73-80,104-128,130-164,164-193,200-227
1s52 d1s52b_ B:73-80,104-128,130-164,164-193,200-227
1uaz d1uazb_ B:79-86,110-134,136-170,170-199,206-233
1s52 d1s52a_ A:73-80,104-128,130-164,164-193,200-227
1ucq d1ucqa_ A:73-80,104-128,130-164,164-192,200-227
1xji d1xjia1 A:73-80,104-128,130-164,164-192,200-227
1brx d1brxa_ A:73-80,104-128,130-152,167-192,200-227
1bm1 d1bm1a_ A:73-80,104-128,131-164,164-193,200-226
3. 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
1tff d1tffa_ A:39-46,48-65,67-89,91-113,114-125
4. a.39.1 EF-hand Duplication: consists of two EF-hand units: each is made of two helices connected with calcium-binding loop !
EF Hand-like core: 4 helices; array of 2 hairpins, opened
1qxp d1qxpb2 B:516-520,660-683,692-702,849-873,882-893
1qxp d1qxpa2 A:515-520,660-683,692-702,850-873,882-893
5. a.123.1 Nuclear receptor ligand-binding domain
Nuclear receptor ligand-binding domain multihelical; 3 layers or orthogonally packed helices
1r20 d1r20a_ A:229-233,239-267,332-340,341-360,412-439
2r40 d2r40a1 A:229-233,239-267,332-340,341-360,412-439
1r1k d1r1ka_ A:229-233,239-267,332-340,341-360,412-439
6. c.68.1 Nucleotide-diphospho-sugar transferases
Nucleotide-diphospho-sugar transferases 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
2cu2 d2cu2a2 A:73-79,83-99,193-206,205-218,220-228
7. e.40.1 Cullin homology domain
Cullin homology domain 3 domains: (1) 4-helical bundle; (2) alpha+beta; (3) "winged helix"-like
2hye d2hyec3 C:584-592,592-606,609-618,620-636,668-675
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 862 (enumeration index: query25.137) of S5
3abw B:116-121,145-170,172-206,207-233,240-271
3abw D:116-121,145-170,172-206,207-233,240-271
2x60 A:76-81,85-98,196-209,208-218,222-233
3a8p B:584-591,664-701,706-714,715-726,729-742
3hao A:73-80,104-128,130-164,164-193,200-226
3hao B:73-80,104-128,130-164,164-193,200-227
3mq3 A:66-76,77-97,98-108,130-150,160-183
3haq A:73-80,104-128,130-164,164-193,200-226
3han A:73-80,104-128,130-164,164-193,200-226
2ksy A:65-69,94-118,120-143,153-181,189-224
3mbv A:73-80,104-128,130-156,164-193,200-227
3har A:73-80,104-128,130-164,164-192,200-226
2z55 E:78-85,109-133,135-169,169-198,205-232
3qbk B:116-121,145-170,172-206,207-233,240-271
3qbk D:116-121,145-170,172-206,207-233,240-271
2zfe A:73-80,104-128,130-164,164-193,200-227
3a7k B:116-121,145-170,172-206,207-233,240-271
3a7k D:116-121,145-170,172-206,207-233,240-271
2pzi A:453-457,501-516,517-533,535-550,551-567
2pzi B:453-457,501-516,517-533,535-550,551-567
2pzi B:77-81,249-271,323-340,363-375,384-405
3qbl B:116-121,145-170,172-206,207-233,240-271
3qbl D:116-121,145-170,172-206,207-233,240-271
3nsb A:73-80,104-128,130-155,164-193,200-227
3n3c A:66-76,77-97,98-108,130-150,160-183
3a8n A:513-520,593-630,635-643,644-655,658-670
2ei4 A:78-85,109-133,135-169,169-198,205-232
3ns0 A:73-80,104-128,130-155,164-193,200-227
2x5s B:76-80,85-98,196-209,208-218,222-234
2x5s A:76-80,85-98,196-209,208-218,222-234
2x65 B:76-80,85-98,196-209,208-218,222-233
2x65 A:76-80,85-98,196-209,208-218,222-234
2wjk A:75-80,104-128,130-155,166-192,200-227
3hap A:73-80,104-128,130-164,164-192,200-226
3cod B:73-80,104-128,130-164,164-193,200-227
3cod A:73-80,104-128,130-164,164-193,200-227
3has A:73-80,104-128,130-164,164-192,200-226
3a8q B:584-591,664-701,706-714,715-726,729-742
3a8q A:584-591,664-701,706-714,715-726,729-742
3a8q C:584-591,664-701,706-714,715-726,729-742
3a8q D:584-591,664-701,706-714,715-726,729-742
2yrf B:16-22,52-71,75-95,97-114,116-151
2zfy A:80-86,90-108,107-129,131-152,154-165
2x5z A:76-81,85-98,196-209,208-218,222-234
2x5z B:76-80,85-98,196-209,208-218,222-234
2yvk B:16-22,52-72,75-95,97-114,116-151
2yvk D:16-22,52-72,75-95,97-114,116-151
3coc B:73-80,104-128,130-164,164-193,200-227
3coc A:73-80,104-128,130-164,164-193,200-227
3dtp B:283-287,345-366,380-392,394-404,419-451