1. 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
2fdc d2fdcb1 B:158-163,168-180,191-197,198-204,209-218
1t5l d1t5lb1 B:158-163,168-180,191-197,198-204,209-218
1t5l d1t5la1 A:158-163,168-180,191-197,198-204,209-218
2b2n d2b2na1 A:127-132,137-149,160-166,167-172,179-186
2b2n d2b2nb1 B:127-132,137-149,160-166,167-172,179-186
2eyq d2eyqb4 B:127-132,137-149,160-166,167-172,179-186
2eyq d2eyqa4 A:127-132,137-149,160-166,167-172,179-186
1w44 d1w44a_ A:112-117,135-149,255-261,265-274,277-290
1w44 d1w44b_ B:112-117,135-149,255-261,265-274,277-290
1w48 d1w48b_ B:112-117,135-149,255-261,265-274,277-290
1w44 d1w44c_ C:112-117,135-149,255-261,265-274,277-290
1w49 d1w49a_ A:112-117,135-149,255-261,265-274,277-290
1w4a d1w4aa_ A:112-117,135-149,255-261,265-274,277-290
1w48 d1w48a_ A:112-117,135-149,255-261,265-274,277-290
1w48 d1w48c_ C:112-117,135-149,255-261,265-274,277-290
1w4a d1w4ab_ B:112-117,135-149,255-261,265-274,277-290
1w4b d1w4bc_ C:112-117,135-149,255-261,265-274,277-290
1w4a d1w4ac_ C:112-117,135-149,255-261,265-274,277-290
1w49 d1w49c_ C:112-117,135-149,255-261,265-274,277-290
1w4b d1w4ba_ A:112-117,135-149,255-261,265-274,277-290
1w49 d1w49b_ B:112-117,135-149,255-261,265-274,277-290
1w4b d1w4bb_ B:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cm_ M:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cq_ Q:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cs_ S:112-117,135-149,255-261,265-274,277-290
1w4c d1w4ce_ E:112-117,135-149,255-261,265-274,277-290
1w4c d1w4ct_ T:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cw_ W:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cc_ C:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cg_ G:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cr_ R:112-117,135-149,255-261,265-274,277-290
1w4c d1w4ck_ K:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cp_ P:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cf_ F:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cb_ B:112-117,135-149,255-261,265-274,277-290
1w47 d1w47c_ C:112-117,135-149,255-261,265-274,277-290
1w4c d1w4co_ O:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cn_ N:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cj_ J:112-117,135-149,255-261,265-274,277-290
1w47 d1w47b_ B:112-117,135-149,255-261,265-274,277-290
1w47 d1w47a_ A:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cv_ V:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cl_ L:112-117,135-149,255-261,265-274,277-290
1w4c d1w4ch_ H:112-117,135-149,255-261,265-274,277-290
1w4c d1w4ci_ I:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cu_ U:112-117,135-149,255-261,265-274,277-290
1w4c d1w4ca_ A:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cx_ X:112-117,135-149,255-261,265-274,277-290
1w4c d1w4cd_ D:112-117,135-149,255-261,265-274,277-290
1w46 d1w46a_ A:112-117,135-149,255-261,265-274,277-290
1w46 d1w46c_ C:112-117,135-149,255-261,265-274,277-290
1w46 d1w46b_ B:112-117,135-149,255-261,265-274,277-290
2. d.294.1 EndoU-like similarity to the RNase A-like superfamily (
EndoU-like comprises several helices and two three-stranded antiparallel beta-sheets; similar architecture to the RNase A-like fold (scop_cf 54075)
2rhb d2rhbe2 E:245-249,250-262,261-267,275-284,285-291
2rhb d2rhbf2 F:245-249,250-262,261-267,275-284,285-291
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
2ibi d2ibia1 A:266-270,274-289,539-552,555-564,569-575
2hd5 d2hd5a1 A:213-217,221-236,443-460,461-473,474-482
2io9 d2io9a2 A:22-29,58-72,114-122,129-140,141-147
2ioa d2ioaa2 A:22-29,58-72,114-122,129-140,141-147
2iob d2ioba2 A:22-29,58-72,116-122,129-140,141-147
1qmy d1qmyb_ B:36-41,50-64,137-145,147-155,158-164
1qmy d1qmya_ A:36-41,50-64,137-144,148-155,158-164
2jqf d2jqfs1 S:236-241,250-264,338-344,348-355,358-364
2jqf d2jqfr1 R:36-41,50-64,138-144,148-155,158-164
1qol d1qold_ D:36-41,50-64,137-144,148-155,158-164
1qol d1qolh_ H:36-41,49-64,137-144,148-155,158-164
1qmy d1qmyc_ C:36-41,50-64,137-144,148-155,158-164
1qol d1qolg_ G:36-41,49-64,137-144,148-155,158-164
1qol d1qolc_ C:36-41,50-64,137-144,148-155,158-164
1qol d1qolb_ B:36-41,50-64,137-144,148-155,158-164
1qol d1qola_ A:36-41,50-64,137-144,148-155,158-164
1qol d1qole_ E:36-41,50-64,137-144,148-155,158-164
1qol d1qolf_ F:36-41,50-64,137-144,148-155,158-164
2iob d2iobb2 B:22-28,58-72,116-123,128-140,141-147
4. d.154.1 DmpA/ArgJ-like convergent similarity to the Ntn amidohydrolases !
DmpA/ArgJ-like duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
1vz7 d1vz7d_ D:28-34,138-147,153-158,163-171,181-190
1vz8 d1vz8b_ B:28-35,138-147,154-161,162-171,181-190
1vz6 d1vz6b_ B:28-35,138-147,154-161,162-171,181-190
1vz6 d1vz6a_ A:28-35,138-147,154-161,162-171,181-190
1vz7 d1vz7a_ A:28-35,138-147,154-161,162-171,181-190
1vz8 d1vz8d_ D:28-35,138-147,154-161,162-171,181-190
1vz8 d1vz8a_ A:28-35,138-147,154-161,162-171,181-190
1vz7 d1vz7b_ B:28-35,138-147,154-161,162-171,181-190
1vz7 d1vz7c_ C:28-35,140-147,154-158,164-171,181-190
1vz8 d1vz8c_ C:28-35,139-147,154-161,162-171,181-190
5. b.88.1 Mss4-like duplication: tandem repeat of two similar structural motifs !
Mss4-like complex fold made of several coiled beta-sheets
1txj d1txja_ A:9-16,69-76,76-80,131-137,145-150
6. d.108.1 Acyl-CoA N-acyltransferases (Nat)
Acyl-CoA N-acyltransferases (Nat) 3 layers: a/b/a; contains mixed beta-sheet
2cxa d2cxaa1 A:46-50,113-127,128-137,138-150,151-161
7. b.17.1 PEBP-like
PEBP-like sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
1a44 d1a44a_ A:24-29,41-48,61-71,116-126,162-171
1beh d1beha_ A:25-30,42-49,62-72,117-127,164-172
8. c.3.1 FAD/NAD(P)-binding domain
FAD/NAD(P)-binding domain core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
2gqf d2gqfa1 A:145-151,176-186,352-356,357-361,365-369
9. i.14.1 Bacteriophage HK97 procapsid (prohead II)
Bacteriophage HK97 procapsid (prohead II)
1if0 d1if0d_ D:147-160,253-269,272-278,322-328,375-381
10. d.87.1 FAD/NAD-linked reductases, dimerisation (C-terminal) domain both first two domains are of same beta/beta/alpha fold !
CO dehydrogenase flavoprotein C-domain-like core: beta(3,4)-alpha(3); alpha+beta sandwich
1npx d1npxa3 A:290-295,342-350,353-363,370-382,383-394
1nhr d1nhra3 A:290-295,342-350,353-363,370-382,383-394
1nhs d1nhsa3 A:290-295,342-350,353-363,370-382,383-394
2npx d2npxa3 A:290-295,342-350,353-363,370-382,383-394
1nhp d1nhpa3 A:290-295,342-350,353-363,370-382,383-394
1nhq d1nhqa3 A:290-295,342-350,353-363,370-382,383-394
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 685 (enumeration index: query95) of S5
2qqv A:313-325,336-343,369-379,476-485,486-493
3oxh A:9-19,153-166,167-172,180-186,187-195
3f8l A:76-80,84-93,95-109,120-134,136-146
3f8l B:75-80,84-93,95-109,120-134,136-146
3f8l D:76-80,84-93,95-109,120-134,136-147
3fwm A:101-115,120-132,143-149,150-162,167-176
2z3k B:46-50,113-127,128-137,138-150,151-161
2z3k A:46-50,113-127,128-137,138-150,151-161
3ldk A:418-437,468-479,504-514,589-598,599-606
3o4o C:30-37,141-149,153-159,190-201,202-217
3lfi B:418-437,468-479,504-514,589-598,599-606
3lfi A:418-437,468-479,504-514,589-598,599-606
2vhc C:112-117,135-149,255-261,265-274,277-290
2vhc B:112-117,135-149,255-261,265-274,277-290
2vhc A:112-117,135-149,255-261,265-274,277-290
3c26 A:178-183,185-194,196-201,202-211,212-222
2ac1 A:312-325,336-343,369-380,476-485,486-493
3p3k A:13-20,73-80,80-84,135-141,149-154
3mp2 A:21-26,30-45,169-178,181-190,191-197
2nmv A:158-163,168-180,191-197,198-203,209-218
2fe8 B:101-106,110-125,260-267,270-280,282-288
2fe8 A:101-106,110-125,260-269,270-280,282-288
2fe8 C:101-106,110-125,260-269,270-280,282-288
3lf7 A:418-437,468-479,504-514,589-598,599-606
3ml4 A:61-68,93-109,110-119,126-135,136-143
3ml4 D:61-68,93-109,110-119,126-135,136-143
3ml4 B:61-68,93-109,110-119,126-135,136-143
3ml4 C:61-68,93-109,110-119,126-135,136-143
2vps A:29-36,58-72,114-123,127-139,140-146
2xqr K:312-325,336-343,369-379,476-485,486-493
2xqr G:312-325,336-343,369-379,476-485,486-493
2xqr A:312-325,336-343,369-379,476-485,486-493
2xqr C:312-325,336-343,369-379,476-485,486-493
2xqr E:312-325,336-343,369-379,476-485,486-493
2xqr I:312-325,336-343,369-379,476-485,486-493
2dpt B:46-50,113-127,128-137,138-150,151-161
2dpt A:46-50,113-127,128-137,138-150,151-161
3eet B:77-82,92-99,104-116,130-142,143-155
3eet A:77-82,92-99,104-117,128-142,143-155
2dps B:46-50,113-127,128-137,138-150,151-161
2dps A:46-50,113-127,128-137,138-150,151-161
3fpn B:158-163,168-180,190-197,198-205,211-218
3hjh A:127-132,137-149,160-166,167-172,179-186
2z3o A:46-50,113-127,128-137,138-150,151-161
2z3o B:46-50,113-127,128-137,138-150,151-161
2vpm B:29-36,58-72,114-123,127-137,140-146
2vpm A:29-36,58-72,115-123,127-135,140-146
3e9s A:101-106,110-125,260-269,270-280,282-288
2l1u A:45-51,70-78,78-85,90-98,99-109
2be1 A:166-174,194-202,220-239,276-292,294-306
2be1 B:166-174,194-202,220-239,276-292,294-306
3mj5 A:101-106,110-125,260-269,270-280,282-288
3mj5 B:101-106,110-125,260-268,271-280,282-288
3ldr A:418-437,468-479,504-514,589-598,599-606
2vob A:29-36,58-72,114-123,127-137,140-146
2vob B:29-36,58-72,114-123,127-139,140-146
2z3m A:46-50,113-127,128-137,138-150,151-161
2z3m B:46-50,113-127,128-137,138-150,151-161
3lih A:418-437,468-479,504-514,589-598,599-606
2vht C:112-117,135-149,255-261,265-275,276-290
2vht A:112-117,135-149,255-261,265-275,276-290
2vht B:112-117,135-149,255-261,265-275,276-290
3f8m B:75-80,84-93,95-108,122-134,135-146
3f8m A:75-80,84-93,95-109,120-134,135-146
2vhj B:112-117,132-149,255-261,265-274,277-290
2vhj A:112-117,134-149,255-261,265-274,277-290
2vhj C:112-117,132-149,255-261,265-274,277-290
3a2y A:22-29,58-72,114-123,128-140,141-147
2oxb A:315-325,336-343,369-379,476-485,486-493
2hz6 A:73-78,99-107,116-128,154-166,173-183
3lig A:418-437,468-479,504-514,589-598,599-606
2iqy A:25-30,42-49,62-72,117-127,163-172
2xmo B:126-133,157-166,173-177,181-187,190-197
2xmo A:126-133,157-166,173-177,181-187,190-197
2vhq A:112-117,135-149,255-261,265-274,277-290
2vhq B:112-117,135-149,255-261,265-274,277-290
2vhq C:112-117,135-149,255-261,265-274,277-290
2qqu A:312-325,336-343,369-379,476-485,486-493
2d7d A:158-163,168-180,191-197,198-204,210-218
2z3n B:46-50,113-127,128-137,138-150,151-161
2z3n A:46-50,113-127,128-137,138-150,151-161
2iqx A:25-30,42-49,62-72,117-127,163-172
3lem A:418-437,468-479,504-514,589-598,599-606
2z3l A:46-50,113-127,128-137,138-150,151-161
2z3l B:46-50,113-127,128-137,138-150,151-161
2vhu C:112-117,135-149,255-261,265-274,277-290
2vhu A:112-117,135-149,255-261,265-274,277-290
2vhu B:112-117,135-149,255-261,265-274,277-290
2qqw A:312-325,336-343,369-379,476-485,486-493
2z3p A:46-50,113-127,128-137,138-150,151-161
2z3p B:46-50,113-127,128-137,138-150,151-161