1. c.77.1 Isocitrate/Isopropylmalate dehydrogenase-like the constituent families form similar dimers !
Isocitrate/Isopropylmalate dehydrogenase-like consists of two intertwined (sub)domains related by pseudo dyad; duplication ! 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
1ps6 d1ps6a_ A:5-13,27-31,113-121,310-329
1ptm d1ptma_ A:5-13,27-31,113-121,310-329
1ptm d1ptmb_ B:5-13,27-31,113-121,310-329
1ps6 d1ps6b_ B:5-13,27-31,114-121,310-329
1ps7 d1ps7d_ D:5-13,27-31,113-121,311-329
1ps7 d1ps7a_ A:5-13,27-31,114-121,311-329
1ps7 d1ps7c_ C:5-13,27-31,113-121,310-329
1ps7 d1ps7b_ B:5-13,27-31,114-121,310-329
1t0l d1t0ld_ D:8-16,34-38,68-74,328-348
1t0l d1t0lb_ B:8-16,34-38,68-74,328-348
2. 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
2zfj d2zfja1 A:5-13,47-52,323-332,337-352
3cnz d3cnzb1 B:890-897,930-934,1179-1188,1193-1211
1f9v d1f9va_ A:386-394,433-439,692-701,706-722
1mkj d1mkja_ A:9-16,43-48,294-303,308-325
1cz7 d1cz7b_ B:348-356,394-398,639-648,653-668
2zfl d2zfla1 A:6-14,27-32,323-332,337-355
1vfw d1vfwa_ A:6-14,27-32,323-332,337-355
1vfx d1vfxa_ A:6-14,27-32,323-332,337-354
1bg2 d1bg2a_ A:8-16,43-48,294-303,308-323
2zfm d2zfma1 A:6-14,47-52,323-332,337-354
1vfv d1vfva_ A:6-14,27-32,323-332,337-354
2hxf d2hxfc1 C:6-14,27-32,323-332,337-354
3kar d3kara_ A:385-394,433-439,692-701,706-722
1vfw d1vfwa_ A:6-14,47-52,323-332,337-355
2zfm d2zfma1 A:6-14,27-32,323-332,337-354
1f9u d1f9ua_ A:385-394,433-439,692-701,706-722
1i6i d1i6ia_ A:6-14,27-32,323-332,337-354
1i6i d1i6ia_ A:6-14,47-52,323-332,337-354
1n6m d1n6mb_ B:348-356,394-399,639-648,650-668
1vfx d1vfxa_ A:6-14,47-52,323-332,337-354
1vfz d1vfza_ A:5-14,47-52,323-332,337-353
2hxf d2hxfc1 C:6-14,47-52,323-332,337-354
1vfv d1vfva_ A:6-14,47-52,323-332,337-354
2zfl d2zfla1 A:6-14,47-52,323-332,337-355
1ii6 d1ii6a_ A:18-26,62-68,329-337,342-358
2ncd d2ncda_ A:348-356,394-398,639-648,650-670
1i5s d1i5sa_ A:5-14,47-52,323-332,337-352
1cz7 d1cz7c_ C:348-356,394-398,639-648,653-669
2zfi d2zfia1 A:5-14,47-52,323-332,337-352
2zfi d2zfia1 A:5-14,27-32,323-332,337-352
1i5s d1i5sa_ A:5-14,27-32,323-332,337-352
1vfz d1vfza_ A:5-14,27-32,323-332,337-353
1x88 d1x88a1 A:19-26,40-46,328-337,342-359
2uym d2uyma1 A:19-26,62-68,328-337,342-359
1cz7 d1cz7a_ A:348-356,394-398,639-648,650-672
1n6m d1n6ma_ A:348-356,394-398,639-648,650-671
2uyi d2uyib1 B:19-26,40-46,328-337,342-359
1sdm d1sdma_ A:890-897,928-934,1179-1187,1190-1211
2uyi d2uyia1 A:19-26,62-68,328-337,342-359
1cz7 d1cz7d_ D:348-356,394-398,639-648,650-671
1f9t d1f9ta_ A:385-394,433-439,692-701,706-720
2pg2 d2pg2a1 A:19-26,62-68,328-337,342-359
1x88 d1x88b1 B:19-26,62-68,328-337,342-359
1ii6 d1ii6b_ B:18-26,62-68,328-337,342-358
2q2z d2q2za1 A:19-26,40-45,328-337,339-360
3cob d3coba1 A:890-897,911-916,1179-1188,1190-1211
3cnz d3cnza1 A:890-897,928-934,1179-1188,1190-1211
1f9w d1f9wa_ A:385-394,433-439,692-701,706-722
1f9w d1f9wb_ B:385-394,433-439,692-701,706-722
1goj d1goja_ A:8-15,44-51,299-308,313-330
2ieh d2iehb1 B:19-26,40-46,328-337,339-359
2zfj d2zfja1 A:5-13,27-32,323-332,337-352
3cnz d3cnza1 A:890-897,912-916,1179-1188,1190-1211
2gm1 d2gm1d1 D:19-26,61-68,328-337,342-360
1sdm d1sdma_ A:890-897,912-916,1179-1187,1190-1211
1v8k d1v8ka_ A:72-80,94-99,370-380,385-403
1goj d1goja_ A:8-15,29-34,299-308,313-330
2fme d2fmea1 A:19-26,61-68,328-337,342-359
3cob d3coba1 A:890-897,927-934,1179-1188,1190-1211
2fme d2fmeb1 B:19-26,61-68,328-337,342-359
1x88 d1x88a1 A:19-26,61-68,328-337,342-359
1v8j d1v8ja_ A:72-80,94-99,370-380,385-404
1ry6 d1ry6a_ A:1-9,23-28,300-309,311-330
2g1q d2g1qa1 A:19-26,61-68,328-337,342-359
3cob d3cobc1 C:890-897,912-916,1179-1188,1190-1210
2gm1 d2gm1e1 E:19-26,61-68,328-337,342-360
2gm1 d2gm1a1 A:19-26,61-68,328-337,342-360
2gm1 d2gm1b1 B:19-26,61-68,328-337,342-360
3cob d3cobc1 C:890-897,927-934,1179-1188,1190-1210
2fl2 d2fl2a1 A:19-26,60-68,328-337,342-359
2fl6 d2fl6a1 A:19-26,60-68,328-337,342-359
2q2z d2q2za1 A:19-26,59-68,328-337,339-360
2fl6 d2fl6b1 B:19-26,59-68,328-337,342-359
3cjo d3cjoa1 A:19-26,59-68,328-337,342-359
2g1q d2g1qb1 B:19-26,59-68,328-337,342-359
1q0b d1q0ba_ A:19-26,59-68,328-337,342-359
2uyi d2uyib1 B:19-26,59-68,328-337,342-359
1q0b d1q0bb_ B:19-26,59-68,328-337,342-359
2ieh d2iehb1 B:19-26,59-68,328-337,339-359
2fl2 d2fl2b1 B:19-26,59-68,328-337,342-359
2fky d2fkya1 A:19-26,59-68,328-337,342-359
2pg2 d2pg2b1 B:19-26,59-68,328-337,342-359
1yrs d1yrsb1 B:19-26,59-68,328-337,342-359
2ieh d2ieha1 A:19-26,59-68,328-337,342-359
2q2y d2q2ya1 A:19-26,59-68,328-337,342-359
1yrs d1yrsa1 A:19-26,59-68,328-337,342-359
2uym d2uymb1 B:19-26,59-68,328-337,342-359
2q2y d2q2yb1 B:19-26,59-68,328-337,342-359
3cjo d3cjob1 B:19-26,59-68,328-337,342-359
2fky d2fkyb1 B:19-26,59-68,328-337,342-360
2q2z d2q2zb1 B:19-26,59-68,328-337,342-359
1ry6 d1ry6a_ A:1-9,42-54,300-309,311-330
1v8k d1v8ka_ A:72-80,114-125,370-380,385-403
1v8j d1v8ja_ A:72-80,114-125,370-380,385-404
3. i.10.1 Microtubule complexes
Microtubule complexes
1ia0 d1ia0k_ K:6-14,27-32,323-332,337-354
1ia0 d1ia0k_ K:6-14,47-52,323-332,337-354
4. b.81.1 Trimeric LpxA-like enzymes superhelical turns are made of three short strands; duplication: the sequence hexapeptide repeats correspond to individual strands !
Single-stranded left-handed beta-helix superhelix turns are made of parallel beta-strands and (short) turns
1thj d1thjc_ C:151-158,157-164,169-174,175-182
1thj d1thjb_ B:151-158,157-164,169-174,175-182
1qre d1qrea_ A:151-158,157-164,169-174,175-182
1thj d1thja_ A:151-158,157-164,169-174,175-182
1qrf d1qrfa_ A:151-158,157-164,169-174,175-182
1qrm d1qrma_ A:151-158,157-164,169-174,175-182
1qrl d1qrla_ A:151-158,157-164,169-174,175-182
1qrg d1qrga_ A:151-158,157-164,169-174,175-182
1qq0 d1qq0a_ A:151-158,157-164,169-174,175-182
1qrm d1qrma_ A:135-141,140-147,151-158,175-182
1qrl d1qrla_ A:135-141,140-147,151-158,175-182
1qrg d1qrga_ A:135-141,140-147,151-158,175-182
1thj d1thja_ A:135-141,140-147,151-158,175-182
1thj d1thjc_ C:135-141,140-147,151-158,175-182
1qrf d1qrfa_ A:135-141,140-147,151-158,175-182
1qre d1qrea_ A:135-141,140-147,151-158,175-182
1thj d1thjb_ B:135-141,140-147,151-158,175-182
1qq0 d1qq0a_ A:135-141,140-147,151-158,175-182
5. c.76.1 Alkaline phosphatase-like
Alkaline phosphatase-like core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
1fsu d1fsua_ A:83-87,329-334,346-350,375-383
1p49 d1p49a_ A:66-70,379-384,396-400,425-432
6. c.41.1 Subtilisin-like
Subtilisin-like 3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
2ixt d2ixta1 A:28-34,80-84,133-139,248-268
1ea7 d1ea7a_ A:28-34,80-84,133-139,248-268
2ixt d2ixtb1 B:28-34,80-84,133-139,248-268
7. c.2.1 NAD(P)-binding Rossmann-fold domains
NAD(P)-binding Rossmann-fold domains core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456 ! The nucleotide-binding modes of this and the next two folds/superfamilies are similar
2vuu d2vuuc1 C:144-151,186-191,212-219,316-326
1k6j d1k6ja_ A:144-151,186-191,212-219,316-326
2vuu d2vuua1 A:144-151,186-191,212-219,316-326
2vuu d2vuue1 E:144-151,186-191,212-219,316-326
2vuu d2vuug1 G:144-151,186-191,212-219,316-326
2vuu d2vuud1 D:144-151,186-191,212-219,316-326
2vut d2vutd1 D:144-151,186-191,212-219,316-326
8. c.51.6 XCC0632-like short crossover loop between strands 2 and 3; the antiparallel part of the beta-sheet (strands 3, 4 and 5) and the C-terminal helix are quite long
Anticodon-binding domain-like 3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
2iqi d2iqif1 F:70-74,84-88,122-136,176-209
2iqi d2iqia1 A:70-74,84-88,122-136,176-209
9. c.19.1 FabD/lysophospholipase-like
FabD/lysophospholipase-like core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
1nm2 d1nm2a1 A:91-97,157-164,227-232,256-268
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 64 (enumeration index: query16) of S4
2h58 A:445-453,468-472,737-746,751-766
2h58 A:445-453,485-492,737-746,751-766
3b6u B:10-17,54-59,309-318,323-340
3b6u A:10-17,54-59,309-318,323-340
3brk X:368-374,373-380,385-390,392-401
3kl3 D:11-23,45-49,263-268,284-298
2x7e A:19-26,61-68,328-337,342-359
2x7e B:19-26,59-68,328-337,342-359
3kwe A:137-143,142-149,154-159,160-167
3kwe A:120-126,125-132,137-143,160-167
2rep A:310-318,369-374,632-641,646-661
2w5t A:289-293,506-513,521-526,525-538
3t41 B:135-141,195-199,239-244,391-411
3t41 A:135-140,195-199,239-244,391-411
3h4s A:888-897,928-934,1179-1188,1193-1209
2ycl A:92-100,117-122,288-293,296-312
2fj0 A:138-144,156-160,219-226,470-480
3l9h B:19-26,62-68,328-337,342-359
3l9h A:19-26,59-68,328-337,342-359
3kvr B:155-159,172-179,200-209,248-261
3kvr A:155-159,172-179,200-209,248-261
2gez A:90-98,98-103,119-123,123-134
3gbj C:5-13,52-58,322-331,336-351
3gbj A:5-14,27-32,322-331,336-351
3gbj B:5-14,27-32,322-331,336-351
3gbj B:5-14,52-58,322-331,336-351
3gbj A:5-14,52-58,322-331,336-351
3gbj C:5-13,27-32,322-331,336-351
3ow5 A:151-158,157-164,169-174,175-182
3ow5 A:135-141,140-147,151-158,175-182
3map A:8-16,34-38,68-74,328-348
3map B:8-16,34-38,68-74,328-348
3nbq C:156-160,173-180,201-210,249-262
3nbq D:156-160,173-180,201-210,249-262
3nbq B:156-160,173-180,201-210,249-262
3nbq A:156-160,173-180,201-210,249-262
3edl D:73-80,114-125,370-380,385-403
3edl D:73-80,94-99,370-380,385-403
3kl5 C:11-23,45-49,263-269,284-298
3kl5 A:11-23,45-49,262-268,284-298
2x7d B:19-26,62-68,328-337,342-359
2x7d A:19-26,40-46,329-337,342-359
2x7d A:19-26,60-68,329-337,342-359
2xae A:19-26,62-68,328-337,342-359
2xae B:19-26,62-68,328-337,342-360
2xae C:19-26,62-68,328-337,342-358
2wbe C:8-15,48-54,313-322,327-344
3d43 A:28-34,80-84,133-139,248-268
3d43 B:28-34,80-84,133-139,248-268
3k5e A:19-26,61-68,328-337,342-359
3k5e B:19-26,61-68,328-337,342-359
2owm A:40-48,94-100,385-393,396-414
2owm A:40-48,61-65,385-393,396-414
3mas A:8-16,34-38,68-74,328-348
3mas B:8-16,34-38,68-74,328-348
3kwd A:137-143,142-149,154-159,160-167
3kwd A:120-126,125-132,137-143,160-167
3ken A:19-26,62-68,328-337,342-360
3ku4 C:155-159,172-179,200-209,248-261
3ku4 D:155-159,172-179,200-209,248-261
3ku4 B:155-159,172-179,200-209,248-261
3ku4 A:155-159,172-179,200-209,248-261
3p0e E:162-167,179-186,207-216,256-268
3p0e C:162-167,179-186,207-216,256-268
3p0e A:162-167,179-186,207-216,256-268
3p0e F:162-167,179-186,207-216,255-268
3p0e B:162-167,179-186,207-216,256-268
3p0e D:162-167,179-186,207-216,256-268
3otm A:151-158,157-164,169-174,175-182
3otm A:135-141,140-147,151-158,175-182
3otz A:151-158,157-164,169-174,175-182
3otz A:135-141,140-147,151-158,175-182
2i9l L:49-58,127-138,144-152,153-176
2i9l J:49-58,127-138,144-152,153-176
2i9l I:49-58,127-138,144-152,153-176
2i9l K:49-58,127-138,144-152,153-176
2h9a A:92-100,117-122,288-293,296-312
3eue A:156-160,173-180,201-210,249-262
3b6v B:11-18,55-60,334-343,348-366
3b6v A:11-18,55-60,334-343,348-365
3l9a X:161-168,167-173,211-216,218-230
3mar B:9-16,34-38,68-74,328-348
1t5c A:6-14,30-35,300-309,312-329
1t5c A:6-14,45-49,300-309,312-329
1t5c B:6-14,45-49,300-309,312-329
1t5c B:6-14,30-35,300-309,312-329
3bfn A:44-51,84-90,337-346,351-363
3k3b A:18-26,61-68,328-337,342-358
3k3b B:18-26,62-68,328-337,342-358
3l1c B:349-356,394-399,639-648,650-671
3l1c A:348-356,394-399,639-648,650-671
3p0f A:162-166,179-186,207-216,256-268
3hqd A:19-26,62-68,328-337,342-359
3hqd B:19-26,62-68,328-337,342-359
2x7c B:19-26,61-68,328-337,342-359
2x7c A:19-26,40-46,328-337,342-359
2x7c A:19-26,59-68,328-337,342-359
3euf C:156-160,173-180,201-210,249-262
3euf D:156-160,173-180,201-210,249-262
3euf B:156-160,173-180,201-210,249-262
3euf A:156-160,173-180,201-210,249-262
3dc4 A:7-16,45-50,289-298,303-324
3dcb A:6-16,45-50,289-298,300-321
3ou9 A:151-158,157-164,169-174,175-182
3ou9 A:135-141,140-147,151-158,175-182
2wog A:19-26,62-68,328-337,342-360
2wog B:19-26,62-68,328-337,342-360
2wog C:18-26,62-68,329-337,342-358
3lxy A:6-14,28-32,115-122,311-329
3oup A:151-158,157-164,169-174,175-182
3oup A:135-141,140-147,151-158,175-182
2y5w A:13-20,51-55,303-311,316-333
2y5w B:13-20,50-55,303-311,316-333
2y5w A:13-20,34-38,303-311,316-333
2o0a A:376-382,404-410,611-620,621-640
3kwc B:137-143,142-149,154-159,160-167
3kwc C:120-126,125-132,137-143,160-167
3kwc F:120-126,125-132,137-143,160-167
3kwc C:137-143,142-149,154-159,160-167
3kwc D:120-126,125-132,137-143,160-167
3kwc B:120-126,125-132,137-143,160-167
3kwc A:120-126,125-132,137-143,160-167
3kwc E:120-126,125-132,137-143,160-167
3kwc E:137-143,142-149,154-159,160-167
3kwc F:137-143,142-149,154-159,160-167
3kwc A:137-143,142-149,154-159,160-167
3kwc D:137-143,142-149,154-159,160-167
2gry A:196-204,238-249,494-504,506-523
2gry A:196-204,218-223,494-504,506-523
3lre B:12-19,71-76,324-333,338-355
3lre A:12-19,71-76,324-333,338-353
3lre A:12-19,33-38,324-333,338-353
3lre B:12-19,33-38,324-333,338-355
3dco N:7-16,45-50,289-298,303-324
3gtn A:11-23,45-49,262-268,284-298
2heh A:258-266,300-312,556-566,571-587
2heh A:258-266,280-285,556-566,571-587
3c8v A:334-340,344-351,356-362,380-388
3c8v D:334-340,344-351,356-362,380-388
3c8v B:334-340,344-351,356-362,380-388
3c8v C:334-340,344-351,356-362,380-388
2y65 D:13-20,51-55,302-311,316-333
2y65 C:13-20,51-55,302-311,316-333
2y65 A:13-20,50-55,302-311,316-333
2y65 B:13-20,50-55,302-311,314-333
3kuk B:155-159,172-179,200-209,248-261
3kuk A:155-159,172-179,200-209,248-261
3nwn A:6-14,23-27,309-318,323-340
3nwn A:6-14,51-57,309-318,323-340
2xrf C:162-166,179-186,207-216,256-268
2xrf B:162-166,179-186,207-216,256-268
2xrf A:162-167,179-186,207-216,256-268
3ed4 D:82-86,357-362,374-378,403-410
3ed4 A:82-86,357-362,374-378,403-410
3ed4 C:82-86,357-362,374-378,403-410
3kvy B:155-159,172-179,200-209,248-261
3kvy A:155-159,172-179,200-209,248-261
1ypy B:49-58,134-138,144-152,153-172
1ypy A:48-58,127-135,143-152,153-175
1ypy B:49-58,127-135,144-152,153-172
2x2r B:19-26,62-68,328-337,342-360
2x2r A:19-26,62-68,328-337,342-360
2x2r C:19-26,62-68,329-337,342-358
2vvg A:6-13,55-60,304-313,318-336
2vvg B:6-13,55-60,304-313,318-335
2hxh C:5-14,47-52,323-332,337-352
2hxh C:5-14,27-32,323-332,337-352
2p4n K:8-16,43-48,294-303,308-323
2qej C:49-56,69-76,84-90,131-148
2cf2 B:91-97,157-164,227-232,256-268
2cf2 K:91-97,157-164,227-232,256-268
2cdh 5:91-97,157-164,227-232,256-268
2cdh 4:91-97,157-164,227-232,256-268
2cdh O:91-97,157-164,227-232,256-268
2cdh P:91-97,157-164,227-232,256-268
2cdh 9:91-97,157-164,227-232,256-268
2cdh N:91-97,157-164,227-232,256-268
2cdh 8:91-97,157-164,227-232,256-268
2cdh 7:91-97,157-164,227-232,256-268
2cdh Q:91-97,157-164,227-232,256-268
2cdh R:91-97,157-164,227-232,256-268
2cdh M:91-97,157-164,227-232,256-268
2cdh 6:91-97,157-164,227-232,256-268