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
3d31 d3d31b2 B:27-33,187-195,211-219,231-239
3d31 d3d31a2 A:27-33,187-195,211-219,231-239
1g3i d1g3iv_ V:76-82,95-119,236-251,288-294
1g3i d1g3iw_ W:76-82,95-120,238-251,288-294
1g3i d1g3iu_ U:76-82,95-120,236-251,288-294
1yyf d1yyfa1 A:77-83,95-116,235-250,287-293
1kyi d1kyib_ B:76-82,95-119,236-251,288-294
1g3i d1g3ix_ X:76-82,95-119,236-251,288-294
1kyi d1kyif_ F:76-82,95-119,236-251,288-294
1e94 d1e94e_ E:76-83,95-117,235-250,287-293
1g3i d1g3ib_ B:76-83,95-120,236-251,288-294
1g3i d1g3ia_ A:76-83,95-120,236-251,288-294
1do0 d1do0c_ C:76-83,95-120,235-250,288-293
1g3i d1g3is_ S:76-82,95-120,236-251,288-294
1kyi d1kyie_ E:76-82,95-119,236-251,288-294
1kyi d1kyia_ A:76-83,95-119,236-251,288-294
1e94 d1e94f_ F:76-83,95-120,235-250,287-293
1yyf d1yyfb1 B:77-83,95-116,235-250,287-293
1g4b d1g4bl_ L:76-83,95-120,235-250,287-293
1g4b d1g4bf_ F:76-83,95-120,235-250,287-293
1kyi d1kyid_ D:76-82,95-119,236-251,288-294
1do0 d1do0f_ F:76-83,95-120,235-250,288-293
1kyi d1kyic_ C:76-82,95-119,236-251,288-294
1g4b d1g4bk_ K:76-83,95-120,235-250,287-293
1g4b d1g4be_ E:76-83,95-120,235-250,287-293
1do2 d1do2d_ D:77-83,91-120,235-250,288-293
1g3i d1g3it_ T:76-82,95-121,236-251,288-294
1g3i d1g3ie_ E:76-83,95-120,236-251,288-294
1g41 d1g41a_ A:76-83,95-120,236-251,288-294
1g3i d1g3id_ D:76-83,95-120,236-251,288-294
1ht2 d1ht2g_ G:76-83,95-120,235-250,287-293
1hqy d1hqye_ E:76-83,95-120,235-250,287-293
1ht1 d1ht1f_ F:76-83,95-120,235-250,287-293
1ht1 d1ht1g_ G:76-83,95-120,235-250,287-293
1ht2 d1ht2f_ F:76-83,95-120,235-250,287-293
1ht2 d1ht2e_ E:76-83,95-120,235-250,287-293
1ht1 d1ht1i_ I:76-83,95-120,235-250,287-293
1im2 d1im2a_ A:76-83,95-121,236-251,288-294
1ht2 d1ht2h_ H:76-83,95-120,235-250,287-293
1ht1 d1ht1e_ E:76-83,95-120,235-250,287-293
1do2 d1do2c_ C:76-82,95-120,235-250,287-293
1hqy d1hqyf_ F:76-83,95-120,235-250,287-293
1do0 d1do0e_ E:76-83,95-120,235-250,287-293
1do2 d1do2b_ B:76-83,91-120,235-250,288-293
1do0 d1do0b_ B:76-83,95-120,235-250,287-293
1g3i d1g3if_ F:76-83,95-122,236-251,288-294
1g3i d1g3ic_ C:76-83,95-121,236-251,288-294
1do2 d1do2a_ A:76-83,95-120,235-250,287-293
1g4a d1g4ae_ E:77-83,95-120,235-250,287-293
1do0 d1do0d_ D:76-83,95-120,235-250,287-293
1g4a d1g4af_ F:77-82,95-120,235-250,287-293
1do0 d1do0a_ A:76-83,95-120,235-250,287-293
2. i.19.1 Bacteriophage T4 3D cryo-EM reconstruction
Bacteriophage T4 3D cryo-EM reconstruction
1pdj d1pdje_ E:119-123,127-141,165-176,186-192
1pdj d1pdjf_ F:119-123,127-141,165-176,186-192
1pdj d1pdjd_ D:119-123,127-141,165-176,186-192
3. b.106.1 Phage tail proteins
Phage tail proteins core: barrel; n=6, S=10; greek-key; topologically similar to the FMN-binding split barrel
1k28 d1k28d1 D:119-123,127-141,165-176,186-192
1wth d1wthd1 D:118-123,127-141,165-176,186-191
4. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
1s1h d1s1ht_ T:383-390,500-516,534-551,553-558
5. d.52.3 Prokaryotic type KH domain (KH-domain type II) Prokaryotic and eukaryotic domains share a KH-motif but have different topologies !
Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
1hh2 d1hh2p3 P:231-240,278-288,322-333,334-341
1l2f d1l2fa3 A:231-240,278-288,322-333,334-341
2atw d2atwc3 C:216-225,263-273,307-318,319-326
1k0r d1k0ra3 A:216-225,263-273,307-318,319-326
2atw d2atwa3 A:216-225,263-273,307-318,319-327
2asb d2asba3 A:216-225,263-273,307-318,319-327
1k0r d1k0rb3 B:216-225,263-273,307-318,319-326
1k0r d1k0ra3 A:253-260,263-273,307-318,319-326
1k0r d1k0rb3 B:253-260,263-273,307-318,319-326
2atw d2atwc3 C:253-259,263-273,307-318,319-326
1l2f d1l2fa3 A:268-274,278-288,322-333,334-341
1hh2 d1hh2p3 P:268-275,278-288,322-333,334-341
2atw d2atwa3 A:253-259,263-273,307-318,319-327
2asb d2asba3 A:253-259,263-273,307-318,319-327
6. c.109.1 PEP carboxykinase N-terminal domain
PEP carboxykinase N-terminal domain contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain
1ii2 d1ii2b2 B:3-8,10-23,114-126,281-285
1ii2 d1ii2a2 A:3-8,10-23,114-126,281-285
2pc9 d2pc9a2 A:13-18,20-32,122-134,293-297
2py7 d2py7x2 X:22-26,28-38,141-153,308-312
1j3b d1j3ba2 A:13-18,20-32,122-134,293-297
2pxz d2pxzx2 X:22-26,28-38,141-153,308-312
1j3b d1j3bb2 B:13-18,20-32,122-134,293-297
2pc9 d2pc9c2 C:13-18,20-32,122-134,293-297
1xkv d1xkvb2 B:13-18,20-32,122-134,293-297
1xkv d1xkva2 A:13-18,20-32,122-134,293-297
2pc9 d2pc9b2 B:13-18,20-32,122-134,293-297
2pc9 d2pc9d2 D:13-18,20-32,122-134,293-297
1os1 d1os1a2 A:21-26,28-38,141-153,308-312
1m51 d1m51a2 A:41-46,49-64,163-175,353-359
1khb d1khba2 A:41-46,49-64,163-175,353-359
1nhx d1nhxa2 A:41-46,49-64,163-175,353-359
1khg d1khga2 A:41-46,49-64,163-175,353-359
1khe d1khea2 A:41-46,49-64,163-175,353-359
1khf d1khfa2 A:41-46,49-64,163-175,353-359
2gmv d2gmva2 A:41-46,49-64,163-175,353-359
2gmv d2gmvb2 B:41-46,49-64,163-175,353-359
1k3d d1k3da2 A:18-26,28-38,141-153,308-312
2olq d2olqa2 A:18-26,28-38,141-153,308-312
1oen d1oena2 A:18-26,28-38,141-153,308-312
2olr d2olra2 A:18-26,28-38,141-153,308-312
1k3c d1k3ca2 A:18-26,28-38,141-153,308-312
1aq2 d1aq2a2 A:18-26,28-38,141-153,308-312
1ayl d1ayla2 A:18-26,28-38,141-153,308-312
7. c.1.9 Metallo-dependent hydrolases the beta-sheet barrel is similarly distorted and capped by a C-terminal helix ! has transition metal ions bound inside the barrel !
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
1rjp d1rjpa3 A:63-68,80-87,397-414,427-433
1rjr d1rjra3 A:63-68,80-87,397-414,427-433
1rk6 d1rk6a3 A:63-68,80-87,397-414,427-433
1rjq d1rjqa3 A:63-69,80-87,397-414,427-433
1v4y d1v4ya3 A:63-69,80-87,397-414,427-433
1m7j d1m7ja3 A:63-69,80-87,397-414,427-433
1v51 d1v51a3 A:63-69,80-87,397-414,427-433
1rk5 d1rk5a3 A:63-69,80-87,397-414,427-433
1onx d1onxa2 A:64-70,88-96,324-341,354-361
1onw d1onwa2 A:64-70,88-96,329-341,354-361
1onx d1onxb2 B:64-70,88-96,329-341,354-361
1onw d1onwb2 B:64-70,88-96,329-341,354-361
1nfg d1nfgd2 D:53-59,72-84,357-374,388-396
1gkp d1gkpd2 D:310-318,343-356,359-376,391-397
1k1d d1k1dc2 C:310-317,344-357,360-377,392-399
2plm d2plma2 A:51-57,88-107,309-326,338-345
1p1m d1p1ma2 A:51-57,88-107,309-326,338-345
1j6p d1j6pa2 A:51-57,88-107,309-326,338-345
8. d.169.1 C-type lectin-like
C-type lectin-like unusual fold
1bch d1bch11 1:109-114,120-132,140-152,153-157
2msb d2msba_ A:110-115,120-132,140-152,153-157
1bch d1bch21 2:109-114,120-132,140-152,153-157
1afa d1afa21 2:109-114,120-132,140-152,153-157
1fif d1fifb1 B:109-114,120-132,140-152,153-157
1bcj d1bcj21 2:109-114,120-132,140-152,153-157
1kmb d1kmb11 1:109-114,120-132,140-152,153-157
1kmb d1kmb21 2:109-114,120-132,140-152,153-157
1kmb d1kmb31 3:109-114,120-132,140-152,153-157
1fif d1fifa1 A:109-114,120-132,140-152,153-157
2kmb d2kmb31 3:109-114,120-132,140-152,153-157
3kmb d3kmb31 3:109-114,120-132,140-152,153-157
1fih d1fiha1 A:109-114,120-132,140-152,153-157
4kmb d4kmb31 3:109-114,120-132,140-152,153-157
2kmb d2kmb21 2:109-114,120-132,140-152,153-157
1bcj d1bcj11 1:109-114,120-132,140-152,153-157
1afb d1afb21 2:109-114,120-132,140-152,153-157
1afd d1afd31 3:109-114,120-132,140-152,153-157
4kmb d4kmb11 1:109-114,120-132,140-152,153-157
2kmb d2kmb11 1:109-114,120-132,140-152,153-157
1fih d1fihb1 B:109-114,120-132,140-152,153-157
1afa d1afa31 3:109-114,120-132,140-152,153-157
1kwv d1kwvc1 C:109-114,120-132,140-152,153-157
1kwt d1kwtc1 C:109-114,120-132,140-152,153-157
1kwu d1kwuc1 C:109-114,120-132,140-152,153-157
1kx1 d1kx1c1 C:109-114,120-132,140-152,153-157
1afb d1afb31 3:109-114,120-132,140-152,153-157
1kwx d1kwxc1 C:109-114,120-132,140-152,153-157
1rtm d1rtm31 3:109-114,120-132,140-152,153-157
1kww d1kwwc1 C:109-114,120-132,140-152,153-157
1afd d1afd11 1:109-114,120-132,140-152,153-157
1kwz d1kwzc1 C:109-114,120-132,140-152,153-157
1kx1 d1kx1f1 F:109-114,120-132,140-152,153-157
1kwy d1kwyc1 C:109-114,120-132,140-152,153-157
1afb d1afb11 1:109-114,120-132,140-152,153-157
1afd d1afd21 2:109-114,120-132,140-152,153-157
1buu d1buua1 A:109-114,120-132,140-152,153-157
1kx0 d1kx0a1 A:109-114,120-132,140-152,153-157
1afa d1afa11 1:109-114,120-132,140-152,153-157
1kx0 d1kx0c1 C:109-114,120-132,140-152,153-157
9. d.92.1 Metalloproteases ("zincins"), catalytic domain
Zincin-like contains mixed beta sheet with connection over free side of the sheet
2ima d2imab1 B:125-129,275-300,309-322,323-327
2ima d2imaa1 A:125-129,275-300,309-322,323-327
2imc d2imcb1 B:125-129,275-300,309-322,323-327
2imb d2imba1 A:125-129,275-300,309-322,323-327
3bok d3boka1 A:125-129,275-301,309-322,323-327
3bon d3bona1 A:125-129,275-301,309-322,323-327
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
1qtm d1qtma1 A:305-313,337-346,352-364,367-372
4ktq d4ktqa1 A:305-313,337-346,352-364,367-372
11. c.94.1 Periplasmic binding protein-like II Similar in architecture to the superfamily I but partly differs in topology !
Periplasmic binding protein-like II consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication ! mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
2onr d2onra1 A:144-149,153-171,172-184,188-192
2ons d2onsa1 A:144-149,153-171,172-184,188-192
12. c.12.1 Ribosomal proteins L15p and L18e
Ribosomal proteins L15p and L18e core: three turns of irregular (beta-beta-alpha)n superhelix
2qam d2qaml1 L:73-80,79-86,128-139,139-144
2qao d2qaol1 L:73-80,79-86,128-139,139-144
2z4l d2z4ll1 L:73-80,79-86,128-139,139-144
2z4n d2z4nl1 L:73-80,79-86,128-139,139-144
13. d.58.11 EF-G C-terminal domain-like
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1wdt d1wdta5 A:284-295,397-410,429-444,446-451
2dy1 d2dy1a4 A:284-294,397-410,429-444,446-451
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 153 (enumeration index: query159) of S4
1ybq B:64-70,88-96,329-341,354-361
1ybq A:64-70,88-96,329-341,354-361
2faf A:59-64,67-82,183-195,372-378
2faf B:59-64,67-82,183-195,372-378
2qf2 A:41-46,49-64,163-175,353-359
2qf2 B:41-46,49-64,163-175,353-359
3qix A:125-129,275-300,309-322,323-327
2rka A:41-46,49-64,163-175,353-359
2rka C:41-46,49-64,163-175,353-359
3cg1 B:151-156,160-178,180-191,192-196
3c8a A:125-129,275-301,309-322,323-327
2aqv A:64-70,88-96,329-341,354-361
2aqv B:64-70,88-96,329-341,354-361
1yvy A:16-21,23-33,134-146,299-306
1yvy B:1016-1021,1023-1033,1134-1146,1302-1306
3cij A:144-149,153-171,172-184,188-192
3cij B:144-149,153-171,172-184,188-192
3k5m A:151-161,200-216,224-241,244-248
2oem A:104-112,265-274,280-293,295-300
3prd A:43-49,151-165,192-209,212-218
3ooq B:59-64,101-111,328-345,359-366
3ooq D:59-64,101-111,328-345,359-366
3k58 A:151-161,200-216,224-241,244-248
1z47 A:222-229,229-237,239-248,350-355
3c89 A:125-129,275-301,309-322,323-327
3mof A:41-46,49-64,163-175,353-359
3mof B:41-46,49-64,163-175,353-359
2rk7 B:41-46,49-64,163-175,353-359
2rk7 A:41-46,49-64,163-175,353-359
3oss D:4-13,13-26,48-64,65-699
3t8l B:88-94,101-113,315-332,345-352
3t8l A:88-94,101-113,315-332,345-352
3c8b A:125-129,275-301,309-322,323-327
2rkd A:41-46,49-64,163-175,353-359
2aqo B:64-70,88-96,329-341,354-361
3ds9 A:125-129,275-300,309-322,323-327
2g7p A:124-128,274-300,308-321,322-326
1ylh A:18-26,28-38,141-153,308-312
2g7k A:124-128,274-300,308-321,322-326
3ls9 A:59-65,103-122,359-376,389-396
3ozx A:368-375,519-527,548-561,563-569
3ozx B:367-375,519-527,548-561,563-569
3ozx B:99-106,270-278,299-310,570-576
3ozx A:99-106,270-278,299-310,570-576
2xzn 3:91-97,118-132,166-179,181-188
3dtb B:41-46,49-64,163-175,353-359
3dtb A:41-46,49-64,163-175,353-359
3o53 A:262-268,272-284,283-299,310-314
3gip B:62-67,79-86,396-413,426-432
3gip A:62-67,79-86,396-413,426-432
3cg3 A:146-151,155-173,175-186,187-191
2fah D:59-64,67-82,183-195,372-378
2fah C:59-64,67-82,183-195,372-378
2fah B:59-64,67-82,183-195,372-378
2fah A:59-64,67-82,183-195,372-378
2zvi B:107-116,268-278,283-296,298-303
2zvi D:107-116,268-278,283-296,298-303
2zvi A:107-116,268-278,283-296,298-303
1zzv A:2-8,9-22,45-57,59-65
2qey A:41-46,49-64,163-175,353-359
3ady A:82-90,90-103,127-140,142-150
3tuz G:32-38,200-208,224-232,292-305
3tuz C:31-38,200-208,224-232,292-305
3dt2 A:41-46,49-64,163-175,353-359
2cy1 A:35-43,77-87,122-137,139-144
2cy1 A:67-74,77-87,122-137,139-144
2qzy A:59-64,67-82,183-195,372-378
2qzy B:59-64,67-82,183-195,372-378
2g7n A:124-128,274-300,308-321,322-326
3moe A:41-46,49-64,163-175,353-359
3tui C:32-38,200-208,224-232,292-305
3tui D:32-38,200-208,224-232,292-305
3tui G:31-38,200-208,224-232,292-305
3ezj C:7-13,13-26,48-64,66-71
3ezj E:7-13,13-26,48-64,66-71
3ezj A:7-13,13-26,48-64,65-71
3ezj G:7-13,13-26,48-64,65-71
1ytm B:1013-1021,1023-1033,1134-1146,1302-1306
1ytm A:16-21,23-33,134-146,302-306
3nqb B:88-94,101-113,315-332,345-352
3nqb A:88-94,101-113,315-332,345-352
3giq B:62-67,79-86,396-413,426-432
3giq A:62-67,79-86,396-413,426-432
3gwc F:181-188,188-201,205-224,230-236
3gwc A:181-188,188-201,205-224,230-236
3gwc B:181-188,188-201,205-224,230-236
3gwc G:181-188,188-201,205-224,230-236
3bk7 A:368-375,517-525,546-559,561-566
3bk7 A:103-110,273-281,302-313,569-574
3cfz A:149-154,158-176,177-189,191-197
3hpa A:89-95,127-146,378-395,408-415
3prb A:43-49,151-165,192-209,212-222
3prb B:43-49,151-165,192-209,212-222
2z6b D:119-127,127-141,165-176,186-191
2xzm 3:91-97,118-132,166-179,181-188
2qf1 A:41-46,49-64,163-175,353-359
2cxc A:35-43,77-87,122-137,139-144
2cxc A:67-74,77-87,122-137,139-144
2rk8 B:41-46,49-64,163-175,353-359
2rk8 A:41-46,49-64,163-175,353-359
3dse A:125-129,275-300,309-322,323-327
3dt4 A:41-46,49-64,163-175,353-359
3dt4 C:41-46,49-64,163-175,353-359
2qew A:41-46,49-64,163-175,353-359
3ddb A:125-129,275-301,309-322,323-327
3qiz A:125-129,275-300,309-322,323-327
2rke A:41-46,49-64,163-175,353-359
3gr5 A:32-37,41-54,75-88,88-95
3tuj D:32-38,200-208,224-232,297-305
3tuj C:32-39,200-208,224-232,297-305
3hzg A:181-188,188-201,205-224,230-236
3gs9 A:99-108,109-119,148-161,162-168
3t81 B:88-94,101-113,315-332,345-352
3t81 A:88-94,101-113,315-332,345-352
3dt7 A:41-46,49-64,163-175,353-359
3dt7 B:41-46,49-64,163-175,353-359
2vun D:63-67,83-92,302-319,331-338
2vun C:63-67,83-92,302-319,331-338
2vun B:63-67,83-92,302-319,331-338
2vun A:63-67,83-92,302-319,331-338
3qqc A:11-15,41-55,78-87,134-140
1ygg A:21-26,28-38,141-153,308-312
2af6 G:181-188,188-201,205-224,230-236
2af6 A:181-188,188-201,205-224,230-236
2af6 B:180-188,188-201,205-224,230-236
2af6 F:181-188,188-201,205-224,230-236
2af6 C:180-188,188-201,205-224,230-236
2af6 E:181-188,188-201,205-224,230-236
3hm7 A:59-65,76-88,357-374,388-396
3hm7 B:59-65,76-88,357-374,388-396
2gq2 C:181-188,188-201,205-224,230-236
2gq2 A:180-188,188-201,205-224,230-236
2gq2 B:180-188,188-201,205-224,230-236
1yqt A:99-106,269-277,298-309,564-570
1yqt A:364-371,513-521,542-555,557-563
3moh B:41-46,49-64,163-175,353-359
3moh A:41-46,49-64,163-175,353-359
2nyy A:125-129,275-301,309-322,323-327
2nz9 A:125-129,275-300,309-322,323-327
2nz9 B:125-129,275-301,309-322,323-327