1. c.66.1 S-adenosyl-L-methionine-dependent methyltransferases
S-adenosyl-L-methionine-dependent methyltransferases core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
2okc d2okcb1 B:298-308,313-328,327-337,347-356,360-368
2ar0 d2ar0b1 B:305-314,319-334,333-342,353-362,376-382
2ar0 d2ar0a1 A:305-314,319-334,333-342,353-362,376-382
2okc d2okca1 A:298-308,313-328,327-336,347-356,361-367
2f8l d2f8la1 A:236-246,251-265,264-274,284-293,303-309
2ih5 d2ih5a1 A:157-166,171-185,185-192,202-211,214-223
2jg3 d2jg3a1 A:157-166,171-184,185-192,202-211,213-224
2ih2 d2ih2d1 D:157-166,171-185,185-192,202-211,214-223
2ibt d2ibtd1 D:157-166,171-185,185-192,202-211,214-223
2np7 d2np7a1 A:157-166,171-185,185-192,202-211,214-223
1g38 d1g38d1 D:157-166,171-185,185-192,202-211,214-223
2ibs d2ibsa1 A:157-166,171-184,185-192,202-211,213-224
1aqj d1aqja1 A:157-166,171-184,185-192,202-211,213-224
2adm d2adma1 A:157-166,171-184,185-192,202-211,213-224
2adm d2admb1 B:157-166,171-184,185-192,202-211,213-224
1nw5 d1nw5a_ A:100-107,118-130,132-142,155-164,206-210
1boo d1booa_ A:91-98,110-124,125-135,156-165,221-225
1eg2 d1eg2a_ A:100-107,118-130,132-143,155-164,206-211
1nw8 d1nw8a_ A:100-107,118-130,132-143,155-164,206-211
2ibs d2ibsd1 D:157-166,171-185,185-192,202-211,214-224
2jg3 d2jg3d1 D:157-166,171-185,185-192,202-211,214-224
1nw6 d1nw6a_ A:100-107,118-130,132-143,155-164,206-211
2ih4 d2ih4a1 A:157-166,171-185,185-192,202-211,214-224
1nw7 d1nw7a_ A:100-107,118-130,132-143,155-164,206-211
2ih2 d2ih2a1 A:157-166,171-185,185-192,202-211,214-224
1aqi d1aqib1 B:157-166,171-185,185-192,202-211,214-224
1aqi d1aqia1 A:157-166,171-185,185-192,202-211,214-224
2ih4 d2ih4d1 D:157-166,171-185,185-192,202-211,214-224
2np6 d2np6d1 D:157-166,171-185,185-192,202-211,214-224
1g38 d1g38a1 A:157-166,171-185,185-192,202-211,214-224
2ibt d2ibta1 A:157-166,171-185,185-192,202-211,214-224
1aqj d1aqjb1 B:157-166,171-185,185-192,202-211,214-224
2np6 d2np6a1 A:157-166,171-185,185-192,202-211,214-224
2. d.58.10 Acylphosphatase/BLUF domain-like
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1v3z d1v3zb_ B:3-13,18-31,32-40,42-51,86-91
1w2i d1w2ia_ A:3-13,18-31,32-40,42-51,86-91
1v3z d1v3za_ A:3-13,18-31,32-40,42-51,86-91
1w2i d1w2ib_ B:3-13,18-31,32-40,42-51,86-91
1yrx d1yrxa1 A:16-26,30-49,50-58,59-68,103-109
1x0p d1x0ph1 H:7003-7013,7017-7036,7037-7045,7046-7055,7092-7098
1x0p d1x0pc1 C:2003-2013,2017-2036,2037-2045,2046-2055,2092-2098
1x0p d1x0pd1 D:3003-3013,3017-3036,3037-3045,3046-3055,3092-3098
1x0p d1x0pe1 E:4003-4013,4017-4036,4037-4045,4046-4055,4092-4098
1x0p d1x0pg1 G:6003-6013,6017-6036,6037-6045,6046-6055,6092-6098
2byc d2bycb1 B:504-514,517-537,538-545,547-556,593-598
1urr d1urra_ A:6-16,21-34,35-43,45-54,93-97
1x0p d1x0pb1 B:1003-1013,1017-1036,1037-1045,1046-1055,1092-1098
1x0p d1x0pi1 I:8003-8013,8017-8036,8037-8045,8046-8055,8092-8098
1x0p d1x0pj1 J:9003-9013,9017-9036,9037-9045,9046-9055,9092-9098
1yrx d1yrxb1 B:15-26,30-49,50-58,59-68,103-109
1yrx d1yrxc1 C:15-26,30-49,50-58,59-68,103-109
2byc d2byca1 A:4-14,17-37,38-45,47-56,93-98
1x0p d1x0pf1 F:5003-5013,5017-5036,5037-5045,5046-5055,5092-5098
1x0p d1x0pa1 A:103-113,117-136,137-145,146-155,192-198
1ulr d1ulra_ A:2-11,16-29,30-38,40-48,84-88
2acy d2acya_ A:6-16,21-34,35-43,45-54,93-97
1gxu d1gxua_ A:4-16,21-34,36-43,44-51,87-91
1gxt d1gxta_ A:4-16,21-34,36-43,44-51,87-91
3. d.139.1 PurM C-terminal domain-like
PurM C-terminal domain-like 3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
2z1e d2z1ea2 A:163-171,225-239,240-246,299-308,312-319
2hs3 d2hs3a3 A:171-180,240-254,255-262,306-316,319-325
3d54 d3d54i3 I:173-180,240-254,255-262,307-316,318-325
3d54 d3d54a3 A:173-180,240-254,255-261,307-316,318-325
3d54 d3d54e3 E:173-180,240-254,255-261,307-316,318-325
1t3t d1t3ta6 A:432-440,506-520,521-527,573-582,585-592
3c9r d3c9ra2 A:147-155,211-224,225-230,278-287,290-294
1vk3 d1vk3a3 A:171-180,240-254,255-262,307-316,319-325
3c9s d3c9sa2 A:149-155,211-224,225-230,278-287,290-294
3c9t d3c9tb2 B:148-155,211-224,225-230,278-287,290-294
3c9u d3c9ua2 A:147-155,211-224,225-230,278-287,290-294
3c9s d3c9sb2 B:147-155,211-224,225-230,278-287,290-294
2hry d2hrya3 A:171-180,240-254,255-261,306-316,319-325
3c9u d3c9ub2 B:149-155,211-224,225-230,278-287,290-294
2hs0 d2hs0a3 A:171-180,240-254,255-262,307-316,319-325
2z1f d2z1fa2 A:163-171,225-239,240-247,299-307,312-319
3c9r d3c9rb2 B:148-155,211-224,225-230,278-287,290-294
2hru d2hrua3 A:171-180,240-254,255-262,307-316,319-325
3c9t d3c9ta2 A:149-155,211-224,225-230,278-287,290-294
1vqv d1vqvb2 B:148-155,211-224,224-230,278-287,289-294
2hs4 d2hs4a3 A:171-180,240-254,255-261,307-316,319-325
1vqv d1vqva2 A:149-155,211-224,226-230,278-286,290-294
2zod d2zodb2 B:162-170,224-237,238-243,321-328,331-336
2zau d2zaub2 B:162-170,224-237,238-243,321-328,331-336
2zau d2zauc2 C:162-170,224-237,238-243,321-328,331-336
2zau d2zaua2 A:162-170,224-237,238-243,321-328,331-336
2yye d2yyeb2 B:162-170,224-237,238-243,321-328,331-336
2zod d2zoda2 A:162-170,224-237,238-243,321-328,331-336
2yye d2yyea2 A:162-170,224-237,238-243,321-328,331-336
1cli d1clic2 C:2177-2186,2251-2261,2264-2270,2326-2336,2340-2344
1cli d1clia2 A:177-186,251-261,264-270,326-336,340-344
1t3t d1t3ta7 A:823-832,888-902,903-909,951-960,963-969
1cli d1clib2 B:1177-1186,1251-1261,1266-1270,1326-1335,1341-1345
1cli d1clid2 D:3177-3186,3251-3261,3266-3270,3326-3335,3341-3345
4. 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
3bq2 d3bq2a2 A:1-9,77-96,97-103,105-112,240-244
3bq0 d3bq0a2 A:1-9,77-96,96-103,105-112,240-244
3bq1 d3bq1a2 A:2-9,77-96,96-103,105-111,240-244
1k1q d1k1qb2 B:2-9,77-96,96-103,105-111,240-252
1k1s d1k1sa2 A:2-9,77-97,96-103,105-111,240-252
1k1q d1k1qa2 A:1-9,77-96,97-103,105-112,240-252
5. b.97.1 Cytolysin/lectin some topological similarity to osmotin !
Cytolysin/lectin sandwich, 10 strands in 2 sheets;
1iaz d1iazb_ B:6-10,15-27,31-40,68-77,168-179
1o72 d1o72b_ B:4-8,13-25,29-39,66-75,165-175
1o71 d1o71b_ B:4-8,13-25,29-39,66-75,165-175
1o71 d1o71a_ A:4-8,13-25,29-39,66-75,165-175
1iaz d1iaza_ A:6-10,15-27,31-41,68-77,168-178
1o72 d1o72a_ A:4-8,13-25,29-39,66-75,165-175
1gwy d1gwya_ A:4-8,13-25,29-39,66-75,165-175
1gwy d1gwyb_ B:3-8,13-25,29-39,66-75,165-175
6. b.47.1 Trypsin-like serine proteases
Trypsin-like serine proteases barrel, closed; n=6, S=8; greek-key ! duplication: consists of two domains of the same fold
2flr d2flrh1 H:50-56,55-60B,80-92,102-110,250-255
1dva d1dvai_ I:50-56,55-60B,80-92,102-110,250-255
1dva d1dvah_ H:50-56,55-60B,80-92,102-110,250-255
1o5d d1o5dh_ H:50-56,55-60B,80-92,102-110,250-255
2f9b d2f9bh1 H:50-56,55-60B,80-92,102-110,250-255
2aei d2aeih1 H:50-56,55-60B,80-92,102-110,250-255
2bz6 d2bz6h1 H:50-56,55-60B,80-92,102-110,250-255
2a2q d2a2qh1 H:50-56,55-60B,80-92,102-110,250-255
1qfk d1qfkh_ H:186-192,191-198,220-232,242-249,399-404
1kli d1klih_ H:50-56,55-60B,80-92,102-110,250-255
2zp0 d2zp0h1 H:50-56,55-60B,80-92,102-110,250-255
1w7x d1w7xh1 H:50-56,55-60B,80-92,102-109,250-255
2puq d2puqh1 H:186-192,191-198,220-232,242-249,399-404
2flb d2flbh1 H:50-56,55-60B,80-92,102-109,250-255
1j9c d1j9ch_ H:50-56,55-60B,80-92,102-109,250-255
1klj d1kljh_ H:50-56,55-60B,80-92,102-110,250-255
2aer d2aerh1 H:50-56,55-60B,80-92,102-110,250-255
2b7d d2b7dh1 H:50-56,55-60B,80-92,102-109,250-255
1w8b d1w8bh1 H:50-56,55-60B,80-92,102-109,250-255
2fir d2firh1 H:50-56,55-60B,80-92,102-109,250-255
1dan d1danh_ H:50-56,55-60B,80-92,102-110,250-255
1cvw d1cvwh_ H:50-56,55-60B,80-92,102-109,250-255
1z6j d1z6jh1 H:50-56,55-60B,80-92,102-109,250-255
1ygc d1ygch1 H:50-56,55-60B,80-92,102-109,250-255
2b8o d2b8oh1 H:50-56,55-60B,80-92,102-109,250-255
1wun d1wunh1 H:50-56,55-60B,80-92,102-110,250-255
1w0y d1w0yh1 H:50-56,55-60B,80-92,102-110,250-255
2c4f d2c4fh1 H:50-56,55-60B,80-92,102-110,250-255
1w2k d1w2kh1 H:50-56,55-60B,80-92,102-110,250-255
2ec9 d2ec9h1 H:50-56,55-60B,80-92,102-109,250-255
1wss d1wssh1 H:50-56,55-60B,80-92,102-110,250-255
1wtg d1wtgh1 H:50-56,55-60B,80-92,102-109,250-255
1wv7 d1wv7h1 H:50-56,55-60B,80-92,102-109,250-255
1wqv d1wqvh1 H:50-56,55-60B,80-92,102-109,250-255
7. d.65.1 Hedgehog/DD-peptidase zinc-binding motif !
Hedgehog/DD-peptidase alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
1lbu d1lbua2 A:158-163,168-180,182-186,195-200,204-208
8. b.53.1 Ribosomal protein L25-like
Ribosomal protein L25-like barrel, closed; n=6, S=10; complex topology
2v49 d2v49z1 Z:3-10,14-22,23-30,36-40,80-91
1vsp d1vspt1 T:7-11,14-22,22-31,32-41,82-91
9. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
487d d487dn_ N:3-9,13-24,25-33,35-43,85-94
10. c.56.6 LigB-like circular permutation of the common fold, most similar to the PNP fold !
Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
1b4u d1b4ud_ D:2-11,206-221,256-269,270-281,291-296
1b4u d1b4ub_ B:2-11,206-221,256-269,270-281,291-296
1bou d1boud_ D:2-11,206-221,256-269,270-281,291-296
1bou d1boub_ B:2-11,206-221,256-269,270-281,291-296
1b4u d1b4ud_ D:2-11,239-254,256-269,270-281,291-296
1b4u d1b4ub_ B:2-11,239-254,256-269,270-281,291-296
1bou d1boub_ B:2-11,239-254,256-269,270-281,291-296
1bou d1boud_ D:2-11,237-254,256-269,270-281,291-296
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
2qmw d2qmwa1 A:46-55,60-71,73-83,166-175,254-263
2qmw d2qmwb1 B:47-55,61-71,73-83,166-175,254-264
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 714 (enumeration index: query848.849) of S5
2bjd B:13-23,28-41,42-50,52-61,97-101
2bjd A:13-23,28-41,42-50,52-61,97-101
2i6r D:152-160,212-225,226-232,285-294,297-303
2i6r C:152-160,212-225,226-232,285-294,297-303
2i6r B:152-160,211-225,226-232,285-294,297-303
2i6r A:152-160,212-225,226-232,285-294,297-303
2z1t A:162-170,222-236,237-244,296-305,316-322
3amu A:0-9,17-34,40-45,56-66,237-245
2z1u A:162-170,222-236,237-244,296-305,315-322
3m84 A:177-186,255-265,268-274,331-341,341-347
3m84 B:177-186,255-265,268-274,331-341,341-347
3br8 A:2-11,16-29,30-38,40-48,85-89
2bje E:6-16,21-34,35-43,45-54,90-94
2bje G:6-16,21-34,35-43,45-54,90-94
2bje A:6-16,21-34,35-43,45-54,90-94
2bje C:6-16,21-34,35-43,45-54,90-94
3fd5 A:193-201,270-282,285-291,351-360,360-367
3fd5 B:193-201,270-282,285-291,351-360,362-366
2hlu A:2-11,16-29,30-38,40-48,85-90
3lkd B:352-359,366-380,381-391,397-406,413-419
3lkd A:352-359,366-380,381-391,397-406,413-419
3k1q A:927-932,969-981,984-989,1025-1030,1120-1128
3u02 A:1-9,15-33,39-44,55-64,238-247
3u02 D:1-9,16-34,39-43,56-64,238-247
3u02 C:1-9,17-33,39-44,55-64,238-247
3u02 B:1-9,16-33,39-44,55-64,238-247
3e1b C:2-9,13-24,25-32,37-43,85-94
3t2d A:1-11,22-40,42-51,52-61,285-292
3kiz A:181-189,291-300,305-310,364-372,379-385
3kiz B:181-189,292-300,305-310,364-372,379-385
2iyg B:16-26,30-49,50-58,59-68,105-110
2iyg A:16-26,30-49,50-58,59-68,105-110
3gfx B:2-11,19-35,36-44,45-54,92-97
3gfx A:2-11,19-35,36-44,45-54,91-97
2ozv B:171-179,179-191,193-205,208-220,220-229
2ozv A:171-179,179-191,193-205,208-220,230-234
2ozv B:171-179,179-191,193-205,208-220,230-234
2ozv A:171-179,179-191,193-205,208-220,220-229
3t2g A:1-11,22-40,42-51,52-61,285-291
2y7h B:303-312,317-332,331-340,351-360,374-380
2y7h C:303-312,317-332,331-340,351-360,374-380
3khk B:388-396,405-417,418-426,436-444,458-465
3khk A:387-396,405-417,418-426,436-445,458-465
2yxz B:150-158,212-224,225-231,283-292,295-299
2yxz D:150-158,212-224,225-230,283-291,294-299
2yxz A:150-158,212-224,225-231,283-292,295-299
2yxz C:150-158,212-224,225-231,283-292,295-299
2y7c B:303-312,317-332,331-340,351-360,374-380
2y7c C:303-312,317-332,331-340,351-360,374-380
3amt A:0-9,17-34,40-45,56-66,237-245
2fhm A:2-11,16-29,30-38,40-48,85-89
3opn A:149-157,175-194,194-203,213-221,223-227
3awi F:308-312,319-340,345-355,396-407,497-501
2w4c A:6-16,21-34,35-43,45-54,93-97
2k7j A:6-17,22-35,36-44,46-56,94-98
3gfz B:2-11,19-35,36-44,45-54,92-97
3gfz A:2-11,19-35,36-44,45-54,91-97
3gg1 A:2-11,19-35,36-44,45-54,91-97
3gg1 B:2-11,19-35,36-44,45-54,92-97
3mwb A:50-58,63-74,76-87,177-187,270-279
2iyi B:16-26,30-49,50-58,59-68,105-110
2iyi A:16-26,30-49,50-58,59-68,105-110
2l2b A:4-9,13-25,29-37,66-75,165-175
3ll7 A:200-208,211-220,221-231,232-242,254-260
3mcq A:147-155,211-224,225-232,284-293,296-302
3mdo A:180-189,290-299,301-308,362-371,374-382
3mdo B:180-188,291-299,301-308,362-371,374-382
3p4e A:178-187,251-261,266-270,326-334,342-346
3ela H:186-192,191-198,220-232,242-249,399-404
2vh7 A:6-16,21-34,35-43,45-54,93-97
3luy A:55-64,69-79,82-92,175-184,275-285
3lpm A:170-178,180-192,192-204,207-219,224-228
3lpm B:168-178,180-192,192-204,207-219,224-228
3fd6 A:193-201,270-282,285-291,351-360,362-366
3fd6 B:193-201,270-282,285-291,351-359,361-366
2kb2 A:4-14,22-38,39-47,48-57,94-100
3kcr V:4-9,13-24,24-32,37-44,85-94
3t2f A:1-11,22-40,42-51,52-61,285-292
2z01 A:174-183,250-261,263-270,326-335,335-342
3fik V:2-9,13-24,25-33,34-43,85-94
2v9y A:607-616,684-694,698-704,759-768,775-780
2v9y B:607-616,684-694,697-704,759-769,775-780
2w4p A:6-16,21-34,35-43,45-54,93-98
2hfo C:6-16,20-39,40-47,49-58,93-99
2hfo J:6-16,20-39,40-47,49-58,96-101
2hfo E:6-16,20-39,40-47,49-58,95-101
2hfo I:6-16,20-39,40-47,49-58,95-101
2hfo F:6-16,20-39,40-47,49-58,95-101
2hfo A:6-16,20-39,40-47,49-58,95-101
2hfo H:6-16,20-39,40-47,49-58,95-101
2hfo G:6-16,20-39,40-47,49-58,95-101
2hfo B:6-16,20-39,40-47,49-58,95-100
3t2e A:1-11,22-40,42-51,52-61,285-292
2rb9 C:166-174,225-239,240-246,299-308,311-317
2rb9 B:166-174,225-239,240-246,299-308,311-317
2rb9 D:166-174,225-239,240-246,299-308,311-317
2rb9 A:166-174,225-239,240-246,299-308,311-317
3lim A:5-10,15-27,31-41,68-77,168-178
3lim B:5-10,15-27,31-41,68-77,168-178
3lim E:5-10,15-27,31-41,68-77,168-178
3lim C:5-10,15-27,31-41,68-77,168-178
3lim D:5-10,15-27,31-41,68-77,168-178
3lim F:5-10,15-27,31-41,68-77,168-178
2btu A:174-183,250-261,263-269,325-334,336-341
3trg A:8-18,23-36,37-45,47-56,91-95
2hlt A:2-11,16-29,30-38,40-48,85-89
2hfn I:6-16,20-39,40-47,49-58,95-101
2hfn E:6-16,20-39,40-47,49-58,95-101
2hfn F:6-16,20-39,40-47,49-58,95-101
2hfn H:6-16,20-39,40-47,49-58,95-101
2hfn G:6-16,20-39,40-47,49-58,95-101
2hfn A:6-16,20-39,40-47,49-58,95-101
2hfn J:6-16,20-39,40-47,49-58,95-101
2hfn B:6-16,20-39,40-47,49-58,95-101
2hfn C:6-16,20-39,40-47,49-58,95-101
2wdj Z:3-10,14-22,22-31,32-41,80-91
1y9o A:13-23,28-41,42-48,52-61,97-101
3gfy A:2-11,19-35,36-44,45-54,91-97
3gfy B:2-11,19-35,36-44,45-54,92-97
3t2c A:1-11,22-40,42-51,52-61,285-292
3ac6 A:195-202,263-277,278-284,331-339,342-348
3ac6 A:560-568,624-638,639-645,683-692,694-700
3gg0 B:2-11,19-35,36-44,45-54,91-97
3gg0 A:2-11,19-35,36-44,45-54,91-97
3mzi B:2-13,17-36,37-44,46-56,92-98
3mzi D:3-13,17-36,37-44,46-55,93-98
3mzi E:3-13,17-36,37-44,46-55,93-98
3mzi F:3-13,17-36,37-44,46-55,93-97
3mzi A:3-13,17-36,37-44,46-55,94-98
2zzu H:50-56,55-60B,80-92,102-110,250-255
2dka B:28-33,36-55,58-64,71-80,132-140
3t2b A:1-11,22-40,42-51,52-61,285-292
2gv1 A:4-13,18-31,33-40,42-50,88-92
2qmx A:46-55,60-70,70-81,169-179,266-278
2qmx B:46-54,60-70,70-81,169-179,266-278
3qty B:177-186,255-265,269-274,331-340,343-347
3qty A:177-186,255-265,269-274,331-340,343-347
2k7k A:6-16,22-35,36-44,46-56,94-98
3au7 A:0-8,19-34,40-45,56-66,237-245
3s1s A:457-467,474-488,487-496,508-517,522-529
2zwl H:50-56,55-60B,80-92,102-109,250-255
2w4d E:3-13,18-31,32-40,42-51,86-90
2w4d C:3-13,18-31,32-40,42-51,86-90
2w4d A:3-13,18-31,32-40,42-51,86-90
2w4d B:3-13,18-31,32-40,42-51,86-90
2w4d D:3-13,18-31,32-40,42-51,86-90
2w4d F:3-13,18-31,32-40,42-51,86-90