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
1u2z d1u2zc_ C:235-241,247-253,263-280,292-303,304-322
1u2z d1u2zb_ B:235-241,247-253,263-280,292-303,304-323
1u2z d1u2za_ A:235-241,247-253,263-280,292-303,304-323
2. a.56.1 CO dehydrogenase ISP C-domain like contains 2Fe-2S cluster !
CO dehydrogenase ISP C-domain like core: 4 helices, bundle
1jrp d1jrpe1 E:47-54,72-77,103-121,124-133,272-279
1jro d1jroe1 E:47-54,71-77,103-121,124-133,272-279
3. 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
1r0x d1r0xb_ B:614-621,622-629,629-638,637-648,654-670
1r0x d1r0xa_ A:614-621,622-629,629-638,637-648,654-670
1r0y d1r0ya_ A:614-621,622-629,629-638,637-648,654-670
1q3h d1q3ha_ A:614-621,622-629,629-638,637-648,654-670
1r0w d1r0wa_ A:614-621,622-629,629-638,637-648,654-670
1r0x d1r0xc_ C:614-621,622-629,629-638,637-648,654-670
1xf9 d1xf9b_ B:614-621,622-629,629-638,637-648,654-670
1q3h d1q3hc_ C:614-621,622-629,629-638,637-648,654-670
1r0y d1r0yc_ C:614-621,622-629,629-638,637-648,654-670
1r0y d1r0yb_ B:614-621,622-629,629-638,637-648,654-670
1r0w d1r0wb_ B:614-621,622-629,629-638,637-648,654-670
1q3h d1q3hb_ B:614-621,622-629,629-638,637-648,654-670
1r10 d1r10b_ B:614-621,622-629,629-638,637-648,654-670
1xfa d1xfaa_ A:614-621,622-629,629-638,637-648,654-670
1r0y d1r0yd_ D:614-621,622-629,629-638,637-648,654-670
1xf9 d1xf9c_ C:614-621,622-629,629-638,637-648,654-670
1xf9 d1xf9a_ A:614-621,622-629,629-638,637-648,654-670
1xf9 d1xf9d_ D:614-621,622-629,629-638,637-648,654-670
1xfa d1xfab_ B:614-621,622-629,629-638,637-648,654-670
1q3h d1q3hd_ D:614-621,622-629,629-638,637-648,654-670
1r0w d1r0wd_ D:614-621,622-629,629-638,637-648,654-670
1r0z d1r0zc_ C:614-621,622-629,629-638,637-648,654-670
1r0w d1r0wc_ C:614-621,622-629,629-638,637-648,654-670
1r0z d1r0zd_ D:614-621,622-629,629-638,637-648,654-670
1r0z d1r0za_ A:614-621,622-629,629-638,637-648,654-670
1r0x d1r0xd_ D:614-621,622-629,629-638,637-648,654-670
1r0z d1r0zb_ B:614-621,622-629,629-638,637-648,654-670
4. d.371.1 YehR-like
YehR-like beta(3)-alpha-beta(2)-alpha(3)-beta; 2 layers, a/b; antiparallel beta-sheet, order: 612354
2joe d2joea1 A:28-41,78-88,92-101,105-112,114-126
5. a.6.1 Putative DNA-binding domain
Putative DNA-binding domain core: 3 helices; architecture is similar to that of the "winged helix" fold but topology is different
1sbx d1sbxa_ A:100-106,107-116,123-132,135-147,178-192
6. c.123.1 CoA-transferase family III (CaiB/BaiF)
CoA-transferase family III (CaiB/BaiF) consist of two different alpha/beta domains; N-terminal domain has a SurE-like topology with a left-handed beta-alpha-beta unit
1vgq d1vgqb_ B:262-269,278-285,288-297,298-305,316-332
1t3z d1t3zb_ B:262-269,278-285,288-297,298-305,316-332
1vgr d1vgrb_ B:262-269,278-285,288-297,298-305,316-331
1p5r d1p5rb_ B:262-269,278-285,288-297,298-305,316-331
2vjl d2vjlb1 B:262-269,278-285,288-297,298-305,316-331
7. 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
1uiu d1uiua_ A:247-254,391-398,402-414,425-441,443-462
1zlq d1zlqa1 A:247-254,391-398,416-425,425-441,443-462
1zlq d1zlqb1 B:247-254,391-398,416-425,425-441,443-462
3e3k d3e3ka1 A:246-254,391-399,416-425,425-441,443-462
3dp8 d3dp8b1 B:246-254,391-398,416-425,425-441,443-462
3dp8 d3dp8a1 A:246-254,391-399,416-425,425-441,443-462
1uiv d1uivb_ B:1246-1254,1391-1399,1416-1425,1425-1441,1443-1462
1uiv d1uiva_ A:246-254,391-399,416-425,425-441,443-462
3dp8 d3dp8c1 C:246-254,391-399,416-425,425-441,443-462
3e3k d3e3kb1 B:246-254,391-397,416-426,425-441,443-462
1uiu d1uiub_ B:1247-1254,1391-1397,1416-1426,1425-1441,1443-1462
1uiu d1uiua_ A:247-254,391-398,416-426,425-441,443-462
3e3k d3e3kc1 C:246-254,391-399,416-426,425-441,443-462
8. b.52.1 Barwin-like endoglucanases
Double psi beta-barrel barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
2pic d2pica1 A:117-122,145-151,152-163,190-199,219-231
2pjj d2pjja1 A:117-123,145-151,152-163,190-199,219-231
2ae0 d2ae0x1 X:117-123,145-151,152-163,190-199,219-231
9. 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
1t5o d1t5oc_ C:11-16,25-29,31-42,46-66,110-145
1t5o d1t5ob_ B:11-16,25-29,31-42,46-66,110-145
1t9k d1t9kb_ B:13-19,28-33,34-45,49-68,113-145
1t9k d1t9ka_ A:13-19,28-33,34-45,49-68,113-145
1t5o d1t5oa_ A:11-16,25-29,31-42,46-66,110-145
1t5o d1t5od_ D:11-16,25-29,31-42,46-66,110-145
10. c.97.1 Cytidine deaminase-like contains extra C-terminal strand 5, order 21345 !
Cytidine deaminase-like core: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands, order 2134; strand 1 is antiparallel to the rest
1m9n d1m9na2 A:432-439,440-448,451-471,521-533,545-556
1g8m d1g8ma2 A:432-439,440-448,451-471,521-533,545-556
1pl0 d1pl0a2 A:431-438,439-447,450-470,520-532,544-555
1pkx d1pkxc2 C:431-438,439-447,450-470,520-532,544-555
1pkx d1pkxd2 D:431-438,439-447,450-470,520-532,544-555
1pkx d1pkxb2 B:431-438,439-447,450-470,520-532,544-555
1p4r d1p4rb2 B:431-438,439-447,450-470,520-532,544-555
1thz d1thzb2 B:432-439,440-448,451-471,521-532,545-556
1pl0 d1pl0b2 B:431-438,439-447,450-470,520-532,544-555
1pl0 d1pl0d2 D:431-438,439-447,450-470,520-532,544-555
11. a.170.1 BRCA2 helical domain
BRCA2 helical domain multihelical; contains a 3-helical bundle surrounded by several shorter helices
1miu d1miua1 A:2499-2503,2505-2509,2517-2529,2537-2560,2569-2588
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 668 (enumeration index: query26) of S5
3izr E:84-92,135-140,142-154,182-193,196-203
2iu3 A:432-439,440-448,451-471,521-533,545-556
3f7w A:124-128,129-133,139-160,163-177,249-270
3lvu D:313-321,489-497,501-510,527-540,542-561
3lvu A:313-321,489-497,501-510,527-540,542-561
3lvu C:312-321,489-498,501-510,527-540,542-561
3lvu B:313-321,489-497,502-510,527-540,542-561
2xzm M:13-18,20-25,27-36,39-51,62-76
2kpq A:17-22,24-29,31-43,47-64,67-83
2w3r E:47-54,71-77,104-121,124-133,272-279
3czb A:152-156,205-210,210-221,265-276,275-288
3mw0 B:247-254,391-398,416-425,425-441,443-462
3mw0 A:247-254,391-398,416-425,425-441,443-462
3mvy A:247-254,391-398,416-425,425-441,443-462
3mvy B:247-254,391-398,416-425,425-441,443-462
3mvw A:247-254,391-398,416-425,425-441,443-462
3mvw B:247-254,391-398,416-425,425-441,443-462
3czq C:16-22,23-29,36-46,198-213,220-230
3czq D:16-22,23-29,36-46,198-213,220-230
3czq B:16-22,23-29,36-46,198-213,220-230
3czq A:16-22,23-29,36-46,198-213,220-230
3mis A:39-52,78-86,86-98,101-118,124-144
2ec6 A:112-117,118-123,473-506,513-524,697-710
3mvx B:247-254,391-398,416-425,425-441,443-462
3mvx A:247-254,391-398,416-425,425-441,443-462
3mz9 A:247-254,391-398,416-425,425-441,443-462
3mz9 B:247-254,391-398,416-425,425-441,443-462
2w55 C:47-54,71-77,103-121,124-133,272-279
3eq5 D:143-150,151-160,167-176,179-191,222-236
3eq5 A:144-150,151-160,167-176,179-191,222-236
3eq5 B:144-150,151-160,167-176,179-191,222-236
3eq5 E:144-150,151-160,167-176,179-191,222-236
3eq5 G:143-150,151-160,167-176,179-191,222-235
3eq5 C:144-150,151-160,167-176,179-191,222-236
2b1g C:432-439,440-448,451-471,521-533,545-556
2b1g A:432-439,440-448,451-471,521-533,545-556
2b1g D:432-439,440-448,451-471,521-533,545-556
2xzn M:13-18,20-25,27-36,39-51,62-76
3mzb A:247-254,391-398,416-425,425-441,443-462
3mzb B:247-254,391-398,416-425,425-441,443-462
3qim B:247-254,391-398,416-425,425-441,443-462
3qim A:246-254,391-399,416-425,425-441,443-462
3mvz A:247-254,391-398,416-425,425-441,443-462
3mvz B:247-254,391-398,416-425,425-441,443-462
2iu0 A:432-439,440-448,451-471,521-533,545-556
2noo A:246-254,391-399,416-425,425-441,443-462