1. e.3.1 beta-lactamase/transpeptidase-like
beta-lactamase/transpeptidase-like contains a cluster of helices and an alpha+beta sandwich
1iyq d1iyqa_ A:28-41,217-225,257-267,275-288
1iyp d1iypa_ A:28-41,217-225,257-267,275-288
1iyo d1iyoa_ A:28-41,217-225,257-267,275-288
1htz d1htzb_ B:26-41,217-226,258-267,271-290
1htz d1htzf_ F:26-41,217-226,258-267,271-290
1bza d1bzaa_ A:28-41,217-225,257-267,275-287
1htz d1htza_ A:26-41,217-226,258-267,271-290
1htz d1htzc_ C:26-41,217-226,258-267,271-290
1htz d1htze_ E:26-41,217-226,258-267,271-290
1s0w d1s0wb_ B:26-41,217-225,256-265,269-288
1s0w d1s0wa_ A:26-41,217-225,256-265,269-288
4blm d4blma_ A:31-41,217-226,257-268,275-291
1i2w d1i2wb_ B:30-41,217-225,257-268,275-290
1mbl d1mbla_ A:31-41,217-225,257-267,275-291
2b5r d2b5ra1 A:26-41,217-225,256-265,269-288
1jtg d1jtgc_ C:26-41,217-225,256-265,269-288
2b5r d2b5rb1 B:26-41,217-225,256-265,269-288
1jtg d1jtga_ A:26-41,217-225,256-265,269-288
1i2s d1i2sa_ A:31-41,217-225,257-268,275-290
1htz d1htzd_ D:26-41,217-225,258-267,271-290
1i2s d1i2sb_ B:31-41,217-225,257-268,275-290
1o7e d1o7eb_ B:32-41,217-226,258-267,271-291
1jtd d1jtda_ A:27-41,217-225,256-265,269-288
3c7v d3c7vc1 C:28-41,217-225,256-265,269-288
3c7v d3c7va1 A:26-41,217-225,256-265,269-288
2g2w d2g2wa1 A:28-41,217-225,258-267,271-290
1i2w d1i2wa_ A:31-41,217-225,257-268,275-290
3c7u d3c7ua1 A:27-41,217-225,256-265,269-288
1o7e d1o7ea_ A:32-41,217-225,257-267,271-291
1n4o d1n4oa_ A:32-41,217-225,257-267,271-291
3c7u d3c7uc1 C:27-41,217-225,256-265,269-288
2blm d2blmb_ B:32-41,217-226,257-267,275-295
1pio d1piob_ B:32-41,217-226,258-267,275-290
2blm d2blma_ A:32-41,217-226,257-268,275-295
1n4o d1n4ob_ B:32-41,217-225,258-267,271-291
1ome d1omeb_ B:32-41,217-226,258-267,275-290
2. i.7.1 Reovirus components
Reovirus components
1ej6 d1ej6b_ B:528-547,588-601,603-609,814-826
3. d.130.1 S-adenosylmethionine synthetase
S-adenosylmethionine synthetase duplication: consists of 3 similar intertwined domains ! structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
1o90 d1o90b1 B:30-51,79-92,105-115,370-379
1o9t d1o9tb1 B:30-51,79-92,105-115,370-379
1o93 d1o93b1 B:30-51,79-92,105-115,370-379
1o9t d1o9ta1 A:30-51,79-92,105-115,370-379
1o92 d1o92b1 B:30-51,79-92,105-115,370-379
1o90 d1o90a1 A:30-51,79-92,105-115,370-379
1qm4 d1qm4b1 B:30-51,79-92,105-115,370-379
1o92 d1o92a1 A:30-51,79-92,105-115,370-379
1o93 d1o93a1 A:30-51,79-92,105-115,370-379
1qm4 d1qm4a1 A:30-51,79-92,105-115,370-379
1fug d1fuga1 A:14-35,63-76,89-98,350-359
4. 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
2hly d2hlya1 A:8-27,29-50,95-99,158-173
5. d.352.1 FlaG-like
FlaG-like alpha(2)-beta(3)-alpha; 2 layers: a/b; antiparallel beta-sheet, order: 123; partial similatity to the dsRBD-like fold(sop_cf 54767)
2hc5 d2hc5a1 A:9-23,36-55,78-87,86-106
6. c.56.5 Zn-dependent exopeptidases core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest !
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
2ewb d2ewba1 A:213-224,271-291,294-306,333-350
1bpn d1bpna1 A:213-224,266-275,294-306,333-350
7. d.284.1 PurS-like segment-swapped dimer: the swapped segment is made of the first helix and second strand; a single long strand is formed by strands 2 and 3 of each subunit !
PurS-like consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
1t3t d1t3ta3 A:48-61,85-99,102-116,1101-1114
8. c.1.20 tRNA-guanine transglycosylase
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
1iq8 d1iq8a1 A:196-204,233-244,246-251,339-353
1it8 d1it8a1 A:196-204,233-244,246-251,339-353
1j2b d1j2bb2 B:196-204,233-244,246-251,339-353
1j2b d1j2ba2 A:196-204,233-244,246-251,339-353
9. c.52.1 Restriction endonuclease-like
Restriction endonuclease-like core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
1bam d1bama_ A:19-36,56-73,103-113,199-212
1bam d1bama_ A:19-36,56-73,137-144,199-212
1esg d1esgb_ B:19-36,56-73,137-144,199-212
1esg d1esgb_ B:19-36,56-73,103-113,199-212
10. c.36.1 Thiamin diphosphate-binding fold (THDP-binding) there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules ! two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules !
Thiamin diphosphate-binding fold (THDP-binding) 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
2bp7 d2bp7a1 A:43-54,109-124,270-276,278-296
2bp7 d2bp7e1 E:43-54,109-124,270-276,278-296
2bp7 d2bp7g1 G:43-54,109-124,270-276,278-296
11. e.28.1 Reovirus inner layer core protein p3
Reovirus inner layer core protein p3 large protein without apparent domain division; has a number of all-alpha regions and one all beta domain near the C-end
1uf2 d1uf2b_ B:296-311,349-367,369-375,594-614
12. c.1.15 Xylose isomerase-like different families share similar but non-identical metal-binding sites !
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
1a0e d1a0ed_ D:47-54,73-93,95-100,347-376
1a0e d1a0ea_ A:47-54,73-93,95-100,347-376
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 218 (enumeration index: query84) of S4
3sh8 B:31-41,217-226,257-268,275-291
2j8y C:17-32,202-210,238-249,253-274
2j8y A:17-32,202-210,238-249,253-274
2j8y B:17-32,202-210,238-249,253-274
3g31 A:27-41,217-225,257-267,275-290
3g31 B:27-41,217-225,257-267,275-290
3kr5 H:338-348,395-417,420-433,460-477
3kr5 E:338-348,395-417,420-433,460-477
3kr5 J:338-348,395-417,420-433,460-477
3kr5 C:338-348,395-417,420-433,460-477
3kr5 D:338-348,395-417,420-433,460-477
3kr5 I:338-348,395-417,420-433,460-477
3kr5 B:338-348,395-417,420-433,460-477
3kr5 K:338-348,395-417,420-433,460-477
3kr5 L:338-348,395-417,420-433,460-477
2p74 A:27-41,217-225,257-268,275-290
2hc9 A:217-227,271-293,296-308,335-353
3k1q B:465-484,524-538,540-545,749-762
3sh7 B:32-41,217-226,257-268,275-291
3sh9 B:31-41,217-226,257-268,275-291
3sh9 A:31-41,217-225,257-268,275-291
3gmw A:28-41,217-225,256-265,269-288
3gmw C:28-41,217-225,256-265,269-288
3hvf B:28-41,217-225,257-267,275-290
3t8w I:338-348,395-417,420-433,460-477
3t8w J:338-348,395-417,420-433,460-477
3t8w F:338-348,395-417,419-433,460-477
3t8w L:338-348,395-417,420-433,460-477
3t8w B:338-348,395-417,420-433,460-477
3t8w G:338-348,395-417,420-433,460-477
3t8w C:338-348,395-417,420-433,460-477
3t8w H:338-348,395-417,420-433,460-477
3t8w E:338-348,395-417,420-433,460-477
3t8w K:338-348,395-417,420-433,460-477
3t8w D:338-348,395-417,420-433,460-477
3t8w A:338-348,395-417,420-433,460-477
2jbf C:17-32,202-210,238-251,253-274
2jbf B:17-32,202-210,238-251,253-274
2jbf A:17-32,202-210,238-249,253-274
2jbf D:17-32,202-210,238-249,253-275
1yms B:27-41,217-225,257-267,275-290
3so4 B:16-37,65-78,91-101,355-365
3so4 D:16-37,65-78,91-101,355-365
3so4 C:16-37,65-78,91-101,355-365
3s82 A:17-38,69-82,95-105,370-379
3g2z B:27-41,217-225,257-267,275-290
3g2z A:27-41,217-225,257-268,275-290
3m2j B:30-41,217-225,257-268,275-291
3jyi E:26-41,217-225,256-265,269-288
3jyi B:26-41,217-225,256-265,269-288
3jyi A:26-41,217-225,256-265,269-288
3jyi C:26-41,217-225,256-265,269-288
3jyi F:26-41,217-225,256-265,269-288
3jyi D:26-41,217-225,256-265,269-288
3qty A:67-78,79-99,100-112,220-227
3qty B:67-78,79-99,100-112,220-227
1xxm B:26-41,217-225,256-265,269-288
1xxm A:26-41,217-225,256-265,269-288
2j9o C:17-32,202-210,238-249,253-274
2j9o A:17-32,202-210,238-249,253-274
2j9o D:17-32,202-210,238-251,253-276
2j9o B:17-32,202-210,238-251,253-275
3ij3 A:192-202,245-267,270-282,309-326
3e2k B:30-41,217-226,257-268,275-291
3e2l B:31-41,217-226,257-267,275-291
2j7v C:17-32,202-210,238-249,253-275
2j7v A:17-32,202-210,238-249,253-274
2j7v B:17-32,202-210,238-251,253-275
1we4 A:28-41,217-225,257-267,275-288
3m2k B:30-41,217-225,257-268,275-291
3m2k A:31-41,217-226,257-268,275-291
3p98 A:26-41,217-225,257-266,270-289
3p98 B:26-41,217-225,257-267,270-289
3hlw B:27-41,217-225,257-267,275-290
3hlw A:27-41,217-225,257-267,275-290
3kqz C:338-348,395-417,420-433,460-477
3kqz I:338-348,395-417,420-433,460-477
3kqz F:338-348,395-417,420-433,460-477
3zxi B:37-46,88-105,266-272,310-322
3zxi A:37-46,88-105,266-272,310-322
3kqx I:338-348,395-417,420-433,460-477
3kqx K:338-348,395-417,420-433,460-477
3kqx C:338-348,395-417,420-433,460-477
3hre A:27-41,217-225,257-267,275-290
3g35 A:28-41,217-225,257-267,275-290
3g35 B:27-41,217-225,257-268,275-290
3p09 B:20-33,209-217,249-258,267-286
2afr A:32-47,58-72,192-197,202-221
3g2y B:27-41,217-225,257-267,275-290
3g2y A:27-41,217-225,255-267,275-290
3bfd C:25-41,217-225,257-268,275-288
3s1s A:580-598,774-786,800-806,850-871
2wk0 B:31-41,217-225,257-267,275-290
3g32 A:27-41,217-225,257-267,275-290
3g32 B:28-41,217-225,257-267,275-290
3m84 B:67-78,79-99,100-112,220-227
3ggg B:18-31,39-53,56-62,179-194
3n4i A:28-41,217-225,258-267,271-290
2wuq A:3-19,236-245,273-285,291-316
2wuq B:3-19,236-245,273-285,291-313
3g34 A:27-41,217-225,257-267,275-290
3g34 B:27-41,217-225,257-267,275-290
1w7f B:31-41,217-225,257-268,275-290
1w7f A:31-41,217-225,257-268,275-290
3kr4 B:338-348,395-417,420-433,460-477
3kr4 C:338-348,395-417,420-433,460-477
3kr4 E:338-348,395-417,420-433,460-477
3kr4 A:338-348,395-417,420-433,460-477
3kr4 G:338-348,395-417,420-433,460-477
3kr4 H:338-348,395-417,420-433,460-477
3kr4 L:338-348,395-417,420-433,460-477
3kr4 J:338-348,395-417,420-433,460-477
3kr4 D:338-348,395-417,420-433,460-477
3kr4 K:338-348,395-417,420-433,460-477
2pid A:37-46,88-105,266-272,310-322
3kiz B:58-73,74-97,99-111,255-262
3kiz A:58-73,74-97,99-111,255-262
2hb6 B:217-227,271-293,296-308,335-353
2hb6 A:217-227,271-293,296-308,335-353