1. d.153.1 N-terminal nucleophile aminohydrolases (Ntn hydrolases) N-terminal residue provides two catalytic groups, nucleophile and proton donor !
Ntn hydrolase-like 4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
2e0w d2e0wa1 A:43-47,48-55,55-69,562-569
2e0w d2e0wb1 B:43-47,48-55,55-69,562-569
2. d.142.2 DNA ligase/mRNA capping enzyme, catalytic domain has a circularly permuted topology !
ATP-grasp Consists of two subdomains with different alpha+beta folds ! shares functional and structural similarities with the PIPK and protein kinase superfamilies
1dgs d1dgsb3 B:2109-2117,2216-2225,2236-2248,2282-2290
1dgs d1dgsa3 A:109-117,216-225,236-248,282-290
1v9p d1v9pa3 A:111-120,221-230,239-251,284-293
1tae d1taea_ A:114-122,222-233,239-251,284-293
1tae d1taeb_ B:114-122,222-233,239-251,284-293
1tae d1taed_ D:114-122,222-233,239-251,284-293
1tae d1taec_ C:114-122,222-233,239-251,284-293
1b04 d1b04a_ A:108-116,216-224,233-245,278-287
1ta8 d1ta8a_ A:114-122,222-230,239-251,284-293
1b04 d1b04b_ B:108-116,216-224,233-245,278-287
1x9n d1x9na3 A:562-569,654-666,674-686,719-727
1a0i d1a0ia2 A:28-34,143-153,166-178,218-223
1s68 d1s68a_ A:29-35,114-126,134-146,205-211
1xdn d1xdna_ A:80-87,202-215,226-238,284-290
3. i.8.1 RNA polymerase
RNA polymerase
1hqm d1hqmd_ D:1118-1123,1159-1164,1168-1182,1185-1190
1l9u d1l9um_ M:1117-1122,1158-1163,1167-1181,1184-1189
1l9u d1l9ud_ D:1117-1122,1158-1163,1167-1181,1184-1189
4. e.29.1 beta and beta-prime subunits of DNA dependent RNA-polymerase The catalytic site is formed by the association of two double-psi beta-barrel domains, one from each subunit !
beta and beta-prime subunits of DNA dependent RNA-polymerase Multidomain subunits of complex domain organization
1ynj d1ynjd1 D:1117-1122,1157-1163,1167-1181,1184-1189
3dxj d3dxjd1 D:1117-1122,1157-1163,1167-1181,1184-1189
2cw0 d2cw0n1 N:1117-1122,1157-1163,1167-1181,1184-1189
5. b.103.1 MoeA N-terminal region -like
MoeA N-terminal region -like complex fold made of bifurcated and coiled b-sheets
1uz5 d1uz5a2 A:24-30,148-156,160-171,173-179
1g8l d1g8lb2 B:26-32,145-153,157-168,170-176
1t3e d1t3eb2 B:341-347,466-474,478-489,491-497
2nro d2nrob2 B:26-32,145-153,157-168,170-176
1g8l d1g8la2 A:26-32,145-153,157-168,170-176
2nqm d2nqmb2 B:26-32,145-153,157-168,170-176
2nqm d2nqma2 A:26-32,145-153,157-168,170-176
1t3e d1t3ea2 A:341-347,466-474,478-489,491-497
2nrs d2nrsb2 B:26-32,145-153,157-168,170-176
2nrp d2nrpb2 B:26-32,145-153,157-168,170-176
2nqs d2nqsb2 B:26-32,145-153,157-168,170-176
2nqk d2nqkb2 B:26-32,145-153,157-168,170-176
2nqn d2nqnb2 B:26-32,145-153,157-168,170-176
2nqn d2nqna2 A:26-32,145-153,157-168,170-176
2nqv d2nqva2 A:26-32,145-153,157-168,170-176
2nqk d2nqka2 A:26-32,145-153,157-168,170-176
1g8r d1g8rb2 B:26-32,145-153,157-168,170-176
2fu3 d2fu3a2 A:341-347,466-474,478-489,491-497
1g8r d1g8ra2 A:26-32,145-153,157-168,170-176
2nqv d2nqvb2 B:26-32,145-153,157-168,170-176
2fu3 d2fu3b2 B:341-347,466-474,478-489,491-497
2nrs d2nrsa2 A:26-32,145-153,157-168,170-176
2nqq d2nqqb2 B:26-32,145-153,157-168,170-176
2nro d2nroa2 A:26-32,145-153,157-168,170-176
2nqq d2nqqc2 C:26-32,145-153,157-168,170-176
2nqr d2nqrb2 B:26-32,145-153,157-168,170-176
2nqr d2nqra2 A:26-32,145-153,157-168,170-176
2nqu d2nqua2 A:26-32,145-153,157-168,170-176
2fts d2ftsa2 A:341-347,466-474,478-489,491-497
2nqs d2nqsa2 A:26-32,145-153,157-168,170-176
2nqq d2nqqa2 A:26-32,145-153,157-168,170-176
1fc5 d1fc5b2 B:26-32,145-153,157-168,170-176
2nqu d2nqub2 B:26-32,145-153,157-168,170-176
1xi8 d1xi8b2 B:26-32,150-158,162-173,175-181
1fc5 d1fc5a2 A:26-32,145-153,157-168,170-176
6. 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
1eu8 d1eu8a_ A:117-125,252-257,257-266,290-301
1a99 d1a99c_ C:130-138,239-244,244-259,273-284
1a99 d1a99b_ B:130-138,239-244,244-259,273-284
1a99 d1a99a_ A:130-138,239-244,244-259,273-284
1a99 d1a99d_ D:130-138,239-244,244-259,273-284
7. b.121.6 Group I dsDNA viruses
Nucleoplasmin-like/VP (viral coat and capsid proteins) sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands ! characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
1dzl d1dzla_ A:153-161,164-172,233-240,327-336
8. d.125.1 Ornithine decarboxylase C-terminal domain
Ornithine decarboxylase C-terminal domain complex alpha+beta motif
1ord d1ordb3 B:639-645,663-670,674-692,708-718
1ord d1orda3 A:639-645,663-670,674-692,708-718
9. d.16.1 FAD-linked reductases, C-terminal domain N-terminal domain is beta/beta/alpha common fold !
FAD-linked reductases, C-terminal domain alpha+beta sandwich
2h94 d2h94a3 A:654-658,701-709,709-718,759-764
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 95 (enumeration index: query101) of S4
2r5i G:153-161,164-172,233-240,327-336
2r5i F:153-161,164-172,233-240,327-336
2r5i E:153-161,164-172,233-240,327-336
2r5i K:153-161,164-172,233-240,327-336
2r5i B:153-161,164-172,233-240,327-336
2r5i H:153-161,164-172,233-240,327-336
2r5i D:153-161,164-172,233-240,327-336
2r5i A:153-161,164-172,233-240,327-336
2r5i O:153-161,164-172,233-240,327-336
2r5i I:153-161,164-172,233-241,327-336
2r5i C:153-161,164-172,233-240,327-336
2r5i N:153-161,164-172,233-240,327-336
2r5i L:153-161,164-172,233-241,327-336
2r5i M:153-161,164-172,233-241,327-336
2r5i J:153-161,164-172,233-240,327-336
2hvr A:29-36,114-126,134-146,204-211
2hvr B:29-35,114-126,134-146,205-211
2r5j D:153-161,164-172,233-240,325-334
2r5j N:153-161,164-172,233-240,325-334
2r5j F:153-161,164-172,233-240,325-334
2r5j C:153-161,164-172,233-240,325-334
2r5j A:153-161,164-172,233-240,325-334
2r5j M:153-161,164-172,233-240,325-334
2r5j B:153-161,164-172,233-240,325-334
2r5j L:153-161,164-172,233-240,325-334
2r5j H:153-161,164-172,233-240,325-334
2r5j I:153-161,164-172,233-240,325-334
2r5j O:152-161,164-172,233-240,325-334
2r5j E:152-161,164-172,233-240,325-334
2r5j J:153-161,164-172,233-240,325-334
2r5j K:153-161,164-172,233-240,325-334
2r5j G:153-161,164-172,233-240,325-334
3bi4 B:289-293,370-378,377-388,448-453
3hhg B:163-169,217-221,222-233,235-241
3hhg H:163-169,217-221,222-233,235-241
3hhg A:163-169,217-221,222-233,235-241
3hhg F:163-169,217-221,222-233,235-241
3bab A:114-122,222-233,239-251,284-293
3rtx B:288-296,353-368,376-399,437-445
2cfm A:243-250,333-345,353-366,397-404
3cnt A:289-293,368-378,377-388,448-453
3cnd A:289-293,370-378,377-388,448-453
3bi5 B:289-293,370-378,377-388,448-454
2qsx B:86-92,136-140,141-152,154-159
2r5h A:153-161,164-172,233-240,327-336
2r5h F:153-161,164-172,233-240,327-336
2r5h K:152-161,164-172,233-240,327-336
2r5h L:152-161,164-172,233-240,327-336
2r5h N:152-161,164-172,233-240,327-336
2r5h I:152-161,164-172,233-240,327-336
2r5h M:153-161,164-172,233-240,327-336
2r5h C:153-161,164-172,233-240,327-336
2r5h H:152-161,164-172,233-240,327-336
2r5h D:152-161,164-172,233-240,327-336
2r5h B:153-161,164-172,233-240,327-336
2r5h J:153-161,164-172,233-240,327-336
2r5h G:152-161,164-172,233-240,327-336
2r5h E:152-161,164-172,233-240,327-336
3jsl B:106-114,214-222,231-243,276-285
3jsl A:106-114,214-222,231-243,276-285
3s24 G:288-295,355-368,376-399,438-445
3s24 E:288-295,355-368,376-399,437-445
3s24 F:288-295,353-368,376-399,438-445
2hvq A:29-35,114-126,134-146,205-211
3iyj C:150-157,160-168,229-236,324-333
3iyj A:148-157,160-168,229-236,324-333
3iyj B:150-157,160-168,229-236,324-333
3iyj E:150-157,160-168,229-236,324-333
3iyj D:150-157,160-168,229-236,324-333
3bnu A:289-293,370-378,377-388,448-453
3bnu B:289-293,370-378,377-388,448-454
3l2p A:415-421,500-514,522-534,569-575
3jtk A:290-295,448-454,457-466,473-480
3jtk B:290-295,448-454,457-466,473-480
1xpq A:289-293,370-378,377-388,448-453
1xpq C:289-293,370-378,377-388,448-453
3cnp B:289-293,370-378,377-388,448-453
3cnp A:289-293,368-378,377-388,448-453
3oae D:153-161,164-172,233-240,327-336
3oae B:153-161,164-172,233-240,327-336
3oae A:153-161,164-172,233-240,327-336
3oae C:153-161,164-172,233-240,327-336
3oae E:153-161,164-172,233-240,327-336
3eql D:1117-1122,1157-1163,1167-1181,1184-1189
3eql N:1117-1122,1157-1163,1167-1181,1184-1189
3h5z A:211-216,373-379,382-391,398-405
1vs0 B:475-481,554-565,573-589,614-620
1vs0 A:475-481,554-565,573-589,613-620
2gh8 C:260-269,270-274,276-283,315-324
2ql3 H:175-181,226-232,233-244,247-251
2ql3 F:175-181,228-232,233-244,247-251
3jsn A:106-114,214-223,231-243,276-285
3k1u A:9-13,16-23,46-53,294-301
3cns B:289-293,370-378,377-388,448-453
3cns A:289-293,370-378,377-388,448-453
3qwu A:71-78,148-159,166-178,211-219
3qwu B:71-78,148-159,166-178,211-219
2owo A:109-117,220-234,238-250,283-292
2y7k B:171-177,223-228,228-239,241-246
3nc0 B:118-126,180-193,200-216,253-262
3nc0 E:118-126,180-193,200-216,253-262
3iwe B:291-295,448-454,457-466,473-480
2vyc H:676-682,700-707,715-732,746-754
2vyc F:676-682,700-707,715-732,746-754
2vyc A:676-682,700-707,715-732,746-754
2vyc C:676-682,700-707,715-732,746-754
2vyc G:676-682,700-707,715-732,746-754
2vyc J:676-682,700-707,715-732,746-754
2vyc B:676-682,700-707,715-732,746-754
2vyc I:676-682,700-707,715-732,746-754
3gde A:243-250,331-343,350-363,394-401
3cji C:63-72,77-85,151-159,255-271
3nbz B:118-126,180-193,200-215,253-262
3ku9 B:293-297,343-351,350-361,401-406
3baa A:114-122,222-230,239-251,284-293
1z6l A:289-293,370-378,377-388,448-453
1z6l B:289-293,370-378,377-388,448-453
2vug B:89-96,166-178,184-196,227-233
2vug A:89-96,166-178,184-196,227-233
3ba9 A:114-122,222-233,239-251,284-293
2hko A:654-658,701-709,709-718,759-764
2r5k C:150-158,161-169,230-237,324-333
2r5k D:150-158,161-169,230-237,324-333
2r5k E:150-158,161-169,230-237,324-333
2r5k A:150-158,161-169,230-237,324-333
2r5k B:149-158,161-169,230-237,324-333
2hix A:253-260,344-356,364-377,409-415
3iu2 A:290-295,448-454,457-466,473-480
3iu2 B:290-295,448-454,457-466,473-480
3bac A:109-118,221-233,239-251,284-293
3ba8 A:114-122,222-233,239-251,284-293
3bnm B:289-293,370-378,377-388,448-454
3bnm A:289-293,370-378,377-388,448-453
3t1b A:162-167,214-218,219-230,232-237
2hiv A:253-260,344-356,364-377,409-415
3cn8 A:289-293,370-378,377-388,448-453
3iu1 B:290-295,448-454,457-466,473-480
3iu1 A:290-295,448-454,457-466,473-480
3bi2 B:289-293,370-378,377-388,448-454
3bi2 A:289-293,370-378,377-388,448-453
3pn1 A:109-118,221-233,239-251,284-293
2c5u A:92-99,172-185,191-199,227-234
2c5u B:92-99,172-185,191-199,228-234
2hvs A:29-36,114-126,134-146,204-211
2hvs B:29-35,114-126,134-146,205-211
3ofl J:153-161,164-172,233-240,327-336
3ofl K:153-161,164-172,233-240,327-336
3ofl F:153-161,164-172,233-240,327-336
3ofl A:153-161,164-172,233-240,327-336
3ofl L:153-161,164-172,233-240,327-336
3ofl B:153-161,164-172,233-240,327-336
3ofl M:153-161,164-172,233-240,327-336
3ofl D:153-161,164-172,233-240,327-336
3ofl N:153-161,164-172,233-240,327-336
3ofl O:153-161,164-172,233-240,327-336
3ofl I:153-161,164-172,233-240,327-336
3ofl G:153-161,164-172,233-240,327-336
3ofl H:153-161,164-172,233-240,327-336
3ofl E:153-161,164-172,233-240,327-336
3ofl C:153-161,164-172,233-240,327-336
1yy5 B:289-293,370-378,377-388,448-453
1yy5 A:289-293,370-378,377-388,448-453