1. 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
1muk d1muka_ A:265-285,326-339,340-355,358-372,783-788
1mwh d1mwha_ A:265-285,326-339,340-355,358-372,783-788
1n38 d1n38a_ A:265-285,326-339,340-355,358-372,783-788
1n35 d1n35a_ A:265-285,326-339,340-355,358-372,783-788
1n1h d1n1ha_ A:265-285,326-339,340-355,358-372,783-788
2. i.7.1 Reovirus components
Reovirus components
1uon d1uona_ A:265-285,326-339,340-355,358-372,783-788
3. c.73.1 Carbamate kinase-like the sheet topology is similar to those of undecaprenyl diphosphate synthase and the N-terminal domain of phosphoglycerate kinase !
Carbamate kinase-like 3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
2j0w d2j0wa1 A:41-54,56-78,80-106,107-134,184-189
2j0x d2j0xa1 A:41-54,56-79,80-106,107-134,184-189
2j0x d2j0xb1 B:41-54,56-79,80-106,107-134,184-189
4. a.104.1 Cytochrome P450
Cytochrome P450 multihelical
1w0e d1w0ea_ A:145-167,171-190,291-325,324-340,462-467
1w0f d1w0fa_ A:145-167,171-190,291-325,324-340,462-467
1tqn d1tqna_ A:145-167,171-190,291-325,324-340,462-467
1w0g d1w0ga_ A:145-167,171-190,291-325,324-340,462-467
1r9o d1r9oa_ A:140-160,165-184,283-317,316-332,455-460
1dt6 d1dt6a_ A:140-160,165-184,280-314,313-329,452-457
1n6b d1n6ba_ A:140-160,165-184,280-314,313-329,452-457
1nr6 d1nr6a_ A:140-160,165-184,280-314,313-329,452-457
1fag d1fagd_ D:115-134,140-159,250-284,283-299,420-425
1fag d1fagb_ B:115-134,140-159,250-284,283-299,420-425
2vku d2vkua1 A:106-129,135-154,254-276,275-293,414-420
1suo d1suoa_ A:141-161,166-185,284-318,317-333,456-461
2q6n d2q6ne1 E:141-161,166-185,284-318,317-333,456-461
3dl9 d3dl9b1 B:151-173,178-197,296-330,329-345,468-473
3czh d3czhb1 B:151-173,178-197,296-330,329-345,468-473
2q6n d2q6na1 A:139-161,166-185,284-318,317-333,456-461
2v0m d2v0mc1 C:145-167,171-190,291-325,324-340,463-467
3c6g d3c6ga1 A:151-173,178-197,296-330,329-345,468-473
2q6n d2q6nf1 F:141-161,166-185,284-318,317-333,456-461
3czh d3czha1 A:151-173,178-197,296-330,329-345,468-473
2q6n d2q6nc1 C:138-161,166-185,284-318,317-333,456-461
2hpd d2hpda_ A:115-133,140-159,250-284,283-299,420-425
1fah d1faha_ A:115-133,140-159,250-284,283-299,420-425
1og2 d1og2a_ A:140-160,165-184,283-317,316-332,456-460
2q6n d2q6ng1 G:141-161,166-185,284-318,317-333,456-461
2vn0 d2vn0a1 A:140-160,165-184,283-317,316-332,455-461
2nnh d2nnha1 A:140-160,165-184,283-317,316-332,456-460
2q6n d2q6nd1 D:141-161,166-185,284-318,317-333,456-461
1pq2 d1pq2b_ B:140-160,165-184,283-317,316-332,456-460
2nni d2nnia1 A:140-160,165-184,283-317,316-332,456-460
2nnj d2nnja1 A:140-160,165-184,283-317,316-332,456-460
1smj d1smjd_ D:115-133,140-159,250-284,283-299,420-425
2nnh d2nnhb1 B:140-160,165-184,283-317,316-332,456-460
1og5 d1og5a_ A:140-160,165-184,283-317,316-332,456-460
1po5 d1po5a_ A:138-161,166-185,281-318,317-333,456-461
1fag d1faga_ A:115-133,140-159,250-284,283-299,420-425
1smj d1smjc_ C:115-133,140-159,250-284,283-299,420-425
1fag d1fagc_ C:115-133,140-159,250-284,283-299,420-425
3c6g d3c6gb1 B:151-173,178-197,296-330,329-345,469-473
2q6n d2q6nb1 B:138-161,166-185,284-318,317-333,457-461
3dl9 d3dl9a1 A:151-173,178-197,296-330,329-345,469-473
1og2 d1og2b_ B:140-160,165-184,283-317,316-332,456-461
1og5 d1og5b_ B:140-160,165-184,283-317,316-332,456-461
1pq2 d1pq2a_ A:140-160,165-184,283-317,316-332,456-461
5. c.7.1 PFL-like glycyl radical enzymes duplication: the N- and C-terminal halves have similar topologies !
PFL-like glycyl radical enzymes contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
3pfl d3pflb_ B:180-188,188-210,212-241,250-269,273-278
3pfl d3pfla_ A:180-188,188-210,212-241,250-269,273-278
1h16 d1h16a_ A:180-188,188-210,212-241,250-270,273-278
1h17 d1h17a_ A:180-188,188-210,212-241,250-270,273-278
1cm5 d1cm5b_ B:180-188,188-210,212-241,250-270,273-278
1cm5 d1cm5a_ A:180-188,188-210,212-241,250-270,273-278
1mzo d1mzoa_ A:180-188,188-210,212-241,250-270,273-278
1mzo d1mzob_ B:180-188,188-210,212-241,250-270,273-278
1h18 d1h18a_ A:180-188,188-210,212-241,250-270,273-278
1h18 d1h18b_ B:180-188,188-210,212-241,250-270,273-278
2pfl d2pflb_ B:180-188,188-210,212-241,250-270,273-278
2pfl d2pfla_ A:180-188,188-210,212-241,250-270,273-278
1r9e d1r9eb_ B:168-176,176-192,195-233,259-279,281-286
1r8w d1r8wb_ B:168-176,176-192,195-233,259-279,281-286
1r8w d1r8wa_ A:168-176,176-192,195-233,259-279,281-286
1r9d d1r9da_ A:168-176,176-192,195-233,259-279,281-286
1r9e d1r9ea_ A:168-176,176-192,195-233,259-279,281-287
1r9d d1r9db_ B:168-176,176-192,195-234,259-279,281-286
6. a.98.1 R1 subunit of ribonucleotide reductase, N-terminal domain
R1 subunit of ribonucleotide reductase, N-terminal domain multihelical consists of two all-alpha subdomains ! subdomain 1 (residues 10-100) is a 4-helical bundle
1rlr d1rlra1 A:54-70,74-95,136-143,144-156,649-656
7. 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
2im9 d2im9a1 A:75-88,117-132,133-147,159-172,266-274
8. 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
3dhw d3dhwc1 C:73-85,98-112,113-129,142-158,160-166
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1192 (enumeration index: query64.1109) of S5
3qu8 C:141-161,166-185,284-318,317-333,456-461
3qu8 A:141-161,166-185,284-318,317-333,456-461
3qu8 D:141-161,166-185,284-318,317-333,457-461
3qu8 B:141-161,166-185,284-318,317-333,457-461
3qu8 E:141-161,166-185,284-318,317-333,457-461
2y8n A:227-235,235-251,257-296,322-342,344-350
2y8n C:227-235,235-251,257-296,322-342,344-350
3kc6 A:540-557,574-585,585-607,611-619,669-675
3ebs A:142-164,169-188,287-321,320-336,460-465
3ebs D:142-164,169-188,287-321,320-336,460-465
3ebs C:142-164,169-188,287-321,320-336,460-465
3ebs B:142-164,169-188,287-321,320-336,460-464
3na1 A:121-151,158-177,288-307,306-325,443-448
3na1 B:121-151,158-177,288-307,306-325,443-448
3me6 D:141-161,166-185,284-318,317-333,456-461
3me6 C:141-161,166-185,284-318,317-333,456-461
3me6 A:141-161,166-185,284-318,317-333,456-461
3me6 B:141-161,166-185,284-318,317-333,456-461
3qf7 B:130-139,152-166,712-739,768-788,792-798
3el3 A:131-147,153-172,260-294,293-309,430-436
3el3 B:131-147,153-172,260-294,293-309,430-436
2wv2 A:139-159,166-184,277-309,312-326,442-447
3mq3 A:77-97,98-108,130-150,160-183,199-210
3khm A:139-159,166-185,277-310,312-327,442-448
3n9z A:121-151,158-177,288-307,306-325,444-448
3n9z B:121-151,158-177,288-307,306-325,444-448
3tuz G:73-85,98-111,113-129,142-158,160-166
2yaj A:227-235,235-251,257-296,322-342,344-350
2yaj C:227-235,235-251,257-296,322-342,344-350
2r7v A:236-255,281-299,300-314,315-333,679-684
3ibd A:141-161,166-185,287-318,317-333,456-461
1z11 A:142-164,169-188,287-321,320-336,460-465
1z11 B:142-164,169-188,287-321,320-336,460-464
1z11 D:142-164,169-188,287-321,320-336,460-465
1z11 C:142-164,169-188,287-321,320-336,460-465
3e6i B:137-162,167-186,285-319,318-334,457-462
3e6i A:140-162,167-186,285-319,318-334,457-462
3e4e B:142-162,167-186,285-319,318-334,457-463
3e4e A:142-162,167-186,285-319,318-334,457-463
2fdv D:142-164,169-188,287-321,320-336,460-465
2fdv B:142-164,169-188,287-321,320-336,459-464
2fdv C:142-164,169-188,287-321,320-336,460-465
2fdv A:142-164,169-188,287-321,320-336,460-465
2uwh C:115-133,140-159,250-284,283-299,420-425
2uwh E:108-133,140-159,250-284,283-299,420-425
3mzs B:122-152,160-178,288-307,306-325,444-448
3mzs C:129-152,159-178,288-307,306-325,444-448
3n3c A:77-97,98-108,130-150,160-183,199-210
3r1b D:141-161,166-185,279-318,317-333,457-461
3r1b B:141-161,166-185,278-318,317-333,456-461
3r1b C:141-161,166-185,286-318,317-333,456-461
3hhg F:4-18,19-28,30-46,60-90,154-163
3qi8 A:115-133,140-159,250-284,283-299,420-425
3qi8 B:115-133,140-159,250-284,283-299,420-425
2r7q A:236-255,281-299,300-314,315-333,679-684
3nxu A:145-167,171-190,291-325,324-340,463-467
2q9g A:153-172,179-198,288-322,321-337,457-463
3koh B:139-162,167-186,285-319,318-334,457-462
3koh A:142-162,167-186,285-319,318-334,457-463
2r7o A:236-256,281-299,300-314,315-333,679-684
2pg5 B:142-164,169-188,287-321,320-336,460-465
2pg5 A:142-164,169-188,287-321,320-336,460-465
2pg5 D:142-164,169-188,287-321,320-336,460-465
2pg5 C:142-164,169-188,287-321,320-336,460-465
3qkt C:128-137,149-164,180-761,793-813,817-823
3qkt D:128-137,149-162,727-761,793-813,817-823
3qkt B:128-137,149-162,726-761,793-813,817-823
3qkt A:128-137,149-164,180-761,793-817,817-823
3g5n B:141-161,166-185,284-318,317-333,456-461
3g5n A:141-161,166-185,283-318,317-333,456-461
3g5n D:141-161,166-185,284-318,317-333,456-461
3g5n C:141-161,166-185,285-318,317-333,456-461
2pg7 B:142-164,169-188,287-321,320-336,460-465
2pg7 D:142-164,169-188,287-321,320-336,460-465
2pg7 C:142-164,169-188,287-321,320-336,460-465
2pg7 A:142-164,169-188,287-321,320-336,460-465
3fvy A:27-53,251-269,271-288,289-304,307-314
3k1o A:135-159,166-185,277-309,312-326,442-448
3l4d B:138-158,165-184,276-309,311-326,442-448
3l4d A:140-158,165-184,276-308,311-326,442-448
3mdm A:153-173,179-198,288-322,321-337,457-463
3qku B:128-137,149-161,743-761,793-813,817-823
3qku A:128-137,149-162,189-761,793-817,817-823
2r7x A:236-255,281-299,300-314,315-333,679-684
2r7x B:236-255,281-299,300-314,315-333,679-684
3g1q C:139-159,166-185,277-309,312-326,442-448
2p85 D:142-164,169-188,287-321,320-336,460-464
2p85 A:142-164,169-188,287-321,320-336,459-464
2p85 C:142-164,169-188,287-321,320-336,460-464
2p85 B:142-164,169-188,287-321,320-336,460-464
2p85 F:142-164,169-188,287-321,320-336,460-464
2p85 E:142-164,169-188,287-321,320-336,460-464
2fdy D:142-164,169-188,287-321,320-336,460-465
2fdy C:142-164,169-188,287-321,320-336,460-465
2fdy B:142-164,169-188,287-321,320-336,459-465
2fdy A:142-164,169-188,287-321,320-336,460-465
3csk A:26-53,260-278,280-297,298-313,316-326
3mdr A:146-172,179-198,288-322,321-337,457-463
2hi4 A:159-184,187-206,303-337,336-352,479-483
3tk3 C:141-161,166-185,284-318,317-333,456-461
3tk3 A:141-161,166-185,284-318,317-333,456-461
3tk3 B:141-161,166-185,284-318,317-333,456-461
3tk3 D:141-161,166-185,284-318,317-333,456-461
3pm0 A:161-186,192-211,316-350,349-365,490-496
2r7w A:236-255,281-299,300-314,315-333,679-684
2pnq A:77-97,98-110,130-151,160-183,199-210
2pnq B:77-97,98-110,130-151,160-183,199-210
3mvr A:141-161,166-185,284-318,317-333,456-461
3mvr B:141-161,166-185,284-318,317-333,456-461
3r2v A:541-557,574-585,585-607,611-619,669-675
2r7s A:236-255,281-299,300-314,315-333,679-684
2q9f A:146-172,179-198,288-322,321-337,457-463
3lc4 A:142-162,167-186,285-319,318-334,457-462
3lc4 B:142-162,167-186,285-319,318-334,457-462
3gph B:137-162,167-186,285-319,318-334,457-463
3gph A:140-162,167-186,285-319,318-334,457-463
2r7t A:236-255,281-299,300-314,315-333,679-684
2r7u A:236-255,281-299,300-314,315-333,679-684
3na0 B:160-190,197-216,327-346,345-364,483-487
3kw4 A:141-161,166-185,284-318,317-333,456-461
3gw9 A:139-159,166-185,277-309,312-326,442-448
1z10 A:142-164,169-188,287-321,320-336,460-465
1z10 B:142-164,169-188,287-321,320-336,460-465
1z10 D:142-164,169-188,287-321,320-336,460-465
1z10 C:142-164,169-188,287-321,320-336,460-465
3g93 D:141-161,166-185,285-318,317-333,457-461
3g93 C:141-161,166-185,283-318,317-333,457-461
3g93 B:141-161,166-185,285-318,317-333,456-461
3g93 A:137-161,166-185,284-318,317-333,456-461
2fdu C:142-164,169-188,287-321,320-336,460-465
2fdu A:142-164,169-188,287-321,320-336,460-465
2fdu D:142-164,169-188,287-321,320-336,460-465
2fdu B:142-164,169-188,287-321,320-336,460-465
2pg6 C:142-164,169-188,287-321,320-336,460-465
2pg6 D:142-164,169-188,287-321,320-336,460-465
2pg6 B:142-164,169-188,287-321,320-336,460-465
2pg6 A:142-164,169-188,287-321,320-336,460-465
3qoa A:141-161,166-185,284-318,317-333,456-461
3n9y B:121-151,158-177,288-307,306-325,444-448
2p1g B:27-34,59-74,83-95,108-120,191-200
2p1g A:26-34,59-74,81-95,108-120,191-200
3khw B:541-557,574-585,585-607,611-619,669-675
2r7r A:236-255,281-299,300-314,315-333,679-684
2fdw B:142-164,169-188,287-321,320-336,459-465
2fdw A:142-164,169-188,287-321,320-336,460-465
2fdw D:142-164,169-188,287-321,320-336,460-465
2fdw C:142-164,169-188,287-321,320-336,460-465
3r1a D:138-161,166-185,284-318,317-333,456-461
3r1a A:138-161,166-185,284-318,317-333,456-461
3r1a B:138-161,166-185,284-318,317-333,456-461
3r1a G:138-161,166-185,284-318,317-333,456-461
3r1a C:138-161,166-185,284-318,317-333,456-461
3r1a E:138-161,166-185,284-318,317-333,456-461
3r1a H:138-161,166-185,284-318,317-333,457-461
3r1a F:138-161,166-185,284-318,317-333,456-461
2f9q C:147-168,173-192,291-325,324-340,464-468
2f9q B:147-168,173-192,291-325,324-340,464-468
2f9q A:147-168,173-192,291-325,324-340,464-468
2f9q D:147-168,173-192,291-325,324-340,464-468
3org B:165-176,177-186,208-228,236-257,272-276
3org D:165-176,177-186,208-228,236-257,272-276
3org C:165-176,177-186,208-228,236-257,272-276
3org A:165-176,177-186,208-228,236-257,272-276