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
1nhu d1nhua_ A:406-416,418-437,442-448,449-455,455-468
1nb7 d1nb7a_ A:406-416,418-437,442-448,449-455,455-468
1nhv d1nhva_ A:406-416,418-437,442-448,449-455,455-468
1csj d1csja_ A:406-416,418-437,442-448,449-455,455-468
1nhu d1nhub_ B:406-416,418-437,442-448,449-455,455-468
2o5d d2o5da1 A:406-416,418-437,442-448,449-455,455-468
1csj d1csjb_ B:406-416,418-437,442-448,449-455,455-468
2d41 d2d41b1 B:406-416,418-437,442-448,449-455,455-468
2d3u d2d3ua1 A:406-416,418-437,442-448,449-455,455-468
2d41 d2d41a1 A:406-416,418-437,442-448,449-455,455-468
2i1r d2i1ra1 A:406-416,418-437,442-448,449-455,455-468
2ijn d2ijna1 A:406-416,418-437,442-448,449-455,455-468
2ijn d2ijnb1 B:406-416,418-437,442-448,449-455,455-468
2i1r d2i1rb1 B:406-416,418-437,442-448,449-455,455-468
1nhv d1nhvb_ B:406-416,418-437,442-448,449-455,455-468
1nb6 d1nb6a_ A:406-416,418-437,442-448,449-455,455-468
2gc8 d2gc8a1 A:406-416,418-437,442-448,449-455,455-468
2hwi d2hwia1 A:406-416,418-437,442-448,449-455,455-468
2gc8 d2gc8b1 B:406-416,418-437,442-448,449-455,455-468
2d3u d2d3ub1 B:406-416,418-437,442-448,449-455,455-468
1c2p d1c2pa_ A:406-416,418-437,442-448,449-455,455-468
1c2p d1c2pb_ B:406-416,418-437,442-448,449-455,455-468
2hwh d2hwha1 A:406-416,418-437,442-448,449-455,455-468
2o5d d2o5db1 B:406-416,418-437,442-448,449-455,455-468
2d3z d2d3za1 A:406-416,418-437,442-448,449-455,455-468
1nb7 d1nb7b_ B:406-416,418-437,442-448,449-455,455-468
2brk d2brka1 A:406-416,418-437,442-448,449-455,455-468
2hwh d2hwhb1 B:406-416,418-437,442-448,449-455,455-468
2hwi d2hwib1 B:406-416,418-437,442-448,449-455,455-468
1os5 d1os5a_ A:406-416,418-437,442-448,449-455,455-468
1nb6 d1nb6b_ B:406-416,418-437,442-448,449-455,455-468
1nb4 d1nb4b_ B:406-416,418-437,442-448,449-455,455-468
1gx6 d1gx6a_ A:406-416,418-437,442-448,449-455,455-468
1nb4 d1nb4a_ A:406-416,418-437,442-448,449-455,455-468
1gx5 d1gx5a_ A:406-416,418-437,442-448,449-455,455-468
2. 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 d2e0wb1 B:294-311,319-341,466-472,473-483,483-502
2e0w d2e0wa1 A:294-311,319-341,466-472,473-482,483-502
2nlz d2nlzc1 C:271-287,293-315,423-429,430-440,440-459
2nlz d2nlza1 A:271-287,293-315,423-429,430-440,440-459
2nlz d2nlzd1 D:271-287,293-315,423-429,430-440,440-459
2nlz d2nlzb1 B:271-287,293-315,423-429,430-440,440-459
2i3o d2i3od1 D:255-271,281-299,396-402,403-413,416-432
2i3o d2i3ob1 B:255-271,281-299,396-402,403-413,416-432
2i3o d2i3oa1 A:255-271,281-299,396-402,403-413,416-432
2i3o d2i3oc1 C:255-271,281-299,396-402,403-413,416-432
3. d.17.4 NTF2-like has a beta-alpha(2)-beta insertion after the main helix !
Cystatin-like Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
2rgq d2rgqa1 A:4-25,26-35,38-43,44-49,49-66
2rgq d2rgqb1 B:4-25,26-35,38-43,44-49,49-66
4. d.58.46 eEF1-gamma domain elaborated with additional structures !
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1pbu d1pbua_ A:289-297,301-314,355-366,367-379,406-419
5. a.93.1 Heme-dependent peroxidases
Heme-dependent peroxidases multihelical; consists of two all-alpha domains
1w4w d1w4wa1 A:29-48,159-173,171-177,217-222,230-240
6atj d6atja_ A:29-48,159-173,171-177,217-222,230-240
1gwt d1gwta_ A:29-48,159-173,171-177,217-222,230-240
1h58 d1h58a_ A:29-48,159-173,171-177,217-222,230-240
1h5c d1h5ca_ A:29-48,159-173,171-177,217-222,230-240
1h55 d1h55a_ A:29-48,159-173,171-177,217-222,230-240
1h5f d1h5fa_ A:29-48,159-173,171-177,217-222,230-240
1h5l d1h5la_ A:29-48,159-173,171-177,217-222,230-240
1h57 d1h57a_ A:29-48,159-173,171-177,217-222,230-240
1h5m d1h5ma_ A:29-48,159-173,171-177,217-222,230-240
1h5h d1h5ha_ A:29-48,159-173,171-177,217-222,230-240
1h5i d1h5ia_ A:29-48,159-173,171-177,217-222,230-240
1h5g d1h5ga_ A:29-48,159-173,171-177,217-222,230-240
1h5d d1h5da_ A:29-48,159-173,171-177,217-222,230-240
1h5k d1h5ka_ A:29-48,159-173,171-177,217-222,230-240
1h5e d1h5ea_ A:29-48,159-173,171-177,217-222,230-240
1h5a d1h5aa_ A:29-48,159-173,171-177,217-222,230-240
1h5j d1h5ja_ A:29-48,159-173,171-177,217-222,230-240
1hch d1hcha_ A:29-48,159-173,171-177,217-222,230-240
1gwo d1gwoa_ A:29-48,159-173,171-177,217-222,230-240
3atj d3atja_ A:29-48,159-173,171-177,217-222,230-240
3atj d3atjb_ B:29-48,159-173,171-177,217-222,230-240
1sch d1scha_ A:29-47,158-172,170-176,209-214,222-232
6. e.51.1 Urocanase
Urocanase 3 domains; d1: alpha+beta [alpha(2)-beta(3); mixed sheet: 213]; d2: alpha/beta of the NAD(P)-binding Rossmann-fold superfamily (scop_sf 51735, most similar to scop_fa 51883 and scop_fa 51736); d3: alpha+beta of the glutamine synthetase/guanido kinase fold (scop_cf 55930); d1 and d3 form a single beta-sheet
1w1u d1w1ua_ A:369-385,414-432,436-443,499-509,511-537
1w1u d1w1ub_ B:369-385,414-432,436-443,499-509,511-537
1uwk d1uwka_ A:369-385,414-432,436-443,499-509,511-537
1uwk d1uwkb_ B:369-385,414-432,436-443,499-509,511-537
1uwl d1uwlb_ B:369-385,414-432,436-443,499-509,511-537
1uwl d1uwla_ A:369-385,414-432,436-443,499-509,511-537
1x87 d1x87b_ B:364-380,409-427,431-438,492-504,506-532
1x87 d1x87a_ A:364-380,409-427,431-439,491-504,506-532
7. 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:204-212,213-224,314-321,323-330,333-350
2j9a d2j9aa1 A:204-212,213-224,314-321,323-330,333-350
1bll d1blle2 E:204-212,213-224,314-321,323-330,333-350
1lan d1lana2 A:204-212,213-224,314-321,323-330,333-350
1lap d1lapa1 A:204-212,213-224,314-321,323-330,333-350
8. d.96.2 ApbE-like duplication: contains two differently decorated beta(2)-alpha(2)-beta(2) subdomains, similar to other T-fold domains; probably does not form the tunnel-shaped oligomers !
T-fold beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234 ! tunnel-shaped: its known members form wide oligomeric barrels different sizes
1vrm d1vrma1 A:67-87,188-210,212-219,220-226,298-313
9. 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
1zm2 d1zm2c2 C:160-168,170-193,208-215,216-221,271-291
1zm2 d1zm2e2 E:159-168,170-193,208-215,216-221,271-291
1zm3 d1zm3e2 E:159-168,170-193,208-215,216-221,271-291
1zm9 d1zm9e2 E:159-168,170-193,208-215,216-221,271-291
1zm4 d1zm4e2 E:159-168,170-193,208-215,216-221,271-291
1zm3 d1zm3a2 A:159-168,170-193,208-215,216-221,271-291
1zm3 d1zm3c2 C:159-168,170-193,208-215,216-221,271-291
1zm9 d1zm9a2 A:159-168,170-193,208-215,216-221,271-291
1zm9 d1zm9c2 C:160-168,170-193,208-215,216-221,271-291
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1117 (enumeration index: query1313) of S5
2v7g B:369-385,414-432,436-443,499-509,511-537
2v7g C:369-385,414-432,436-442,499-509,511-537
2v7g A:369-385,414-432,436-443,499-509,511-537
2v7g D:369-385,414-432,436-442,499-509,511-537
2ax1 B:406-416,418-437,442-448,449-455,455-468
3gsz B:406-416,418-437,442-448,449-455,455-468
3gsz A:406-416,418-437,442-448,449-455,455-468
2wrm A:406-416,418-437,442-448,449-455,455-468
3cso B:406-416,418-437,442-448,449-455,455-468
3cso A:406-416,418-437,442-448,449-455,455-468
3cj3 B:406-416,418-437,442-448,449-455,455-468
3cj3 A:406-416,418-437,442-448,449-455,455-468
2xi2 C:406-416,418-437,442-448,449-455,455-468
2xi2 B:406-416,418-437,442-448,449-455,455-468
3br9 A:406-416,418-437,442-448,449-455,455-468
3br9 B:406-416,418-437,442-448,449-455,455-468
2xhw A:406-416,418-437,442-448,449-455,455-468
3a76 C:1-27,28-36,40-45,48-52,52-63
3a76 B:1-27,28-36,40-45,47-52,52-64
3cj2 B:406-416,418-437,442-448,449-455,455-468
3cj2 A:406-416,418-437,442-448,449-455,455-468
2xwh A:406-416,418-437,442-448,449-455,455-468
3qgd B:406-416,418-437,442-448,449-455,458-468
3qgd A:406-416,418-437,442-448,449-455,455-468
2xwy A:406-416,418-437,442-448,449-455,455-468
3cj4 B:406-416,418-437,442-448,449-455,458-468
3b82 E:159-168,170-193,208-215,216-221,271-291
3b82 C:159-168,170-193,208-215,216-221,271-291
2jc0 B:406-416,418-437,442-448,449-455,455-468
2jc0 A:406-416,418-437,442-448,449-455,455-468
3bsa B:406-416,418-437,442-448,449-455,455-468
3bsa A:406-416,418-437,442-448,449-455,455-468
3se8 G:64-74,98-117,212-219,246-253,474-486
2gir A:406-416,418-437,442-448,449-455,455-468
2gir B:406-416,418-437,442-448,449-455,455-468
2zku A:406-416,418-437,442-448,449-455,455-468
2zku D:406-416,418-437,442-448,449-455,455-468
2zku B:406-416,418-437,442-448,449-455,455-468
2zku C:406-416,418-437,442-448,449-455,455-468
3gnv B:406-416,418-437,442-448,449-455,455-468
3gnv A:406-416,418-437,442-448,449-455,455-468
3qgf B:406-416,418-437,442-448,449-455,458-468
3qgf A:406-416,418-437,442-448,449-455,458-468
3hky B:406-416,418-437,442-448,449-455,455-468
3gol B:406-416,418-437,442-448,449-455,455-468
2o18 D:35-58,163-184,187-193,194-200,275-290
2o18 C:35-58,163-184,187-193,194-200,275-290
2o18 B:35-58,163-184,187-193,194-200,275-290
2o18 A:35-58,163-184,187-193,194-200,275-290
3q0z A:406-416,418-437,442-448,449-455,455-468
3q0z B:406-416,418-437,442-448,449-455,455-468
2ax0 B:406-416,418-437,442-448,449-455,455-468
3d5m B:406-416,418-437,442-448,449-455,455-468
3d5m A:406-416,418-437,442-448,449-455,455-468
3mwv A:406-416,418-437,442-448,449-455,455-468
2fkn C:365-381,410-428,432-439,495-505,507-533
2fkn A:365-381,410-428,432-439,495-505,507-533
2fkn D:365-381,410-428,432-439,495-505,507-533
2fkn B:365-381,410-428,432-439,495-505,507-533
3pnd D:53-76,181-202,205-211,212-218,293-308
3pnd C:53-76,182-202,205-211,212-218,293-308
3pnd B:53-76,182-202,205-211,212-218,293-308
3pnd A:53-76,182-202,205-211,212-218,293-308
2qe2 B:406-416,418-437,442-448,449-455,455-468
3hhk B:406-416,418-437,442-448,449-455,455-468
3hhk A:406-416,418-437,442-448,449-455,455-468
3cde B:406-416,418-437,442-448,449-455,455-468
3cde A:406-416,418-437,442-448,449-455,455-468
2brl A:406-416,418-437,442-448,449-455,455-468
3hhg F:4-18,60-90,154-163,265-273,279-294
3lkh A:406-416,418-437,442-448,449-455,455-468
3lkh B:406-416,418-437,442-448,449-455,455-468
3g86 B:406-416,418-437,442-448,449-455,455-468
3g86 A:406-416,418-437,442-448,449-455,455-468
1z4u A:406-416,418-437,442-448,449-455,455-468
3b8h E:159-168,170-193,208-215,216-221,271-291
3fqk B:406-416,418-437,442-448,449-455,455-468
3fqk A:406-416,418-437,442-448,449-455,455-468
2dxs A:406-416,418-437,442-448,449-455,455-468
2dxs B:406-416,418-437,442-448,449-455,455-468
3gyn B:406-416,418-437,442-448,449-455,455-468
3gyn A:406-416,418-437,442-448,449-455,455-468
3h5u B:406-416,418-437,442-448,449-455,455-468
3h5u A:406-416,418-437,442-448,449-455,455-468
3qgg B:406-416,418-437,442-448,449-455,458-468
3qgg A:406-416,418-437,442-448,449-455,458-468
1yv2 A:406-416,418-437,442-448,449-455,455-468
3jru A:218-226,227-237,327-333,335-341,345-362
3jru B:218-226,227-237,327-333,335-341,345-362
1yvx A:406-416,418-437,442-448,449-455,455-468
3cj5 A:406-416,418-437,442-448,449-455,458-468
3cj5 B:406-416,418-437,442-448,449-455,455-468
2xhu A:406-416,418-437,442-448,449-455,455-468
2xhu B:406-416,418-437,442-448,449-455,455-468
3b78 E:159-168,170-193,208-215,216-221,271-291
3b78 C:159-168,170-193,208-215,216-221,271-291
3b78 A:159-168,170-193,208-215,216-221,271-291
2xhv B:406-416,418-437,442-448,449-455,455-468
2xhv A:406-416,418-437,442-448,449-455,455-468
2wcx A:406-416,418-437,442-448,449-455,455-468
1yuy A:406-416,418-437,442-448,449-455,455-468
2fvc B:406-416,418-437,442-448,449-455,455-468
2fvc A:406-416,418-437,442-448,449-455,455-468
1yvz A:406-416,418-437,442-448,449-455,455-468
3phe A:406-416,418-437,442-448,449-455,455-468
3phe D:406-416,418-437,442-448,449-455,455-468
3phe B:406-416,418-437,442-448,449-455,455-468
3phe C:406-416,418-437,442-448,449-455,455-468
3mf5 A:406-416,418-437,442-448,449-455,458-468
3mww A:406-416,418-437,442-448,449-455,455-468
2qe5 C:406-416,418-437,442-448,449-455,455-468
2qe5 D:406-416,418-437,442-448,449-455,455-468
2qe5 A:406-416,418-437,442-448,449-455,455-468
3d28 B:406-416,418-437,442-448,449-455,455-468
3d28 A:406-416,418-437,442-448,449-455,455-468
3c3o A:33-56,61-83,92-97,109-114,115-138
3igv A:406-416,418-437,442-448,449-455,455-468
3igv B:406-416,418-437,442-448,449-455,455-468
1yvf A:406-416,418-437,442-448,449-455,455-468
3co9 A:406-416,418-437,442-448,449-455,455-468
3co9 B:406-416,418-437,442-448,449-455,455-468
2xxd A:406-416,418-437,442-448,449-455,455-468
2giq A:406-416,418-437,442-448,449-455,455-468
2giq B:406-416,418-437,442-448,449-455,455-468
2xym A:406-416,418-437,442-448,449-455,455-468
3c3q A:33-56,61-83,92-97,109-114,115-138
3qgh A:406-416,418-437,442-448,449-455,458-468
2awz B:406-416,418-437,442-448,449-455,455-468
3cj0 A:406-416,418-437,442-448,449-455,455-468
3bsc B:406-416,418-437,442-448,449-455,455-468
3h8f A:222-230,231-242,331-338,340-347,350-367
3hvo B:406-416,418-437,442-448,449-455,455-468
3hvo A:406-416,418-437,442-448,449-455,455-468
3ciz A:406-416,418-437,442-448,449-455,458-468
2jc1 B:406-416,418-437,442-448,449-455,455-468
2jc1 A:406-416,418-437,442-448,449-455,455-468
3h98 B:406-416,418-437,442-448,449-455,455-468
3h98 A:406-416,418-437,442-448,449-455,455-468
3qge B:406-416,418-437,442-448,449-455,458-468
3c3r A:33-56,61-83,92-97,109-114,115-138
3e51 B:406-416,418-437,442-448,449-455,455-468
3e51 A:406-416,418-437,442-448,449-455,455-468
3gnw B:406-416,418-437,442-448,449-455,455-468
3gnw A:406-416,418-437,442-448,449-455,455-468
2who B:406-416,418-437,442-448,449-455,455-468
2who A:406-416,418-437,442-448,449-455,455-468
3h5s B:406-416,418-437,442-448,449-455,455-468
3h5s A:406-416,418-437,442-448,449-455,455-468
2zit E:159-168,170-193,208-215,216-221,271-291
2zit C:159-168,170-193,208-215,216-221,271-291