1. 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 d2bp7g1 G:43-54,218-232,234-243,259-268,298-307
2bp7 d2bp7a1 A:43-54,218-232,234-243,259-268,298-307
2bp7 d2bp7e1 E:43-54,218-232,234-243,259-268,298-307
1qs0 d1qs0a_ A:47-54,218-232,234-243,259-268,298-307
2bp7 d2bp7c1 C:47-54,218-232,234-243,259-268,298-307
2. 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
1h7a d1h7aa_ A:249-265,485-501,505-510,516-531,532-538
1h78 d1h78a_ A:250-265,485-501,505-510,516-531,532-538
1h79 d1h79a_ A:250-265,485-501,505-510,516-531,532-538
1hk8 d1hk8a_ A:250-265,485-501,505-510,516-531,532-538
1h7b d1h7ba_ A:250-265,485-501,505-510,516-531,532-538
1l1l d1l1lb_ B:362-374,627-643,650-654,657-669,676-680
1l1l d1l1ld_ D:362-374,627-643,650-654,657-669,676-680
1l1l d1l1lc_ C:362-374,627-643,650-654,657-669,676-680
1h16 d1h16a_ A:380-395,643-655,664-670,677-694,703-710
1l1l d1l1la_ A:362-374,627-643,650-654,660-669,676-680
1h18 d1h18a_ A:380-395,643-655,664-670,677-694,703-710
1cm5 d1cm5a_ A:380-395,643-655,664-670,677-694,703-710
1r9e d1r9ea_ A:385-399,679-691,700-706,712-730,732-738
1cm5 d1cm5b_ B:380-395,643-655,664-670,677-694,703-710
1h17 d1h17a_ A:380-395,643-655,664-670,677-694,703-710
3pfl d3pfla_ A:380-395,643-655,664-670,677-694,703-710
2pfl d2pfla_ A:380-395,643-655,664-670,677-694,703-710
1h18 d1h18b_ B:380-395,643-655,664-670,677-694,703-710
2pfl d2pflb_ B:380-395,643-655,664-670,677-694,703-710
3pfl d3pflb_ B:380-395,643-655,664-670,677-694,703-710
1r9d d1r9da_ A:385-399,679-691,700-706,712-730,732-738
1mzo d1mzoa_ A:380-395,643-655,664-670,677-694,703-710
1mzo d1mzob_ B:380-395,643-655,664-670,677-694,703-710
1r9e d1r9eb_ B:385-399,679-691,700-706,712-730,732-738
2bq1 d2bq1f2 F:346-362,642-657,663-668,672-687,689-697
1pem d1pema2 A:346-362,642-658,663-668,672-687,689-697
1peo d1peoa2 A:346-362,642-657,663-668,672-687,692-697
1peu d1peua2 A:346-362,642-657,663-668,672-687,692-697
2bq1 d2bq1e2 E:346-362,642-657,663-668,672-687,692-697
1peq d1peqa2 A:346-362,642-658,663-668,672-687,692-697
1rlr d1rlra2 A:394-410,674-689,695-700,710-725,730-735
6r1r d6r1rb2 B:394-410,674-689,695-700,710-725,730-735
3r1r d3r1ra2 A:394-410,674-689,695-700,710-725,730-735
3r1r d3r1rb2 B:394-410,674-689,695-700,710-725,730-735
3r1r d3r1rc2 C:394-410,674-689,695-700,710-725,730-735
6r1r d6r1ra2 A:394-410,674-689,695-700,710-725,730-735
6r1r d6r1rc2 C:394-410,674-689,695-700,710-725,730-735
7r1r d7r1rb2 B:394-410,674-689,695-700,710-725,730-735
5r1r d5r1rb2 B:394-410,674-689,695-700,710-725,730-735
7r1r d7r1ra2 A:394-410,674-689,695-700,710-725,730-735
5r1r d5r1ra2 A:394-410,674-689,695-700,710-725,730-735
5r1r d5r1rc2 C:394-410,674-689,695-700,710-725,730-735
4r1r d4r1rb2 B:394-410,674-689,695-700,710-725,730-735
4r1r d4r1ra2 A:394-410,674-689,695-700,710-725,730-735
4r1r d4r1rc2 C:394-410,674-689,695-700,710-725,730-735
2r1r d2r1rc2 C:394-410,674-689,695-700,710-725,730-735
2r1r d2r1rb2 B:394-410,674-689,695-700,710-725,730-735
2r1r d2r1ra2 A:394-410,674-689,695-700,710-725,730-735
7r1r d7r1rc2 C:394-410,674-689,695-700,710-725,730-735
1r1r d1r1rb2 B:394-410,674-689,695-700,710-725,730-735
1r1r d1r1rc2 C:394-410,674-689,695-700,710-725,730-735
1r1r d1r1ra2 A:394-410,674-689,695-700,710-725,730-735
2ha9 d2ha9b1 B:157-176,346-358,362-368,371-390,392-401
2ha9 d2ha9a1 A:157-176,346-358,362-368,371-390,392-401
3. c.67.1 PLP-dependent transferases
PLP-dependent transferase-like main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
2gb3 d2gb3c1 C:5-12,98-112,113-121,124-135,135-142
2gb3 d2gb3f1 F:5-12,98-112,113-121,124-135,135-142
2gb3 d2gb3e1 E:5-12,98-112,113-121,124-135,135-142
2gb3 d2gb3b1 B:5-12,98-112,113-121,124-135,135-142
2gb3 d2gb3d1 D:5-12,98-112,113-121,124-135,135-142
2gb3 d2gb3a1 A:5-12,98-112,113-121,124-135,135-142
1o4s d1o4sa_ A:3-10,97-110,112-120,123-134,134-141
1o4s d1o4sb_ B:3-10,97-110,112-120,123-134,134-141
1j32 d1j32b_ B:4-11,98-111,113-121,124-135,135-142
1j32 d1j32a_ A:4-11,98-111,113-121,124-135,135-142
1xi9 d1xi9d_ D:5-12,101-114,116-124,127-138,138-145
1xi9 d1xi9b_ B:5-12,101-114,116-124,127-138,138-145
1gde d1gdea_ A:2-11,95-108,110-118,121-132,132-139
1gd9 d1gd9b_ B:502-511,595-608,610-618,621-632,632-639
1gde d1gdeb_ B:502-511,595-608,610-618,621-632,632-639
1gd9 d1gd9a_ A:2-11,95-108,110-118,121-132,132-139
1dju d1djub_ B:2-11,95-108,110-118,121-132,132-139
1dju d1djua_ A:2-11,95-108,110-118,121-132,132-139
4. c.83.1 Aconitase iron-sulfur domain
Aconitase iron-sulfur domain consists of three similar domains with 3 layers (a/b/a) each; duplication ! core: parallel beta-sheet of 5 strands, order 32145
1b0m d1b0ma2 A:165-175,216-229,235-242,249-264,266-270
5acn d5acna2 A:165-175,216-229,235-242,249-264,265-270
6acn d6acna2 A:165-175,216-229,235-242,249-264,265-270
1b0j d1b0ja2 A:165-175,216-229,235-242,249-264,265-270
8acn d8acna2 A:165-175,216-229,235-242,249-264,265-270
7acn d7acna2 A:165-175,216-229,235-242,249-264,265-270
1aco d1acoa2 A:165-175,216-229,235-242,249-264,265-270
1nit d1nita2 A:165-175,216-229,235-242,249-264,265-270
1fgh d1fgha2 A:165-175,216-229,235-242,249-264,265-270
1nis d1nisa2 A:165-175,216-229,235-242,249-264,265-270
1amj d1amja2 A:165-175,216-229,235-242,249-263,265-270
1ami d1amia2 A:165-175,216-229,235-242,249-263,265-270
1b0k d1b0ka2 A:165-175,216-229,235-242,249-263,265-270
1c96 d1c96a2 A:165-175,216-229,235-242,249-263,265-270
1c97 d1c97a2 A:165-175,216-229,235-242,249-263,265-270
5. d.79.3 L30e-like
Bacillus chorismate mutase-like core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
1dt9 d1dt9a2 A:6-28,304-315,317-324,373-382,388-393
6. 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
1vma d1vmab2 B:2-19,222-238,240-246,252-264,266-272
1vma d1vmaa2 A:2-19,222-238,240-246,252-264,266-272
1w36 d1w36b2 B:450-465,740-747,750-755,783-809,811-818
1w36 d1w36e2 E:450-465,740-747,750-755,783-809,811-818
7. 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
2okc d2okcb1 B:90-98,182-195,209-215,216-231,238-242
2okc d2okca1 A:90-98,182-195,209-215,216-231,238-242
8. f.33.1 Calcium ATPase, transmembrane domain M
Calcium ATPase, transmembrane domain M core: multihelical; consists of three transmembrane regions of 2, 2 and 6 helices, separated by cytoplasmic domains
3b9b d3b9ba4 A:84-120,704-715,715-721,724-731,732-736
2zbe d2zbea4 A:83-118,704-715,715-721,724-731,732-736
2zbe d2zbeb4 B:80-118,704-715,715-721,724-731,732-736
9. d.117.1 Thymidylate synthase/dCMP hydroxymethylase
Thymidylate synthase/dCMP hydroxymethylase contains large mixed beta-sheet
1hvy d1hvya_ A:28-44,159-172,206-216,218-242,243-254
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1126 (enumeration index: query1273) of S5
3g6k C:2-20,26-51,56-61,64-84,102-108
3g6k A:2-20,26-51,56-61,64-86,102-108
3g6k D:2-20,26-51,56-61,64-88,102-108
3g6k F:2-20,26-51,56-61,64-86,102-108
3g6k E:2-21,26-51,56-61,64-84,102-108
3g6k B:2-20,26-51,56-61,64-88,102-108
2y8n C:451-465,790-802,809-816,822-840,842-849
2y8n A:451-465,790-802,809-816,822-840,842-849
2cvx A:384-400,691-707,712-717,720-735,737-746
2zlg A:384-400,691-706,712-717,720-735,737-746
3cny B:2-10,199-208,212-217,252-264,267-272
3cny A:2-10,199-208,212-217,252-264,267-272
3n23 C:118-157,711-722,722-728,732-739,740-744
3n23 A:118-154,711-722,722-728,732-739,740-744
3p96 A:147-166,344-355,355-361,363-370,371-375
2cvv A:384-400,691-707,712-717,720-735,737-746
2o0r B:3-12,93-106,108-116,119-130,130-137
2o0r A:3-12,93-106,108-116,119-130,130-137
1xjm B:278-294,576-590,598-603,606-621,626-631
2cvw A:384-400,691-707,712-717,720-735,737-746
2eud A:384-400,691-706,712-717,720-735,737-746
2cvs A:384-400,691-707,712-717,720-735,737-746
2yaj C:451-465,790-802,809-816,822-840,842-849
2yaj A:451-465,790-802,810-816,822-840,842-849
2jax A:130-140,244-256,257-263,275-285,287-294
2f3o B:378-392,669-681,690-696,703-719,721-728
2f3o A:378-392,669-681,690-696,703-719,721-728
3cis B:130-140,244-256,257-263,275-285,287-294
3cis D:130-140,244-256,257-263,275-285,287-294
3cis H:130-140,244-256,257-263,275-285,287-294
3cis E:130-140,244-253,257-263,275-285,287-293
3cis F:130-140,244-256,257-263,275-285,287-294
3cis C:130-140,244-253,257-263,275-285,287-293
3cis G:130-140,244-253,257-263,275-285,287-293
3cis A:130-140,244-253,257-263,275-285,287-294
2xo4 B:394-410,674-689,695-700,710-725,727-735
2xo4 C:394-410,674-689,695-700,710-725,727-735
2xo4 A:394-410,674-689,695-700,710-725,727-735
3fwk A:2-20,26-51,56-61,64-84,102-108
3hne A:385-401,687-702,708-712,716-731,733-741
3hne B:385-401,687-703,708-713,716-731,733-742
2y7h B:83-91,179-194,211-217,218-233,243-247
2y7h C:83-91,179-194,211-217,218-233,243-247
2y7c B:83-91,179-194,211-217,218-233,243-247
2y7c C:83-91,179-194,211-217,218-233,243-247
1xjg B:278-294,576-591,598-603,606-621,626-631
1xjg A:278-294,576-590,598-603,606-621,626-631
2qf7 A:526-538,696-711,713-719,725-741,743-748
2zp7 D:11-18,99-112,113-122,125-136,135-143
2zp7 C:11-18,99-112,113-122,125-136,135-143
2zp7 F:11-18,99-112,113-122,125-136,135-143
2zp7 B:11-18,99-112,113-122,125-136,135-143
2zp7 E:11-18,99-112,113-122,125-136,135-143
2zp7 A:11-18,99-112,113-122,125-136,135-143
3k70 B:450-465,740-747,750-755,783-809,811-818
3k70 E:450-465,740-747,750-755,783-809,811-818
3hnc B:385-401,687-703,708-713,716-731,733-742
3hnc A:385-401,687-703,708-713,716-731,733-742
2xak A:394-410,674-689,695-700,710-725,727-735
2xak B:394-410,674-689,695-700,710-725,727-735
2xak C:394-410,674-689,695-700,710-725,727-735
2zlf A:384-400,691-707,712-717,720-735,737-746
2cvu A:384-400,691-707,712-717,720-735,737-746
3hnf A:385-401,687-703,708-713,716-731,733-742
3hnf B:385-401,687-703,708-713,716-731,733-742
2zyj B:11-18,99-112,113-122,125-136,135-143
2zyj A:11-18,99-112,113-122,125-136,135-143
2egy A:11-18,99-112,114-122,125-136,136-143
2egy D:11-18,99-112,113-122,125-136,135-143
2egy C:11-18,99-112,113-122,125-136,135-143
2egy B:11-18,99-112,113-122,125-136,135-143
3igs B:2-15,167-178,180-184,189-200,202-207
3bg3 D:549-561,719-734,736-742,748-764,767-772
3bg3 C:549-561,719-734,736-742,748-764,767-772
3o0q B:278-294,576-590,598-603,606-621,626-631
3o0q A:278-294,576-590,598-603,606-621,626-631
2wsi A:2-20,24-50,55-60,63-88,101-107
3paw B:384-400,691-703,712-717,720-735,739-746
3paw C:384-400,691-707,712-717,720-735,737-746
3ihi A:22-38,153-166,200-210,212-236,237-248
2cvy A:384-400,691-706,712-717,720-735,737-746
3k8t A:384-400,691-707,712-717,720-735,737-746
1xje B:278-294,576-590,598-603,606-621,626-631
1xje A:278-294,576-590,598-603,606-621,626-631
3mt0 A:106-116,221-234,236-242,254-264,266-272
2xaw B:394-410,674-689,695-700,710-725,727-735
2xaw C:394-410,674-689,695-700,710-725,727-735
2xaw A:394-410,674-689,695-700,710-725,727-735
3e1y B:7-28,304-316,317-324,373-382,388-393
3e1y A:7-28,304-316,316-324,373-382,388-393
3e1y C:8-26,304-315,316-324,373-382,387-393
3e1y D:8-26,304-315,316-324,373-382,387-393
3snp B:205-215,256-272,276-282,289-304,306-310
3snp A:205-215,256-272,276-282,289-304,306-310
1xjf B:278-294,576-590,598-603,606-621,626-631
1xjf A:278-294,576-590,598-603,606-621,626-631
3r0x A:11-20,278-294,296-305,308-317,356-362
2xax B:394-410,674-689,695-700,710-725,727-735
2xax C:394-410,674-689,695-700,710-725,727-735
3o0n B:278-294,576-590,598-603,606-621,626-631
3o0n A:278-294,576-590,598-603,606-621,626-631
2z1y B:11-18,99-112,113-122,125-136,135-143
2z1y A:11-18,99-112,113-122,125-136,135-143
3g5a A:2-20,26-51,56-61,64-86,102-108
3g5a B:2-20,26-51,56-61,64-88,102-108
3g5a D:2-20,26-51,56-61,64-88,102-108
3g5a F:2-20,26-51,56-61,64-86,102-108
3g5a E:2-20,26-51,56-61,64-83,102-108
3g5a C:2-20,26-51,56-61,64-83,102-108
3loq B:119-129,214-227,229-235,248-257,259-265
3loq A:120-129,214-227,229-235,248-257,259-265
3gg5 D:28-44,159-172,206-216,218-242,243-254
3gpl B:498-510,644-651,654-661,669-680,682-689
3gpl A:498-510,644-651,654-661,669-680,682-689
2x47 A:147-155,236-258,260-265,275-295,299-306
3n2f C:118-154,711-722,722-728,732-739,740-744
3n2f A:118-154,711-722,722-728,732-739,740-744
3ab8 B:130-140,223-233,235-242,251-260,262-268
3ab8 A:130-140,223-233,235-242,251-260,262-268
2x0x A:394-410,674-689,695-700,710-725,730-735
2x0x B:394-410,674-689,695-700,710-725,730-735
2x0x C:394-410,674-689,695-700,710-725,730-735
1xjn A:278-294,576-590,598-603,606-621,626-631
1xjn C:278-294,576-590,598-603,606-621,626-631
1xjn B:278-294,576-590,598-603,606-621,626-631
1xjn D:278-294,576-590,598-603,606-621,626-631
2wgh A:385-401,687-703,708-713,716-731,733-742
2wgh B:385-401,687-703,708-713,716-731,733-742
2xay A:394-410,674-689,695-700,710-725,727-735
1zyz B:384-400,691-707,712-717,720-735,737-746
1zyz A:384-400,691-707,712-718,720-735,737-747
3sn2 A:207-215,256-272,274-282,289-304,306-310
3cbf B:11-18,99-112,113-122,125-136,135-143
3cbf A:11-18,99-112,113-122,125-136,135-143
3ffh B:4-11,89-102,106-112,115-126,127-133
1xjk B:278-294,576-591,598-603,606-621,626-631
1xjk A:278-294,576-590,598-603,606-621,626-631
3ob7 B:28-44,159-172,206-216,218-242,243-254
3ob7 D:28-44,159-172,206-216,218-242,243-254
2zc0 B:8-15,106-119,122-129,132-143,143-150
2zc0 C:8-15,106-119,122-129,132-143,143-150
2zc0 A:8-15,106-119,122-129,132-143,143-150
2zc0 D:8-15,106-119,122-129,132-143,143-150
3ab7 B:130-140,223-233,235-242,251-260,262-268
3ab7 A:130-140,223-233,234-242,251-260,261-268
3o0o B:278-294,576-590,598-603,606-621,626-631
3o0o A:278-294,576-590,598-603,606-621,626-631
3ihh E:22-38,153-166,200-210,212-236,237-248
3ihh B:22-38,153-166,200-210,212-236,237-248
3r0z A:11-20,279-294,296-305,308-317,356-362
1xjj A:278-294,576-590,598-603,606-621,626-631
1xjj B:278-294,576-590,598-603,606-621,626-631
3hnd A:385-401,687-703,708-713,716-731,733-742
3hnd B:385-401,687-703,708-713,716-731,733-742
3olq A:128-138,250-263,263-271,275-293,295-301
3e20 B:4-25,301-312,314-321,372-381,386-392
3e20 K:5-19,301-313,314-321,372-381,386-392
3e20 H:5-19,301-312,314-321,372-381,386-392
3e20 C:4-25,301-312,314-321,372-381,386-392
1zzd A:384-400,691-707,712-717,720-735,737-746
2xaz A:394-410,674-689,695-700,710-725,727-735
2xaz C:394-410,674-689,695-700,710-725,727-735
2xaz B:394-410,674-689,695-700,710-725,727-735