1. c.77.1 Isocitrate/Isopropylmalate dehydrogenase-like the constituent families form similar dimers !
Isocitrate/Isopropylmalate dehydrogenase-like consists of two intertwined (sub)domains related by pseudo dyad; duplication ! 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
1td9 d1td9c_ C:119-126,285-294,298-304,307-323
1xco d1xcob_ B:119-126,285-294,298-304,307-323
1td9 d1td9b_ B:119-125,285-294,298-303,307-323
1xco d1xcof_ F:119-126,285-294,298-304,307-323
1xco d1xcod_ D:119-126,285-294,298-304,307-323
1td9 d1td9d_ D:119-125,285-294,298-303,307-323
1td9 d1td9a_ A:119-125,285-294,298-302,307-323
1td9 d1td9f_ F:119-124,285-294,298-302,307-323
1td9 d1td9e_ E:119-125,285-294,298-302,307-323
1r5j d1r5jb_ B:121-126,289-298,302-306,311-329
1r5j d1r5ja_ A:121-126,289-298,302-306,311-329
1xco d1xcoc_ C:119-125,285-294,298-304,307-323
1xco d1xcoa_ A:119-125,285-294,298-304,307-323
2af3 d2af3c1 C:118-123,291-300,304-308,313-332
2af4 d2af4d1 D:118-125,291-300,304-310,313-332
1xco d1xcoe_ E:119-126,285-293,298-304,307-323
1qzt d1qztd_ D:118-123,291-300,304-308,313-332
2af4 d2af4c1 C:118-125,291-300,304-310,313-333
1vmi d1vmia_ A:117-123,285-295,299-304,308-323
1qzt d1qzta_ A:118-123,290-300,304-308,313-332
1qzt d1qztc_ C:118-123,290-300,304-308,313-332
2af3 d2af3d1 D:118-124,290-300,304-308,313-332
2. 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
1b7b d1b7bb_ B:43-50,167-171,183-190,208-221
1b7b d1b7bd_ D:43-50,167-171,183-190,208-221
1b7b d1b7bc_ C:43-50,167-171,183-190,208-221
1b7b d1b7ba_ A:43-50,166-171,183-190,208-221
1e19 d1e19a_ A:45-52,170-175,187-194,214-227
1e19 d1e19b_ B:45-52,170-175,187-194,214-227
3. 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
1ktv d1ktvb2 B:131-138,175-181,255-264,268-280
1ktv d1ktva2 A:131-138,175-181,255-264,268-280
1efg d1efga2 A:131-138,172-181,255-264,268-280
2efg d2efga2 A:131-138,172-181,255-264,268-280
1elo d1eloa2 A:131-138,172-181,255-264,268-280
1dar d1dara2 A:130-138,172-181,255-264,268-280
1znw d1znwa1 A:21-28,96-103,114-120,121-133
1znx d1znxa1 A:21-28,96-103,114-120,121-133
1s4q d1s4qa_ A:21-28,96-103,114-120,121-133
1zny d1znya1 A:21-28,96-103,114-120,121-133
2an9 d2an9a1 A:3-11,79-86,96-103,104-116
1lvg d1lvga_ A:6-11,78-84,96-102,103-114
2f3r d2f3ra1 A:3-11,79-85,96-103,104-116
1gky d1gkya_ A:2-8,75-81,93-99,100-111
1ex7 d1ex7a_ A:2-8,75-81,93-99,100-111
2an9 d2an9b1 B:3-11,79-85,96-103,104-116
2f3r d2f3rb1 B:3-11,79-85,96-103,104-116
2anb d2anba1 A:3-11,79-85,96-103,104-116
2f3t d2f3tf1 F:3-11,79-85,96-103,104-116
1s96 d1s96b_ B:4-11,79-85,97-103,104-116
1znz d1znza1 A:21-28,96-102,114-120,121-133
2anc d2ancd1 D:4-11,79-85,97-103,104-116
1s96 d1s96a_ A:4-11,79-85,97-103,104-116
2f3t d2f3td1 D:3-11,79-85,96-103,104-116
2f3t d2f3tb1 B:3-11,79-85,96-103,104-116
2anc d2ance1 E:3-11,79-85,96-103,104-116
2f3t d2f3te1 E:3-11,79-85,96-103,104-116
2anc d2ancb1 B:3-11,79-85,96-103,104-116
2anc d2anca1 A:3-11,79-85,96-103,104-116
2f3t d2f3ta1 A:3-11,79-85,96-103,104-116
2anc d2ancc1 C:3-11,79-85,96-103,104-115
2f3t d2f3tc1 C:3-11,79-85,96-103,104-116
4. c.3.1 FAD/NAD(P)-binding domain
FAD/NAD(P)-binding domain core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
1nen d1nena2 A:196-201,358-364,382-386,400-419
1nek d1neka2 A:196-201,358-364,382-386,400-419
5. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
1jqm d1jqmb_ B:132-138,172-181,255-264,268-280
6. d.126.1 Pentein
Pentein, beta/alpha-propeller duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
1g61 d1g61b_ B:4003-4008,4154-4158,4205-4211,4214-4226
1g61 d1g61a_ A:2003-2008,2154-2158,2205-2211,2214-2226
7. c.45.1 (Phosphotyrosine protein) phosphatases II share with the family I the common active site structure with a circularly permuted topology !
(Phosphotyrosine protein) phosphatases II core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423
2cne d2cnea1 A:77-85,182-186,210-216,217-238
1q6p d1q6pa_ A:577-585,682-686,710-716,717-739
8. c.23.16 Class I glutamine amidotransferase-like conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures !
Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
1kwk d1kwka3 A:477-483,522-528,563-568,572-588
1kwg d1kwga3 A:477-483,522-528,563-568,572-588
1a9x d1a9xb2 B:1764-1769,1793-1801,1846-1851,1860-1880
1ce8 d1ce8h2 H:264-269,293-301,346-351,360-380
1a9x d1a9xf2 F:5764-5769,5793-5801,5846-5851,5860-5880
1c30 d1c30f2 F:264-269,293-301,346-351,360-380
1jdb d1jdbi2 I:264-269,293-301,346-351,360-380
1c30 d1c30d2 D:264-269,293-301,346-351,360-380
1bxr d1bxrb2 B:264-269,293-301,346-351,360-380
1c3o d1c3of2 F:264-269,293-301,346-351,360-380
1cs0 d1cs0f2 F:264-269,293-301,346-351,360-380
1cs0 d1cs0d2 D:264-269,293-301,346-351,360-380
1bxr d1bxrd2 D:264-269,293-301,346-351,360-380
1a9x d1a9xd2 D:3764-3769,3793-3801,3846-3851,3860-3880
1ce8 d1ce8f2 F:264-269,293-301,346-351,360-380
1bxr d1bxrf2 F:264-269,293-301,346-351,360-380
1bxr d1bxrh2 H:264-269,293-301,346-351,360-380
1ce8 d1ce8d2 D:264-269,293-301,346-351,360-380
1ce8 d1ce8b2 B:264-269,293-301,346-351,360-380
1jdb d1jdbf2 F:264-269,293-301,346-351,360-381
1kxj d1kxjb_ B:78-84,119-129,171-176,182-199
1kxj d1kxja_ A:78-84,119-129,171-176,182-199
1k9v d1k9vf_ F:378-384,419-429,471-476,482-500
1gpw d1gpwd_ D:78-84,119-129,171-176,182-201
1gpw d1gpwb_ B:78-84,119-129,171-176,182-200
9. c.19.1 FabD/lysophospholipase-like
FabD/lysophospholipase-like core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
1nm2 d1nm2a1 A:91-97,157-164,227-232,278-290
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 72 (enumeration index: query98) of S4
1yq3 A:207-212,368-374,391-395,409-433
2wu5 A:196-201,358-364,382-386,400-419
2wu5 E:196-201,358-364,382-386,400-419
2wu5 I:196-201,358-364,382-386,400-419
2e9y A:47-54,170-175,187-194,215-228
2e9y B:47-54,170-175,187-194,215-228
3l9o A:325-333,528-532,552-560,564-574
2we5 A:43-50,166-171,183-190,208-221
2we5 C:43-50,166-171,183-190,208-221
2we5 B:43-50,166-171,183-190,208-221
2qcd B:253-258,429-434,445-450,458-479
3aeb A:208-213,369-375,392-396,410-434
3ae9 A:208-213,369-375,392-396,410-434
3ae3 A:208-213,369-375,392-396,410-434
3ae1 A:208-213,369-375,392-396,410-434
3aef A:208-213,369-375,392-396,410-434
2fbw A:207-212,368-374,391-395,409-433
2fbw N:207-212,368-374,391-395,409-433
3kzf B:46-55,171-175,188-195,215-228
3kzf C:46-54,172-176,188-195,215-228
3kzf D:46-54,171-176,188-195,215-228
3kzf A:46-54,171-175,188-195,215-228
2fjn A:577-585,682-686,710-716,717-739
2j41 C:6-13,80-86,98-104,105-117
2j41 D:6-13,80-86,98-104,105-117
2j41 B:6-13,80-87,98-104,105-117
2j41 A:5-13,80-87,97-104,108-117
3aec A:208-213,369-375,392-396,410-434
2wdq A:196-201,358-364,382-386,400-419
2wdq I:196-201,358-364,382-386,400-419
2wdq E:196-201,358-364,382-386,400-419
3sfe A:208-213,369-375,392-396,410-434
3abv A:208-213,369-375,392-396,410-434
2kqa A:1-6,59-66,82-86,86-95
2ws3 A:196-201,358-364,382-386,400-419
2ws3 E:196-201,358-364,382-386,400-419
2ws3 I:196-201,358-364,382-386,400-419
1z6g A:5-11,78-85,96-103,103-113
3l76 B:34-44,114-119,129-135,150-167
3l76 A:34-44,114-119,129-135,150-167
1zoy A:208-213,369-375,392-396,410-434
3aeg A:208-213,369-375,392-396,412-434
3aed A:208-213,369-375,392-396,410-434
3a1v B:16-23,51-55,62-70,80-93
3ae8 A:208-213,369-375,392-396,412-434
3sfd A:208-213,369-375,392-396,410-434
2x5q B:9-15,33-38,115-123,146-163
2x5q A:9-15,32-38,115-124,146-163
3u6u A:30-37,131-139,151-157,170-183
3u6u C:30-37,131-139,151-157,170-183
3m4u A:91-96,200-204,224-230,231-252
3m4u B:91-96,200-204,224-230,231-252
3lnc A:5-13,80-87,97-104,105-117
3lnc B:5-13,80-87,97-104,105-117
2qcg B:253-258,429-434,445-450,458-479
1z8f A:20-28,96-103,113-120,121-133
3tr0 A:4-11,77-83,95-101,102-114
2wrk Y:130-138,172-181,255-260,266-280
2fjm B:577-586,682-686,710-716,717-739
3aee A:208-213,369-375,392-396,410-434
3tau B:5-12,79-85,97-103,104-116
3tau A:4-12,79-85,96-103,104-116
3si2 A:242-250,256-260,317-323,341-361
2wdr A:196-201,358-364,382-386,400-419
2wdr E:196-201,358-364,382-386,400-419
2wdr I:196-201,358-364,382-386,400-419
3ae4 A:208-213,369-375,392-396,410-434
1zp0 A:208-213,369-375,392-396,410-434
3llm A:438-444,475-481,484-490,490-501
2j7k A:131-138,172-181,255-264,268-280
1yq4 A:207-212,368-374,391-395,409-433
3ae5 A:208-213,369-375,392-396,412-434
3aea A:208-213,369-375,392-396,413-434
2hg4 F:636-641,700-708,770-776,823-837
2qj3 B:83-91,151-158,219-225,271-283
2h88 A:207-212,368-374,391-395,409-433
2h88 N:207-212,368-374,391-395,409-433
2wp9 E:196-201,358-364,382-386,400-419
2wp9 A:196-201,358-364,382-386,400-419
2wp9 I:196-201,358-364,382-386,400-419
2wu2 I:196-201,358-364,382-386,400-419
2wu2 E:196-201,358-364,382-386,400-419
2wu2 A:196-201,358-364,382-386,400-419
2wdv A:196-201,358-364,382-386,400-419
2wdv E:196-201,358-364,382-386,400-419
2wdv I:196-201,358-364,382-386,400-419
3ae7 A:208-213,369-375,392-396,410-434
2v30 A:253-258,429-434,445-450,458-478
2v30 B:253-258,429-434,445-450,458-478
3ae6 A:208-213,369-375,392-396,413-434
3ae2 A:208-213,369-375,392-396,410-434
2h89 A:207-212,368-374,391-395,409-433
2wqy A:207-212,368-374,391-395,409-433
2wqy N:207-212,368-374,391-395,409-433
2ywj A:70-75,110-118,158-163,169-185
2we4 B:43-50,166-171,183-190,208-221
2we4 C:43-50,166-171,183-190,208-221
2we4 A:43-50,166-171,183-190,208-221
2we4 D:43-50,166-171,183-190,208-221
2qor A:5-11,78-84,96-102,103-113
2acz A:196-201,358-364,382-386,400-419
2cf2 K:91-97,157-164,227-232,278-290
2cf2 B:91-97,157-164,227-232,278-290
2cdh M:91-97,157-164,227-232,278-290
2cdh Q:91-97,157-164,227-232,278-290
2cdh N:91-97,157-164,227-232,278-290
2cdh P:91-97,157-164,227-232,278-290
2cdh 6:91-97,157-164,227-232,278-290
2cdh O:91-97,157-164,227-232,278-290
2cdh 5:91-97,157-164,227-232,278-290
2cdh 9:91-97,157-164,227-232,278-290
2cdh 8:91-97,157-164,227-232,278-290
2cdh 4:91-97,157-164,227-232,278-290
2cdh R:91-97,157-164,227-232,278-290
2cdh 7:91-97,157-164,227-232,278-290