1. e.6.1 Acyl-CoA dehydrogenase NM domain-like flavoprotein: binds FAD; constituent families differ in the numbers of C-terminal domains (four-helical bundles) !
Acyl-CoA dehydrogenase NM domain-like 2 domains: (1) all-alpha: 5 helices; (2) contains an open beta-sheet barrel: n*=5, S*=8; complex topology
1u8v d1u8vb2 B:100-124,170-177,196-203,214-221,271-276
1u8v d1u8vc2 C:100-124,170-177,196-203,214-221,271-276
1u8v d1u8va2 A:100-124,170-177,196-203,214-221,271-276
1u8v d1u8vd2 D:100-124,170-177,196-203,214-221,271-276
2. d.110.2 GAF domain-like alpha(2)-beta(3)-alpha-beta(3)-alpha; antiparallel beta-sheet: order 321654 !
Profilin-like core: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
2o9a d2o9ad1 D:4-23,49-53,115-120,125-136,138-150
2o99 d2o99d1 D:4-23,49-53,115-120,125-136,138-150
2o9a d2o9aa1 A:11-23,49-53,115-120,125-136,138-150
2o99 d2o99a1 A:11-23,49-53,115-120,125-136,138-150
2o9a d2o9ab1 B:11-23,49-53,115-120,125-136,138-150
2o99 d2o99b1 B:11-23,49-53,115-120,125-136,138-150
1td5 d1td5d_ D:11-23,49-53,115-120,125-136,138-150
3. e.3.1 beta-lactamase/transpeptidase-like
beta-lactamase/transpeptidase-like contains a cluster of helices and an alpha+beta sandwich
1htz d1htzc_ C:26-41,178-182,228-240,242-254,258-267
1htz d1htza_ A:26-41,178-182,228-240,242-254,258-267
4. b.8.1 TRAF domain-like has a circularly permuted immunoglobulin-fold topology with extra strand !
TRAF domain-like sandwich; 8 strands in 2 sheets; greek-key
1d0j d1d0jd1 D:334-348,352-360,375-384,387-398,405-415
1ca4 d1ca4d1 D:334-348,352-360,375-384,387-398,405-415
1ca4 d1ca4b1 B:334-348,352-360,375-384,387-398,405-415
1d0j d1d0jc1 C:334-348,352-360,375-384,387-398,405-415
1ca4 d1ca4a1 A:334-348,352-360,375-384,387-398,405-415
1d01 d1d01c1 C:334-348,352-360,375-384,387-398,405-415
1d0a d1d0ad1 D:334-348,352-360,375-384,387-398,405-415
1d0a d1d0aa1 A:334-348,352-360,375-384,387-398,405-415
1ca4 d1ca4c1 C:334-348,352-360,375-384,387-398,405-415
1d0a d1d0af1 F:334-348,352-360,375-384,387-398,405-415
1d0a d1d0ac1 C:334-348,352-360,375-384,387-398,405-415
5. b.30.5 Galactose mutarotase-like probable carbohydrate-binding domain in enzymes acting on sugars !
Supersandwich sandwich; 18 strands in 2 sheets
1txk d1txka2 A:24-39,155-160,202-212,213-225,227-239
1jz3 d1jz3a4 A:906-914,914-922,937-941,954-961,981-991
1jz2 d1jz2c4 C:906-914,914-922,937-941,954-961,981-991
1px4 d1px4a4 A:906-914,914-922,937-941,954-961,981-991
1jz5 d1jz5d4 D:906-914,914-922,937-941,954-961,981-991
3bui d3buia2 A:422-447,595-603,762-770,773-781,887-899
3bvw d3bvwa2 A:422-447,595-603,762-770,773-781,887-899
3bvx d3bvxa2 A:422-447,595-603,762-770,773-781,887-899
6. b.81.1 Trimeric LpxA-like enzymes superhelical turns are made of three short strands; duplication: the sequence hexapeptide repeats correspond to individual strands !
Single-stranded left-handed beta-helix superhelix turns are made of parallel beta-strands and (short) turns
1yp2 d1yp2b1 B:34-41,410-415,421-426,429-434,435-442
1yp2 d1yp2d1 D:34-41,410-415,421-426,429-434,435-442
1yp3 d1yp3b1 B:34-41,410-415,421-426,429-434,435-442
1yp2 d1yp2c1 C:34-41,410-415,421-426,429-434,435-442
1yp3 d1yp3d1 D:34-42,410-415,421-426,429-434,435-442
1yp4 d1yp4d1 D:34-41,410-415,421-426,429-434,436-442
1yp2 d1yp2a1 A:34-41,410-415,421-426,429-434,436-442
1yp4 d1yp4b1 B:34-42,410-415,421-426,429-434,436-442
7. b.61.3 D-aminopeptidase, middle and C-terminal domains
Streptavidin-like barrel, closed; n=8, S=10; meander
1ei5 d1ei5a2 A:112-121,355-365,486-496,498-508,509-519
8. b.69.4 WD40 repeat-like also contains 8-bladed propellers !
7-bladed beta-propeller consists of seven 4-stranded beta-sheet motifs; meander
2ovp d2ovpb2 B:2349-2368,2601-2609,2635-2642,2644-2652,2653-2663
2ovr d2ovrb2 B:2349-2368,2601-2609,2635-2643,2644-2652,2653-2663
2ovq d2ovqb2 B:2349-2368,2601-2609,2635-2643,2644-2652,2653-2663
1nex d1nexb2 B:346-368,652-660,684-691,692-700,701-707
1nex d1nexd2 D:346-368,652-660,684-691,692-700,701-707
9. c.52.1 Restriction endonuclease-like
Restriction endonuclease-like core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
1dmu d1dmua_ A:23-46,154-158,204-222,228-240,291-297
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 889 (enumeration index: query33.49.2122) of S5
3e5z A:7-15,40-48,257-265,268-276,277-284
3e5z B:7-15,40-48,257-265,269-276,277-284
3ei4 F:82-104,309-317,349-357,369-378,379-387
3ei4 D:82-104,309-317,349-357,369-378,379-387
3ei4 B:82-104,309-317,349-357,369-378,379-387
4a0b B:118-137,346-354,386-394,403-412,413-421
4a0b D:118-137,346-354,386-394,403-412,413-421
3ls9 A:103-122,384-388,389-396,421-426,428-433
3tav A:15-41,204-209,210-223,242-255,256-261
3tav B:15-41,204-209,210-223,242-255,256-261
3ozh A:37-57,92-97,332-342,343-353,354-365
3rju A:-1-19,225-229,294-304,305-315,316-327
3rju A:-1-19,54-58,294-304,305-315,316-327
3mx6 B:6-32,188-193,194-207,227-240,241-246
3ei1 B:118-137,346-354,386-394,403-412,413-421
1y54 A:4-24,221-226,310-320,321-331,332-342
1y54 A:4-24,58-64,310-320,321-331,332-342
3mr1 C:6-32,188-193,194-207,227-240,241-246
2f03 A:9-32,109-113,150-168,175-186,233-239
2f03 C:9-32,109-113,149-168,175-186,233-239
3ixd A:5-24,221-226,310-320,321-331,332-342
3dr2 B:25-33,56-65,279-285,289-296,297-304
3dr2 A:25-33,56-65,279-285,289-296,297-304
3dr2 B:25-33,215-224,250-257,258-265,267-275
3dr2 A:25-33,215-224,250-257,258-265,267-275
3hpa A:127-146,403-407,408-415,439-445,447-452
3lsc A:103-122,384-388,390-396,421-426,427-433
3dyp A:906-914,914-922,937-941,954-961,981-991
4a0a B:118-137,346-354,386-394,403-412,413-421
3dyo B:906-914,914-922,937-941,954-961,981-991
2ezv A:9-32,109-113,150-168,175-186,233-239
2ezv B:9-32,109-113,150-168,175-186,233-239
2zc7 B:4-24,221-226,310-320,321-331,332-342
2zc7 B:4-24,58-64,310-320,321-331,332-342
2zc7 A:4-24,221-226,310-320,321-331,332-342
4a09 B:118-137,346-354,386-394,403-412,413-421
3ei2 B:118-137,346-354,386-394,403-412,413-421
3mks B:346-367,652-660,684-691,692-700,701-708
3mks D:346-368,652-660,684-691,692-700,701-707
2r7t A:315-333,631-639,674-678,679-684,685-689
4a08 B:118-137,346-354,386-394,403-412,413-421
3ei3 B:118-137,346-354,386-394,403-412,413-421