1. c.2.1 NAD(P)-binding Rossmann-fold domains
NAD(P)-binding Rossmann-fold domains core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456 ! The nucleotide-binding modes of this and the next two folds/superfamilies are similar
1xwf d1xwfb1 B:213-219,221-235,269-275,278-282
1b3r d1b3ra1 A:213-219,221-235,269-274,278-282
1b26 d1b26e1 E:210-217,218-233,287-292,295-299
1b26 d1b26c1 C:210-217,218-233,287-292,295-299
1b26 d1b26a1 A:210-217,218-233,287-292,295-299
1b26 d1b26b1 B:210-217,218-233,287-292,295-299
1b26 d1b26f1 F:210-217,218-233,287-292,295-299
1b26 d1b26d1 D:210-217,218-233,287-292,295-299
1hrd d1hrda1 A:231-237,239-253,315-321,323-327
1d4f d1d4fb1 B:212-219,221-235,269-274,278-282
1ky5 d1ky5b1 B:1212-1219,1221-1235,1269-1275,1278-1282
1d4f d1d4fc1 C:212-219,221-235,269-275,278-282
1ky5 d1ky5c1 C:2212-2219,2221-2235,2269-2275,2278-2282
1ky5 d1ky5d1 D:3212-3219,3221-3235,3269-3275,3278-3282
1euz d1euzd1 D:211-220,221-236,290-296,298-302
1omo d1omob_ B:127-132,134-149,189-195,199-203
1bvu d1bvuc1 C:212-218,220-235,289-295,297-301
1d4f d1d4fd1 D:212-219,221-235,269-275,278-282
1ky5 d1ky5a1 A:212-219,221-235,269-274,278-282
2h5l d2h5ld1 D:212-219,221-235,269-275,278-282
1k0u d1k0uf1 F:212-219,221-235,269-275,278-282
1d4f d1d4fa1 A:212-219,221-235,269-274,278-282
2h5l d2h5lc1 C:212-219,221-235,269-275,278-282
1euz d1euza1 A:211-220,221-236,290-296,298-302
2h5l d2h5la1 A:212-219,221-235,269-275,278-282
1euz d1euzf1 F:212-220,221-236,290-296,298-302
2h5l d2h5le1 E:212-219,221-235,269-275,278-282
1k0u d1k0ue1 E:212-219,221-235,269-275,278-282
2h5l d2h5lh1 H:212-219,221-235,269-275,278-282
2h5l d2h5lf1 F:212-219,221-235,269-275,278-282
2h5l d2h5lg1 G:212-219,221-235,269-275,278-282
2h5l d2h5lb1 B:212-219,221-235,269-275,278-282
1euz d1euze1 E:211-220,221-236,290-296,298-302
1k0u d1k0ub1 B:212-219,221-235,269-275,278-282
1k0u d1k0ud1 D:212-219,221-235,269-275,278-282
1k0u d1k0ua1 A:212-219,221-235,269-275,278-282
1b3r d1b3rc1 C:212-219,221-235,269-274,278-282
1k0u d1k0uc1 C:212-219,221-235,269-275,278-282
1k0u d1k0ug1 G:212-219,221-235,269-275,278-282
1b3r d1b3rb1 B:212-219,221-235,269-274,278-282
1k0u d1k0uh1 H:212-219,221-235,269-274,278-282
1a7a d1a7aa1 A:212-220,222-236,270-275,279-283
1a7a d1a7ab1 B:212-220,222-236,270-275,279-283
1xwf d1xwfa1 A:212-219,221-235,269-275,278-282
1xwf d1xwfd1 D:212-219,221-235,269-275,278-282
1xwf d1xwfc1 C:212-219,221-235,269-275,278-282
1li4 d1li4a1 A:213-220,222-236,270-275,279-283
1b3r d1b3rd1 D:212-219,221-235,269-274,278-282
1ky4 d1ky4b1 B:1212-1219,1221-1235,1269-1274,1278-1282
1ky4 d1ky4a1 A:212-219,221-235,269-274,278-282
1ky4 d1ky4d1 D:3212-3219,3221-3235,3269-3274,3278-3282
1ky4 d1ky4c1 C:2212-2219,2221-2235,2269-2274,2278-2282
1dxy d1dxya1 A:146-152,154-168,199-204,212-216
2dld d2dldb1 B:147-153,155-169,201-206,214-218
1v8b d1v8bc1 C:257-264,266-280,314-319,323-327
1v8b d1v8bb1 B:257-264,266-280,314-319,323-327
1v8b d1v8ba1 A:257-264,266-280,314-319,323-327
1v8b d1v8bd1 D:257-264,266-280,314-319,323-327
1aup d1aupa1 A:230-237,239-253,315-320,323-327
1k89 d1k89a1 A:230-237,239-253,315-321,323-327
1bgv d1bgva1 A:230-237,239-253,315-321,323-327
1lu9 d1lu9a1 A:119-127,130-144,191-196,200-204
2. c.44.1 Phosphotyrosine protein phosphatases I share the common active site structure with the family II !
Phosphotyrosine protein phosphatases I-like 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
1y1l d1y1la_ A:1-8,9-24,71-77,80-86
1y1l d1y1lb_ B:1-8,9-24,71-77,80-86
1y1l d1y1ld_ D:1-8,9-24,71-77,80-86
1y1l d1y1lc_ C:1-8,9-24,71-77,80-85
3. c.88.1 Glutaminase/Asparaginase
Glutaminase/Asparaginase consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each ! Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5 ! Domain 2 has parallel beta-sheet of 4 strands, order 1234
2d6f d2d6fa2 A:195-201,211-226,231-237,262-266
2d6f d2d6fb2 B:195-201,211-226,231-237,262-266
1zq1 d1zq1a2 A:197-203,213-228,233-239,264-268
1zq1 d1zq1b2 B:197-203,213-228,233-239,264-268
4. c.6.2 Glycoside hydrolase/deacetylase in the different families beta-barrels are similarly distorted but may vary in the number of strands !
7-stranded beta/alpha barrel variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands
2cc0 d2cc0a1 A:5-13,135-146,148-155,180-185
2cc0 d2cc0a1 A:5-13,135-146,148-155,186-191
2cc0 d2cc0b1 B:4-13,135-146,148-155,186-191
5. c.56.1 HybD-like the HybD fold coincides with the consensus core structure !
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
1c8b d1c8bb_ B:514-520,525-538,588-599,622-628
1c8b d1c8ba_ A:514-520,525-538,588-599,622-628
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 129 (enumeration index: query131) of S4
3one B:262-269,271-285,319-324,328-332
3one A:262-269,271-285,319-324,328-332
3ch7 A:38-44,46-61,157-163,200-205
2zj0 C:276-282,284-298,332-338,341-345
2zj0 D:275-282,284-298,332-337,341-345
2zj0 A:275-282,284-298,332-337,341-345
2zj0 B:275-282,284-298,332-338,341-345
3n58 C:250-256,258-272,306-312,315-319
3n58 D:250-256,258-272,306-312,315-319
3n58 A:250-256,258-272,306-312,315-319
3n58 B:250-256,258-272,306-313,315-319
3nj4 B:213-220,222-236,270-275,279-283
3nj4 C:213-220,222-236,270-275,279-283
3nj4 A:212-220,222-236,270-276,279-283
3nj4 D:213-220,222-236,270-275,279-283
2ykd A:5-12,48-59,117-125,196-201
3ico B:35-41,43-57,141-146,181-187
3ico D:35-41,43-57,141-146,181-187
3ico A:35-41,43-57,141-146,181-187
3ico C:35-41,43-57,141-146,181-187
3onf B:262-269,271-285,319-324,328-332
3onf A:262-269,271-285,319-324,328-332
3dhy D:276-282,284-298,332-339,341-345
3dhy A:275-282,284-298,332-337,341-345
3dhy C:276-282,284-298,332-337,341-345
3dhy B:275-282,284-298,332-337,341-345
2gn9 A:164-172,209-224,226-233,265-270
2gn9 B:164-172,209-224,226-233,265-270
3aoe F:218-225,227-241,291-297,299-303
3aoe E:218-225,227-241,291-297,299-303
3grh A:97-102,150-160,172-179,178-184
3grh A:97-102,150-160,172-179,183-190
3kbo A:138-143,145-159,192-197,205-209
3kbo C:138-143,145-159,192-197,205-209
3gvp B:391-399,401-415,449-456,458-462
3gvp C:391-399,401-415,449-456,458-462
3gvp D:392-399,401-415,449-456,458-462
3gvp A:392-399,401-415,449-456,458-462
3k92 A:222-229,230-244,297-303,305-309
3k92 F:222-228,230-244,297-302,305-309
3k92 D:222-228,230-244,297-303,305-309
3lhi A:34-40,42-55,128-133,173-178
3oc6 A:36-42,44-58,140-145,180-186
2gn8 A:164-172,209-224,226-233,265-269
2vqp A:1-8,44-55,113-121,192-197
2j0e A:37-43,45-60,154-162,199-204
2j0e B:37-43,45-60,154-160,199-204
3g1u D:212-219,221-235,269-274,278-282
3g1u B:212-219,221-235,269-274,278-282
3g1u C:212-219,221-235,269-274,278-282
3g1u A:212-219,221-235,269-274,278-282
3kny A:68-72,81-102,107-114,139-152
2gn4 B:164-172,209-224,226-233,264-270
2gn4 A:164-172,209-224,226-233,264-269
3e7f A:37-43,45-60,154-159,199-204
3e7f B:37-43,45-60,154-160,199-204
2c2y A:157-165,167-180,205-211,214-218
3eb9 B:37-43,45-60,154-160,199-204
3eb9 A:37-43,45-60,154-160,199-204
3e15 D:53-59,61-75,152-157,223-229
3e15 C:53-59,61-75,152-157,223-229
3e15 B:53-59,61-75,152-157,223-229
3e15 A:53-59,61-75,152-157,223-229
3ond B:262-269,271-285,319-326,328-332
3ond A:262-269,271-285,319-326,328-332
3h9u B:212-219,221-235,269-274,278-282
3h9u C:212-219,221-235,269-274,278-282
3h9u D:212-219,221-235,269-274,278-282
3h9u A:212-219,221-235,269-274,278-282
2gna B:164-172,209-224,226-233,265-270
2gna A:164-172,209-224,226-233,265-270
3aog B:220-226,228-242,296-302,304-308
3aog K:220-226,228-242,296-302,304-308
3aog G:220-226,228-242,296-301,304-308
2ziz D:275-282,284-298,332-337,341-345
2ziz B:275-282,284-298,332-337,341-345
2ziz C:275-282,284-298,332-338,341-345
2ziz A:275-282,284-298,332-338,341-345
2gn6 B:164-172,209-224,226-233,264-270
2gn6 A:164-172,209-224,226-233,264-269
3ete B:245-251,253-267,320-325,328-332
3k8z E:221-227,229-243,296-302,304-308
3k8z D:221-228,229-243,296-302,304-308
3k8z A:221-228,229-243,296-302,304-308
3k8z F:221-228,229-243,296-302,304-308
3k8z C:221-228,229-243,296-302,304-308
3k8z B:221-228,229-243,296-302,304-308
2w3y B:39-50,53-83,164-181,268-272
2w3y A:39-50,53-83,165-181,268-272
2zj1 D:275-282,284-298,332-337,341-345
2zj1 A:275-282,284-298,332-337,341-345
2zj1 C:275-282,284-298,332-337,341-345
2zj1 B:275-282,284-298,332-337,341-345
3ce6 D:275-282,284-298,332-337,341-345
3ce6 A:275-282,284-298,332-337,341-345
3ce6 C:275-282,284-298,332-337,341-345
3ce6 B:275-282,284-298,332-338,341-345
3mtg A:311-318,320-334,368-375,377-381
3mtg B:311-318,320-334,368-375,377-381