1. b.82.1 RmlC-like cupins
Double-stranded beta-helix one turn of helix is made by two pairs of antiparallel strands linked with short turns ! has appearance of a sandwich of distinct architecture and jelly-roll topology
1zrr d1zrra1 A:1-7,13-20,20-32,119-126,129-137
2. c.55.1 Actin-like ATPase domain duplication contains two domains of this fold !
Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
2d0o d2d0oc2 C:262-269,270-277,280-292,294-300,350-365
2d0o d2d0oa2 A:262-269,270-277,280-292,294-300,350-365
1nbw d1nbwc2 C:264-271,272-279,282-294,295-302,352-367
1nbw d1nbwa2 A:264-271,272-279,282-294,295-302,352-367
2d0p d2d0pa2 A:262-269,270-277,280-291,292-300,350-366
2d0p d2d0pc2 C:261-269,270-278,280-292,294-299,350-362
3. 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
1te5 d1te5a_ A:33-44,45-54,59-69,73-80,207-215
4. d.58.7 RNA-binding domain, RBD
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1cvj d1cvjh1 H:11-17,53-60,61-73,79-87,124-131
1cvj d1cvjb1 B:11-17,53-60,61-73,79-87,124-131
1cvj d1cvjg1 G:11-17,53-60,61-73,79-87,124-131
1cvj d1cvjc1 C:11-17,53-60,61-73,82-87,124-131
1cvj d1cvjf1 F:11-17,53-60,61-73,82-87,124-131
5. d.58.31 Methyl-coenzyme M reductase subunits each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures !
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1e6y d1e6yc_ C:3083-3091,3120-3127,3127-3141,3148-3152,3197-3201
1e6y d1e6yf_ F:6083-6091,6120-6127,6127-6141,6148-6152,6197-6202
6. c.43.1 CoA-dependent acyltransferases
CoA-dependent acyltransferases core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
1s5o d1s5oa1 A:97-104,314-322,326-343,540-545,552-561
1t7o d1t7oa1 A:118-125,335-343,347-364,561-566,573-582
1t7n d1t7na1 A:118-125,335-343,347-364,561-566,573-582
2h3w d2h3wb1 B:118-125,335-343,347-364,561-566,573-582
1ndb d1ndba1 A:118-125,335-343,347-364,561-566,573-582
1ndb d1ndbb1 B:118-125,335-343,347-364,561-566,573-582
2h3w d2h3wa1 A:118-125,335-343,347-364,561-566,573-582
1ndf d1ndfa1 A:118-125,335-343,347-364,561-566,573-582
1t7q d1t7qb1 B:118-125,335-343,347-364,561-566,573-582
2h3u d2h3ua1 A:118-125,335-343,347-364,561-566,573-582
1t7q d1t7qa1 A:118-125,335-343,347-364,561-566,573-582
2h3u d2h3ub1 B:118-125,335-343,347-364,561-566,573-582
2h3p d2h3pb1 B:118-125,335-343,347-364,561-566,573-582
2h3p d2h3pa1 A:118-125,335-343,347-364,561-566,573-582
1ndi d1ndia1 A:118-125,335-343,347-364,561-566,573-582
1ndf d1ndfb1 B:118-125,335-343,347-364,561-566,573-582
1ndi d1ndib1 B:118-125,335-343,347-364,561-566,573-582
1nm8 d1nm8a1 A:97-104,314-322,326-344,540-545,552-561
1t1u d1t1ua1 A:107-113,326-333,338-356,557-562,569-578
7. c.91.1 PEP carboxykinase-like
PEP carboxykinase-like contains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side
2olr d2olra1 A:232-239,241-248,253-260,263-269,332-338
1k3c d1k3ca1 A:232-239,241-248,253-260,263-269,332-338
2py7 d2py7x1 X:232-239,241-248,253-260,263-269,332-338
1ayl d1ayla1 A:232-239,241-248,253-260,263-269,332-338
1k3d d1k3da1 A:232-239,241-248,253-260,263-269,332-338
8. d.58.30 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK common fold is elaborated with additional secondary structures !
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1rb0 d1rb0a_ A:1-10,51-63,65-82,93-102,105-109
1g4c d1g4cb_ B:201-210,251-263,265-283,293-302,305-309
1ex8 d1ex8a_ A:1-10,52-63,65-81,93-102,105-109
9. b.50.1 Acid proteases
Acid proteases barrel, closed; n=6, S=10, complex topology
1eag d1eaga_ A:194-204,205-209,227-239,260-267,279-283
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 621 (enumeration index: query2378) of S5
3hs0 H:1251-1259,1265-1272,1271-1278,1287-1296,1298-1310
2jke A:181-186,197-202,201-209,230-236,262-270
2jke B:181-186,197-202,201-209,230-236,262-270
2fy2 A:97-103,316-323,328-346,547-552,559-568
2bmb A:337-347,389-400,402-420,431-441,447-451
3hsz A:1-10,51-63,65-82,93-102,105-109
2i4b A:151-157,237-243,242-253,255-261,333-337
3zyi B:147-155,161-169,214-221,250-258,274-288
3foa D:112-121,122-133,146-158,166-172,176-189
3foa B:112-121,122-133,146-158,166-171,177-189
3foa A:112-121,122-133,146-158,166-172,176-188
3foa C:112-121,122-133,146-158,166-173,178-189
3fo8 D:112-121,122-133,146-158,166-172,178-189
3ili A:1-10,51-63,65-82,93-102,105-109
2qx0 B:2-12,53-64,66-86,92-103,106-110
2zq0 A:181-186,197-202,201-209,230-236,262-270
2zq0 B:181-186,197-202,201-209,230-236,262-270
3aup A:233-240,241-245,275-290,315-321,358-362
3aup C:233-240,241-245,275-290,315-321,358-362
3aup D:233-240,241-245,275-290,315-321,358-362
3hrz C:1251-1259,1265-1272,1271-1278,1286-1296,1298-1310
2jkp A:181-186,197-202,201-209,230-236,262-270
2jkp B:181-186,197-202,201-209,230-236,262-270
2i4c A:151-157,237-243,242-253,255-261,333-337
2d73 B:181-186,197-202,201-209,230-236,262-270
2d73 A:181-186,197-202,201-209,230-236,262-270
3fp0 A:51-62,175-186,190-209,455-470,476-484
3hsd B:1-10,52-63,65-83,93-102,105-109
3foi E:112-121,122-133,146-158,166-172,176-188
3foi C:112-121,122-133,146-158,166-172,176-188
3foi B:112-121,122-133,146-158,166-172,176-188
3foi F:112-121,122-133,146-158,166-172,176-188
3foi A:112-121,122-133,146-158,166-172,176-188
3foi D:112-121,122-133,146-158,166-172,176-188
2jka B:181-186,197-202,201-209,230-236,262-270
2jka A:181-186,197-202,201-209,230-236,262-270
2cg8 C:119-129,171-181,183-199,210-219,222-226
2cg8 D:119-129,171-181,183-199,210-219,222-226
2cg8 B:119-129,171-181,183-199,210-219,222-226
2cg8 A:119-129,171-181,183-199,211-219,222-226
2d3j A:9-18,29-36,41-49,61-71,147-156
2i49 A:151-157,237-243,242-253,255-261,333-337
2hji A:2-8,15-19,20-32,119-128,129-137
2i48 A:151-157,237-243,242-253,255-261,333-337
3foh E:112-121,122-133,146-158,166-172,176-188
3foh C:112-121,122-133,146-158,166-172,176-188
3foh B:112-121,122-133,146-158,166-172,176-188
3foh F:112-121,122-133,146-158,166-172,176-188
3foh A:112-121,122-133,146-158,166-172,176-188
3foh D:112-121,122-133,146-158,166-172,176-188
2qmh B:140-147,148-155,160-172,173-180,208-212
2qmh E:140-147,148-155,160-172,173-180,209-213
2qzw B:194-204,205-212,227-239,260-267,279-283