1. c.26.2 Adenine nucleotide alpha hydrolases-like share similar mode of ligand (Adenosine group) binding ! can be subdivided into two group with closer relationships within each group than between the groups; the first three families form one group whereas the last two families form the other group !
Adenine nucleotide alpha hydrolase-like core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
1t9g d1t9gr_ R:34-48,131-136,136-140,163-169
2a1u d2a1ua1 A:34-48,131-136,136-140,163-169
2a1t d2a1tr1 R:34-48,131-136,136-140,163-169
1efv d1efva1 A:34-48,131-136,136-140,163-169
1efp d1efpb_ B:36-53,141-146,149-154,175-181
1efp d1efpd_ D:36-53,141-146,149-154,175-181
1t9g d1t9gs_ S:39-56,144-149,152-157,178-184
2a1u d2a1ub1 B:39-56,145-149,152-157,178-184
1efv d1efvb_ B:39-56,145-149,152-157,178-184
1o95 d1o95d_ D:15-29,112-117,117-125,150-156
1o95 d1o95f_ F:15-29,112-117,117-125,150-156
3clu d3clud1 D:15-29,112-117,118-125,150-156
3cls d3clsd1 D:15-29,112-117,118-125,150-156
3clr d3clrd1 D:15-29,112-117,118-125,150-156
3clt d3cltd1 D:15-29,112-117,118-125,150-156
1o96 d1o96d1 D:15-29,112-117,118-125,150-156
1o94 d1o94f_ F:15-29,112-117,118-125,150-156
1o96 d1o96f1 F:15-29,112-117,118-125,150-156
1o94 d1o94d_ D:15-29,112-117,118-125,150-156
1o97 d1o97d1 D:15-29,112-117,118-125,150-156
1o96 d1o96b1 B:15-29,112-117,118-125,150-156
1o96 d1o96z1 Z:15-29,112-116,118-125,150-156
1efp d1efpc1 C:15-27,110-115,115-119,142-148
2. 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
1f6m d1f6mb2 B:121-128,145-152,204-214,237-242
1f6m d1f6mf2 F:121-128,145-152,204-214,237-242
1fcd d1fcdb2 B:117-125,147-155,229-233,248-254
1cl0 d1cl0a2 A:121-128,144-152,204-214,236-242
1f6m d1f6me2 E:121-128,144-152,204-214,237-242
1trb d1trba2 A:121-128,144-152,204-214,237-242
1f6m d1f6ma2 A:121-128,144-152,204-214,237-242
1tdf d1tdfa2 A:121-128,144-152,204-214,237-242
1tde d1tdea2 A:121-128,144-152,204-214,237-242
3. c.12.1 Ribosomal proteins L15p and L18e
Ribosomal proteins L15p and L18e core: three turns of irregular (beta-beta-alpha)n superhelix
1yij d1yijl1 L:65-73,89-93,104-110,117-123
1kqs d1kqsk_ K:65-73,89-93,104-110,117-123
1yhq d1yhql1 L:65-73,89-93,104-110,117-123
1k73 d1k73m_ M:65-73,89-93,104-110,117-123
1kc8 d1kc8m_ M:65-73,89-93,104-110,117-123
1vql d1vqll1 L:65-73,89-93,104-110,117-123
1vqm d1vqml1 L:65-73,89-93,104-110,117-123
1nji d1njim_ M:65-73,89-93,104-110,117-123
1vqp d1vqpl1 L:65-73,89-93,104-110,117-123
1m90 d1m90m_ M:65-73,89-93,104-110,117-122
4. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
3ccv d3ccvl1 L:65-73,89-93,104-110,117-123
3cc2 d3cc2l1 L:65-73,89-93,104-110,117-123
3ccq d3ccql1 L:65-73,89-93,104-110,117-123
5. c.93.1 Periplasmic binding protein-like I Similar in architecture to the superfamily II but partly differs in topology !
Periplasmic binding protein-like I consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication ! parallel beta-sheet of 6 strands, order 213456
1jx6 d1jx6a_ A:30-39,153-159,161-165,173-178
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
1ega d1egab1 B:20-30,32-36,46-54,213-225
7. c.153.1 YerB-like
YerB-like 3 layers: b/b/a; central mixed beta-sheet of 9 strands, order 541329678; strands 3 and 7 are antiparallel to the rest; an unusual "over the other end" connection between strands 3 and 4
2psb d2psba1 A:86-97,229-236,244-251,292-299
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 174 (enumeration index: query109) of S4
3fbs A:117-124,141-148,195-201,216-220
3fbs B:117-124,141-148,195-201,216-220
3f8p A:130-137,155-161,210-218,241-246
3f8p B:130-137,153-161,210-218,241-246
3f8p D:130-137,153-161,210-218,241-246
3s61 A:175-182,208-214,316-326,347-352
3s61 B:175-182,207-214,316-326,347-352
3ic9 A:148-155,172-179,233-241,261-266
3ic9 B:148-155,172-178,233-241,261-266
3ic9 D:148-155,172-178,233-241,261-266
3ic9 C:148-155,172-178,233-241,261-266
3ish C:119-126,143-150,199-209,232-236
3s5w A:175-182,207-214,316-326,347-352
3s5w B:175-182,208-214,316-326,347-352
2fyo A:334-345,586-591,597-602,609-618
1zx9 A:155-162,177-183,238-246,261-266
3uk1 B:135-158,393-400,423-428,452-460
3uk1 A:135-158,393-400,423-428,452-460
3lb8 B:120-128,148-156,213-220,240-245
2q0k A:119-126,142-150,199-209,232-236
2q0k B:119-126,142-150,199-209,232-236
3cxc K:65-73,89-93,104-110,117-123
3f8r C:130-137,153-161,210-218,241-246
3f8r A:130-137,153-161,210-218,241-246
3f8d C:130-137,153-161,210-218,241-246
3f8d D:130-137,153-161,210-218,241-246
3f8d A:130-137,153-161,210-218,241-246
3f8d B:130-137,153-161,210-218,241-246