1. 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
1ct9 d1ct9b2 B:12-28,145-151,153-159,160-168,168-174
1ct9 d1ct9c2 C:12-28,145-151,153-159,160-168,168-174
1ct9 d1ct9d2 D:12-28,145-151,153-159,160-168,168-174
1ct9 d1ct9a2 A:12-28,145-151,153-159,160-168,168-174
1gph d1gph32 3:11-24,180-186,187-193,194-202,203-209
1gph d1gph42 4:11-24,180-186,187-193,194-202,203-209
1gph d1gph12 1:11-24,180-186,187-193,194-202,203-209
1gph d1gph22 2:11-24,180-186,187-193,194-202,203-209
1ao0 d1ao0a2 A:11-24,180-186,187-193,194-202,203-209
1ao0 d1ao0b2 B:11-24,180-186,187-193,194-202,203-209
1ao0 d1ao0d2 D:11-24,180-186,187-193,194-202,203-209
1ao0 d1ao0c2 C:11-24,180-186,187-193,194-202,203-209
2j6h d2j6hb2 B:11-24,178-184,185-191,192-200,201-206
1xff d1xffb_ B:11-24,178-184,185-191,192-200,201-206
2j6h d2j6ha2 A:11-24,178-184,185-191,192-200,201-206
2bpl d2bpla2 A:11-24,178-184,185-191,192-200,201-206
1jxa d1jxab2 B:12-24,178-184,185-191,192-201,201-206
2bpl d2bplb2 B:11-24,178-184,185-191,192-200,201-206
1ecj d1ecjd2 D:11-24,190-197,201-208,209-217,218-224
1ecc d1eccb2 B:11-24,189-198,200-209,209-217,218-224
2bpl d2bplc2 C:11-24,178-184,185-191,192-200,201-206
1xfg d1xfgb_ B:11-27,178-184,185-191,192-200,201-206
1ecf d1ecfb2 B:11-24,190-198,200-208,209-217,218-224
1xff d1xffa_ A:11-27,178-184,185-191,192-200,201-206
1ecg d1ecgb2 B:11-24,190-198,200-208,209-217,218-224
1xfg d1xfga_ A:11-27,178-184,185-191,192-200,201-206
1ecc d1ecca2 A:11-24,190-198,200-208,209-217,218-224
1ecb d1ecbc2 C:11-24,190-198,200-208,209-217,218-224
1ecj d1ecjc2 C:11-24,190-198,200-208,209-217,218-224
1ecj d1ecjb2 B:11-24,190-198,200-208,209-217,218-224
1ecb d1ecbd2 D:11-24,190-198,200-208,209-217,218-224
1ecj d1ecja2 A:11-24,190-198,200-208,209-217,218-224
1ecf d1ecfa2 A:11-24,190-198,200-208,209-217,218-224
1jxa d1jxaa2 A:11-24,178-184,185-191,192-201,201-206
1ecb d1ecbb2 B:11-24,190-198,200-208,209-217,218-224
1ecg d1ecga2 A:11-24,190-198,200-208,209-217,218-224
1ecb d1ecba2 A:11-24,190-198,200-208,209-217,218-224
2. d.89.1 Origin of replication-binding domain, RBD-like
Origin of replication-binding domain, RBD-like alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel sheet 41325
1tbd d1tbda_ A:11-18,52-62,63-72,100-111,113-120
2tbd d2tbda_ A:11-18,53-62,63-71,100-111,113-119
2itl d2itlb1 B:139-146,181-190,191-199,228-239,241-247
2itj d2itjb1 B:139-146,181-190,191-199,228-239,241-247
2ipr d2iprb1 B:139-146,181-190,191-199,228-239,241-247
2if9 d2if9b1 B:139-146,181-190,191-199,228-239,241-247
2fuf d2fufa1 A:139-146,181-190,191-199,228-239,241-247
2ntc d2ntcb1 B:139-146,181-190,191-199,228-239,241-247
2ntc d2ntca1 A:139-146,181-190,191-199,228-239,241-247
2ipr d2ipra1 A:139-146,181-190,191-199,228-239,241-247
2itl d2itla1 A:139-146,181-190,191-199,228-239,241-247
2if9 d2if9a1 A:139-146,181-190,191-199,228-239,241-247
1z1d d1z1db1 B:11-18,53-62,63-71,100-110,113-120
2itj d2itja1 A:139-146,180-190,191-200,228-239,241-247
3. c.66.1 S-adenosyl-L-methionine-dependent methyltransferases
S-adenosyl-L-methionine-dependent methyltransferases core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
2oo3 d2oo3a1 A:12-33,218-227,234-243,247-265,267-275
4. d.268.1 ParB/Sulfiredoxin
ParB/Sulfiredoxin beta*-alpha-beta(2)-alpha-beta-alpha; mixed beta sheet forms a partly open barrel: (n*=4, S*=8)
1vk1 d1vk1a_ A:112-121,139-145,147-152,159-172,194-200
5. c.94.1 Periplasmic binding protein-like II Similar in architecture to the superfamily I but partly differs in topology !
Periplasmic binding protein-like II consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication ! mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
1xs5 d1xs5a_ A:15-33,81-88,201-208,225-237,240-244
6. c.117.1 Amidase signature (AS) enzymes
Amidase signature (AS) enzymes possible duplication: the topologies of N- and C-terminal halves are similar; 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A=10); strands from 5 to 9 are antiparallel to the rest
2gi3 d2gi3a1 A:92-102,175-180,198-205,206-218,420-431
1m21 d1m21b_ B:148-158,236-241,259-266,267-279,481-492
1m21 d1m21a_ A:148-158,236-241,259-266,267-279,481-492
1m22 d1m22b_ B:148-158,236-243,259-266,267-279,480-492
1m22 d1m22a_ A:148-158,236-243,259-266,267-279,480-492
7. d.252.1 CheC-like
CheC-like duplication: tandem repeat of two intertwined alpha-beta-(X)-beta(2) motifs
1squ d1squb_ B:2-22,41-51,53-60,82-108,110-122
1xko d1xkob_ B:2-22,41-51,52-61,82-108,110-122
1xko d1xkoa_ A:2-22,41-51,53-61,82-105,110-122
1squ d1squa_ A:2-22,41-51,53-61,82-108,110-122
8. d.284.1 PurS-like segment-swapped dimer: the swapped segment is made of the first helix and second strand; a single long strand is formed by strands 2 and 3 of each subunit !
PurS-like consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
1t3t d1t3ta3 A:12-27,72-80,102-116,120-132,136-141
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1004 (enumeration index: query1052) of S5
3qk2 A:139-146,181-190,191-199,228-239,241-247
3e4r A:39-49,100-108,210-217,224-246,274-278
2nl8 A:139-146,181-190,191-199,228-239,241-247
3ljp B:164-178,310-320,371-380,411-430,436-442
3ljp A:164-178,310-320,371-380,411-430,436-442
3ooj H:11-27,178-184,185-191,192-200,201-206
3ooj E:11-27,178-184,185-191,192-200,201-206
3ooj D:11-27,178-184,185-191,192-200,202-206
3ooj B:11-27,178-184,185-191,192-200,202-206
3ooj A:11-27,178-184,185-191,192-200,201-206
3ooj G:11-27,178-184,185-191,192-200,201-206
3ooj F:11-27,178-184,185-191,192-200,202-206
3ooj C:11-27,178-184,185-191,192-200,201-206
3iic A:2-22,41-51,52-62,82-108,115-122
3iic B:2-22,41-51,52-62,82-108,111-122
3ksj A:14-24,75-83,185-192,199-221,249-253
3hzh B:4-22,42-51,54-62,83-113,116-126
2jbv B:164-178,310-320,371-380,411-430,436-442
2jbv A:164-178,310-320,371-380,411-430,436-442
3nne E:164-178,310-320,371-380,411-430,436-442
3nne C:164-178,310-320,371-380,411-430,436-442
3nne A:164-178,310-320,371-380,411-430,436-442
3nne G:164-178,310-320,371-380,411-430,436-442
3nne H:164-178,310-320,371-380,411-430,436-442
3nne B:164-178,310-320,371-380,411-430,436-442
3nne F:164-178,310-320,371-380,411-430,436-442
3nne D:164-178,310-320,371-380,411-430,436-442
3hm4 A:8-25,44-53,55-64,82-110,113-124
3hm4 B:6-25,44-54,56-64,82-110,112-124
3qn2 A:139-146,181-190,191-199,228-239,241-247
3h2d A:1-21,41-51,52-62,82-108,110-122
3h2d B:2-22,41-51,52-62,82-108,111-122
3ksx A:39-49,100-108,210-217,224-246,274-278
2dvz A:31-49,106-116,240-248,269-280,281-287
2dvz A:31-49,106-116,240-248,252-270,281-287
3gjy A:65-83,218-225,233-243,251-264,268-272
3h4y A:6-25,44-53,56-64,82-110,113-124
3al0 A:92-102,175-180,198-205,206-218,420-431
2qpq A:20-38,93-103,227-235,239-256,268-274
2qpq C:20-38,92-103,227-236,256-267,268-274
2qpq A:20-38,93-103,227-235,256-267,268-274
2qpq C:20-38,92-103,227-236,239-256,268-274
3qfq B:316-323,356-366,367-376,404-414,417-423
3qfq E:316-323,357-366,367-375,404-414,418-423
3qfq A:316-323,356-366,367-376,404-415,417-423