1. c.19.1 FabD/lysophospholipase-like
FabD/lysophospholipase-like core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
1oxw d1oxwc_ C:2071-2077,2077-2088,2098-2110,2127-2139,2179-2190
1oxw d1oxwb_ B:1071-1077,1077-1088,1098-1110,1127-1139,1179-1190
1oxw d1oxwa_ A:71-77,77-88,98-110,127-139,179-190
1nm2 d1nm2a1 A:91-97,96-108,111-134,202-217,239-253
1cjy d1cjyb2 B:1222-1228,1228-1240,1247-1262,1290-1305,1385-1395
1cjy d1cjya2 A:222-227,228-240,247-262,290-305,385-395
2. d.34.1 DNA-binding domain of Mlu1-box binding protein MBP1 has some topological similarity to the "winged helix" DNA-binding domain, to B1 and B5 domains of PheRS-beta (1PYS CH B) and to methyl-CpG-binding domain !
DNA-binding domain of Mlu1-box binding protein MBP1 beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
1mb1 d1mb1a_ A:22-30,36-44,46-58,79-91,91-100
3. i.19.1 Bacteriophage T4 3D cryo-EM reconstruction
Bacteriophage T4 3D cryo-EM reconstruction
1pdl d1pdlc_ C:153-157,175-185,237-259,270-285,320-334
1pdl d1pdlb_ B:153-157,175-185,237-259,270-285,320-334
1pdl d1pdla_ A:153-157,175-185,237-259,270-285,320-334
4. d.2.1 Lysozyme-like
Lysozyme-like common alpha+beta motif for the active site region
1k28 d1k28a3 A:153-157,175-185,237-259,270-285,320-334
5. e.41.1 Adenylylcyclase toxin (the edema factor) Domain 1 has topological and active site similarity to the Nucleotidyltransferases (eg. 1kny N-domain); domain 3 binds calmodulin !
Adenylylcyclase toxin (the edema factor) 3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha
1k8t d1k8ta_ A:650-655,659-675,686-707,713-739,742-769
6. a.45.1 GST C-terminal domain-like this domains follows the thioredoxin-like N-terminal domain !
GST C-terminal domain-like core: 4 helices; bundle, closed, left-handed twist; right-handed superhelix
3ljr d3ljrb1 B:2-8,11-25,163-180,187-202,202-223
3ljr d3ljra1 A:2-8,11-25,163-180,187-202,202-223
7. 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
1j2z d1j2za_ A:179-186,194-203,203-219,223-236,238-251
2jf2 d2jf2a1 A:167-174,198-206,208-226,228-241,243-256
2jf3 d2jf3a1 A:167-174,198-206,208-226,228-241,243-256
1lxa d1lxaa_ A:167-174,198-206,208-226,228-241,243-256
8. a.29.5 alpha-ketoacid dehydrogenase kinase, N-terminal domain
Bromodomain-like 4 helices; bundle; minor mirror variant of up-and-down topology
1gkx d1gkxa1 A:43-47,54-82,89-110,114-135,152-183
1gkz d1gkza1 A:43-47,54-82,89-110,114-135,152-183
1gjv d1gjva1 A:43-47,54-82,89-110,114-135,152-183
9. c.111.1 Activating enzymes of the ubiquitin-like proteins transfer adenylyl group to the C-terminal carboxyl group of the ubiquitin and MoaD/ThiS-related proteins ! the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds !
Activating enzymes of the ubiquitin-like proteins 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest
3dbl d3dble1 E:167-172,282-291,302-320,335-369,376-387
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 863 (enumeration index: query63.99) of S5
2vz8 B:575-581,580-592,595-614,690-703,731-742
2vz8 A:575-581,580-592,595-614,690-703,731-742
3qat B:88-94,93-105,108-128,207-221,241-255
3qat A:88-94,93-105,108-128,207-221,241-255
2uva G:279-285,285-298,300-327,441-456,485-497
2uva K:279-285,285-298,300-327,441-456,485-497
2uva H:279-285,285-298,300-327,441-456,485-497
2uva I:279-285,285-298,300-327,441-456,485-497
2uva J:279-285,285-298,300-327,441-456,485-497
2uva L:279-285,285-298,300-327,441-456,485-497
2c3n B:2-8,11-25,164-181,188-203,203-220
2c3n A:2-8,11-25,164-181,188-203,203-220
2c3n D:2-8,11-25,164-181,188-203,203-220
2c3n C:2-8,11-25,164-181,188-203,203-220
2vkz G:268-274,273-286,288-315,435-447,474-486
2vkz I:268-274,273-286,288-315,435-447,474-486
2vkz H:268-274,273-286,288-315,435-447,474-486
3hhd C:575-581,580-592,595-614,690-703,731-742
3hhd A:575-581,580-592,595-614,690-703,731-741
3hhd D:575-581,580-592,595-614,690-703,731-742
3hhd B:575-581,580-592,595-614,690-703,731-741
2qo3 A:645-650,650-662,665-684,761-770,796-806
2qo3 B:645-651,650-662,665-684,761-770,796-806
2pz1 A:247-251,278-318,332-352,360-369,429-442
3p1w A:118-127,130-137,141-158,175-184,186-199
3i3a A:162-169,193-201,203-221,223-235,238-251
3i3a B:162-169,193-201,203-221,223-235,238-251
3i3a C:162-169,193-201,203-221,223-235,238-251
2pff H:267-273,273-286,288-315,432-447,474-486
2pff B:267-273,273-286,288-315,432-447,474-486
2pff E:267-273,273-286,288-315,432-447,474-486
2qj3 B:83-91,90-102,105-128,198-212,232-246
2qj3 A:83-91,90-102,105-128,198-212,232-246
2jfk D:575-581,580-592,595-614,690-703,731-742
2jfk B:575-581,580-592,595-614,690-703,731-742
2jfk C:575-581,580-592,595-614,690-703,731-742
2jfk A:575-581,580-592,595-614,690-703,731-742
3kv0 A:27-31,37-56,60-76,100-128,175-204
2dx1 A:176-180,206-247,261-280,289-298,358-370
2uvc G:279-285,285-298,300-327,444-456,485-497
2uvc I:279-285,285-298,300-327,444-456,485-497
2uvc K:279-285,285-298,300-327,441-456,485-497
2uvc J:279-285,285-298,300-327,444-456,485-497
2uvc L:279-285,285-298,300-327,444-456,485-497
2uvc H:279-285,285-298,300-327,444-456,485-497
3g4d A:267-271,289-312,315-329,330-337,338-363
2h1y B:85-92,91-103,106-126,202-217,236-251
2h1y A:85-92,91-103,106-126,205-217,236-247
2c3q A:2-8,11-25,164-181,188-203,203-220
2c3q D:2-8,11-25,164-181,188-203,203-220
2c3q C:2-8,11-25,164-181,188-203,203-220
2c3q B:2-8,11-25,164-181,188-203,203-220
2z6b A:153-157,175-185,237-259,270-285,320-334
3b4r B:77-84,87-97,147-158,162-189,190-210
2c3t A:2-8,11-25,164-181,188-203,203-220
2c3t D:2-8,11-25,164-181,188-203,203-220
2c3t C:2-8,11-25,164-181,188-203,203-220
2c3t B:2-8,11-25,164-181,188-203,203-220
3ko2 B:22-32,86-98,101-118,124-144,151-164
2qc3 A:84-91,90-102,105-128,198-212,232-246
3g87 A:86-91,91-103,106-125,197-212,233-244
2vz9 A:575-581,580-592,595-614,690-703,731-741
2vz9 B:575-580,580-592,595-614,690-703,731-741
2cuy A:83-89,88-100,103-123,195-210,232-246
2cuy B:83-89,88-100,103-123,195-206,232-246
3hmj I:268-274,273-286,288-315,435-447,474-486
3hmj G:268-274,273-286,288-315,435-447,474-486
3hmj H:268-274,273-286,288-315,435-447,474-486
3hsq B:162-169,193-201,203-221,223-235,238-251
3hsq A:162-169,193-201,203-221,223-235,238-251
3hsq C:162-169,193-201,203-221,223-235,238-251
3i3x B:162-169,193-201,203-221,223-234,238-251
3i3x C:162-169,193-201,203-221,223-235,238-251
3i3x A:162-169,193-201,203-221,223-235,238-251
2hg4 C:636-641,641-653,656-675,746-763,787-797
2hg4 F:636-641,641-653,656-675,746-763,787-797
2hg4 D:636-642,641-653,656-675,752-761,787-797
2hg4 E:636-641,641-653,656-675,746-763,787-797
2hg4 A:636-641,641-653,656-675,746-763,787-797
2hg4 B:636-642,641-653,656-675,746-763,787-797
2uv8 H:268-274,273-286,288-315,435-447,474-486
2uv8 I:268-274,273-286,288-315,435-447,474-486
2uv8 G:268-274,273-286,288-315,435-447,474-486
3fd2 A:22-32,86-98,101-118,124-144,151-164
2jfd C:575-581,580-592,595-614,690-703,731-742
2jfd A:575-581,580-592,595-614,690-703,731-742
2jfd D:575-581,580-592,595-614,690-703,731-742
2jfd B:575-581,580-592,595-614,690-703,731-742
3r7p A:30-39,88-103,106-125,129-143,148-156
3ay8 A:4-9,12-26,157-174,180-193,195-215
3r0s A:164-171,195-203,204-222,223-235,237-250
3r0s A:180-186,195-203,204-222,223-235,237-250
2cf2 K:91-97,96-108,111-134,202-217,239-253
2cf2 B:91-97,96-108,111-134,202-217,239-253
2cdh N:91-97,96-108,111-134,202-217,239-253
2cdh 7:91-97,96-108,111-134,202-217,239-253
2cdh 9:91-97,96-108,111-134,202-217,239-253
2cdh O:91-97,96-108,111-134,202-217,239-253
2cdh Q:91-97,96-108,111-134,202-217,239-253
2cdh R:91-97,96-108,111-134,202-217,239-253
2cdh 8:91-97,96-108,111-134,202-217,239-253
2cdh P:91-97,96-108,111-134,202-217,239-253
2cdh 4:91-97,96-108,111-134,202-217,239-253
2cdh 6:91-97,96-108,111-134,202-217,239-253
2cdh M:91-97,96-108,111-134,202-217,239-253
2cdh 5:91-97,96-108,111-134,202-217,239-253
1wth A:153-157,175-185,237-259,270-285,320-334