1. d.118.1 N-acetylmuramoyl-L-alanine amidase-like
N-acetylmuramoyl-L-alanine amidase-like contains mixed beta-sheet
1j3g d1j3ga_ A:11-15,75-80,82-88,113-119
1oht d1ohta_ A:13-17,79-84,86-91,107-115
1yb0 d1yb0b1 B:3-7,54-59,60-66,85-92
1yb0 d1yb0c1 C:3-7,54-59,60-66,85-92
2ar3 d2ar3b1 B:3-7,54-59,60-66,85-92
1yb0 d1yb0a1 A:3-7,54-59,60-66,85-92
2ar3 d2ar3a1 A:3-7,54-59,60-66,85-92
2ar3 d2ar3c1 C:3-7,54-59,60-66,85-92
2. d.115.1 YrdC/RibB
YrdC/RibB core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta; 3 layers; mixed twisted sheet of 7 strands; order 7126354; strands 7 and 1 are parallel to each other
1k7j d1k7ja_ A:65-69,97-103,117-123,183-189
1kk9 d1kk9a_ A:65-69,96-103,117-123,182-187
1jcu d1jcua_ A:64-68,96-102,115-121,177-183
3. d.3.1 Cysteine proteinases the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet !
Cysteine proteinases consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
3gcb d3gcba_ A:267-273,279-287,297-302,440-445
1gcb d1gcba_ A:267-273,279-287,297-302,440-445
1a6r d1a6ra_ A:267-273,279-286,297-302,440-444
2cb5 d2cb5a_ A:266-272,280-288,299-303,441-446
2cb5 d2cb5b_ B:266-272,280-288,299-303,441-446
1cb5 d1cb5b_ B:266-272,280-288,299-303,441-446
1cb5 d1cb5c_ C:266-272,280-288,299-303,441-446
1cb5 d1cb5a_ A:266-272,280-288,299-303,441-446
4. g.3.9 Growth factor receptor domain
Knottins (small inhibitors, toxins, lectins) disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
1n8z d1n8zc3 C:266-270,281-285,287-291,306-312
1s78 d1s78a3 A:266-270,281-285,287-291,306-312
1s78 d1s78b3 B:266-270,281-285,287-291,306-312
1ivo d1ivob3 B:260-264,275-279,281-285,298-304
1m6b d1m6bb3 B:260-264,275-279,280-284,297-304
1yy9 d1yy9a3 A:260-264,275-279,281-285,298-305
1n8y d1n8yc3 C:267-271,282-286,288-292,306-313
1mox d1moxb3 B:260-264,275-279,281-285,298-305
1nql d1nqla3 A:260-264,275-279,281-285,298-304
1m6b d1m6ba3 A:260-264,275-279,280-284,297-303
1ivo d1ivoa3 A:260-264,275-279,281-285,298-305
1igr d1igra3 A:223-227,238-242,244-248,271-275
1n8z d1n8zc3 C:235-239,266-270,271-275,287-291
1mox d1moxa3 A:229-233,260-264,265-269,281-285
1mox d1moxb3 B:229-233,260-264,265-269,281-285
1s78 d1s78b3 B:235-239,266-270,271-275,287-291
1s78 d1s78a3 A:235-239,266-270,271-275,287-291
1ivo d1ivob3 B:229-233,260-264,265-269,281-285
1n8y d1n8yc3 C:236-240,267-271,272-276,288-292
1ivo d1ivoa3 A:229-233,260-264,265-269,281-285
1yy9 d1yy9a3 A:229-233,260-264,265-269,281-285
2dtg d2dtge6 E:230-234,245-249,251-255,282-286
2dtg d2dtge6 E:245-249,277-281,282-286,298-304
1m6b d1m6bb3 B:229-233,260-264,265-269,280-284
1nql d1nqla3 A:229-233,260-264,265-269,281-285
1mox d1moxa3 A:260-264,275-279,281-285,300-305
1m6b d1m6ba3 A:229-233,260-264,265-269,280-284
5. 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
1k1w d1k1wa3 A:140-145,162-168,169-177,261-265
1k1x d1k1xb3 B:140-145,162-168,169-177,261-265
1k1y d1k1yb3 B:140-145,162-168,169-177,261-265
1k1y d1k1ya3 A:140-145,162-168,169-177,261-265
1k1x d1k1xa3 A:140-146,162-168,169-178,261-265
6. b.60.1 Lipocalins bind hydrophobic ligands in their interior !
Lipocalins barrel, closed or opened; n=8, S=12; meander
1avg d1avgi_ I:23-29,36-44,49-57,65-72
7. d.15.10 TGS-like possibly related to the ubiquitin-like and MoaD/ThiS superfamilies; some similarity to the alpha-L RNA-binding motif !
beta-Grasp (ubiquitin-like) core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
1ni3 d1ni3a2 A:80-84,306-315,316-325,381-387
1jal d1jala2 A:61-65,278-287,288-297,353-361
1jal d1jalb2 B:61-66,278-287,288-297,354-361
8. b.3.6 Aromatic compound dioxygenase
Prealbumin-like sandwich; 7 strands in 2 sheets, greek-key ! variations: some members have additional 1-2 strands to common fold
1dlq d1dlqa_ A:119-123,132-143,188-196,282-293
1dlm d1dlmb_ B:119-123,132-143,188-196,282-293
1dlt d1dltb_ B:119-123,132-143,188-196,282-293
1dlt d1dlta_ A:119-123,132-143,188-196,282-293
1dmh d1dmha_ A:119-123,132-143,188-196,282-293
1dmh d1dmhb_ B:119-123,132-143,188-196,282-293
1dlq d1dlqb_ B:119-123,132-143,188-196,282-293
9. d.113.1 Nudix
Nudix beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet ! contains beta-grasp motif
1iry d1irya_ A:3-12,64-75,79-88,132-141
2b06 d2b06a1 A:4-19,68-80,81-94,138-142
10. 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
1yjq d1yjqa2 A:24-30,35-44,46-56,127-133
11. 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
1fnm d1fnma2 A:11-19,68-75,76-83,353-360
2efg d2efga2 A:11-19,68-75,76-83,353-360
12. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
1pn6 d1pn6a_ A:11-19,68-75,76-83,353-360
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 47 (enumeration index: query194) of S4
3rdr A:6-11,60-65,66-72,91-98
3lat A:34-38,86-91,92-98,114-121
3lat B:34-38,86-91,92-98,114-121
3ltf A:225-229,256-260,261-265,276-280
3ltf C:225-229,256-260,261-265,276-280
3ltf C:256-260,271-275,276-280,291-295
3ltf A:256-260,271-275,276-280,291-295
2qkm F:96-105,159-167,168-178,247-252
2qkm B:96-105,159-167,168-178,247-252
3ml3 A:632-639,644-654,659-668,668-682
2wri Y:11-19,69-75,76-83,353-360
3lvt A:143-148,170-177,179-187,276-280
3qgk I:27-35,71-77,78-82,125-130
3hjs A:116-120,130-141,184-192,267-277
2c4c A:212-217,375-382,383-391,482-486
2c4c B:212-217,375-382,383-391,482-486
3loh E:245-249,277-281,282-286,298-304
3loh E:230-234,245-249,251-255,282-286
3i51 A:116-120,131-141,184-191,267-277
3h09 B:892-899,902-913,914-924,928-937
3h09 A:892-899,902-913,914-924,928-937
3frn A:24-29,54-61,79-86,107-116
2e01 A:267-273,279-287,297-302,440-445
3cng B:37-48,95-107,108-120,169-174
3cng C:37-48,95-107,108-120,169-175
3cng D:37-48,95-107,108-120,169-174
3cng A:37-48,95-107,108-120,169-174
2xex A:9-17,66-73,74-81,354-360
2xex B:9-17,66-73,74-81,354-360
3id9 A:20-28,78-87,92-103,151-156
3id9 B:20-28,74-87,92-103,151-156
2bry A:212-217,375-382,383-391,482-486
2bry B:212-217,375-382,384-391,482-487
2l47 A:3-7,54-59,60-66,85-92
2dby A:64-69,283-291,293-302,358-366
2pqv B:12-23,71-83,84-100,144-151
2pqv A:12-23,71-83,84-100,144-148
2a91 A:267-271,282-286,288-292,306-313
2a91 A:236-240,267-271,272-276,288-292
3hhx A:116-120,130-141,184-192,267-277
3mzw A:235-239,266-270,271-275,287-291
3mzw A:266-270,281-285,287-291,305-312
3zr0 A:3-15,63-75,79-89,132-141
3zr0 B:3-13,64-75,79-89,132-141
2wyh A:143-148,171-178,180-188,277-281
2wyh B:143-148,171-178,180-188,277-281
3u2p A:226-230,257-261,262-266,277-281
3u2p A:257-261,272-276,277-281,296-301
2ohf A:81-85,304-313,314-323,379-388
3hmb B:3-8,57-62,63-69,88-95
3hmb A:3-8,57-62,63-69,88-96
3hmb C:3-8,57-62,63-69,88-95
2ahx B:257-261,272-276,277-281,294-301
2ahx A:226-230,257-261,262-266,277-281
2ahx B:226-230,257-261,262-266,277-281
2ahx A:257-261,272-276,277-281,294-301
3t43 A:46-51,60-67,86-93,150-154
3t43 B:45-51,60-67,86-93,150-154
3exq A:8-21,70-81,86-96,139-145
2e00 A:267-273,279-287,297-302,440-445
3n85 A:235-239,266-270,271-275,287-291
3n85 A:266-270,281-285,287-291,305-312
3fk9 B:1-12,56-71,72-86,131-140
3fk9 A:1-12,56-71,72-86,131-140
3n9t A:118-122,128-139,182-190,275-287
2wrk Y:11-19,69-75,76-83,353-360
2eqa A:65-69,98-105,117-123,182-187
2hr7 A:245-249,277-281,282-286,298-304
2hr7 A:230-234,245-249,251-255,282-286
2hr7 B:230-234,245-249,251-255,282-286
2xsy Y:11-19,69-75,76-83,353-360
3q93 B:3-15,63-75,79-89,132-141
3q93 A:3-15,63-75,79-89,132-141
3ltg A:225-229,256-260,261-265,276-280
3ltg C:256-260,271-275,276-280,291-295
3ltg C:225-229,256-260,261-265,276-280
3ltg A:256-260,271-275,276-280,291-295
3qga I:27-35,71-77,78-82,125-130
3njp B:229-233,260-264,265-269,281-285
3njp B:260-264,275-279,281-285,299-305
3njp A:229-233,260-264,265-269,281-285
3njp A:260-264,275-279,281-285,298-305
3hgi A:116-120,130-141,184-192,267-277
3i4v A:116-120,130-141,184-192,267-277
3i4y A:116-120,131-141,184-191,267-277
3hjq A:116-120,130-141,184-192,267-277
2wyi B:143-148,171-178,180-188,277-281
2wyi A:143-148,171-178,180-188,277-281
2e02 A:267-273,279-287,297-302,440-445
3be1 A:235-239,266-270,271-275,287-291
3be1 A:266-270,281-285,287-291,305-312
3p11 A:229-233,260-264,265-269,280-284
3p11 A:260-264,275-279,280-284,297-304
3zr1 A:3-15,63-75,79-89,132-141
3zr1 B:3-13,64-75,79-89,132-141
3l7v A:59-63,92-98,123-130,203-208
2dwq A:64-69,283-291,293-302,358-366
2dwq B:64-68,283-291,293-302,358-366
2dzz A:267-273,279-287,297-302,440-445
3aje A:65-69,98-105,117-123,182-187
2xuy Y:11-19,69-75,76-83,353-360
3hkp A:116-120,130-141,184-192,267-277
3hj8 A:116-120,130-141,184-192,267-277
3hhy A:116-120,130-141,184-192,267-277
2e03 A:267-273,279-287,297-302,440-445
1tmx A:121-125,132-143,185-193,279-291
1tmx B:121-125,132-143,185-193,280-291
3i2t A:225-229,256-260,261-265,276-280
3i2t A:256-260,271-275,276-280,291-295
2dzy A:267-273,279-287,297-302,440-445
1zn0 B:11-19,68-75,76-83,353-360
2om7 L:11-19,68-75,76-83,353-360