1. b.2.3 Bacterial adhesins
Common fold of diphtheria toxin/transcription factors/cytochrome f sandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
1tr7 d1tr7b1 B:1-6,8-13,14-23,41-46,141-152
1kiu d1kiud1 D:1-6,8-13,14-23,41-46,141-152
1kiu d1kiub1 B:1-6,8-13,14-23,41-46,141-152
1kiu d1kiuh1 H:1-6,8-13,14-23,41-46,141-152
1kiu d1kiuf1 F:1-6,8-13,14-23,41-46,141-152
1uwf d1uwfa1 A:1-6,8-13,14-23,41-46,141-152
1tr7 d1tr7a1 A:1-6,8-13,14-23,41-46,141-152
2vco d2vcob1 B:1-6,8-13,14-23,41-46,141-152
1qun d1qund1 D:1-6,8-13,15-23,41-46,141-152
1qun d1qunf1 F:1-6,8-13,15-23,41-46,141-152
1qun d1qunh1 H:1-6,8-13,15-23,41-46,141-152
1qun d1qunb1 B:1-6,8-13,15-23,41-46,141-152
1qun d1qunl1 L:1-6,8-13,16-23,41-46,141-152
1qun d1qunp1 P:1-6,8-13,16-23,41-46,141-152
1qun d1qunn1 N:1-6,8-13,16-23,41-46,141-152
1qun d1qunj1 J:1-6,8-13,16-23,41-46,141-152
1klf d1klfb1 B:1-6,8-13,14-23,41-46,140-152
1klf d1klff1 F:1-6,8-13,14-23,41-46,140-152
1klf d1klfd1 D:1-6,8-13,14-23,41-46,140-152
1klf d1klfh1 H:1-6,8-13,14-23,41-46,140-152
1kiu d1kiul1 L:1-6,8-13,14-22,41-46,140-152
1kiu d1kiun1 N:1-6,8-13,14-22,41-46,140-152
1kiu d1kiuj1 J:1-6,8-13,14-22,41-46,140-152
1kiu d1kiup1 P:1-6,8-13,14-22,41-46,140-152
2vco d2vcoa1 A:1-6,9-13,14-23,41-46,140-152
1klf d1klfn1 N:1-6,8-13,15-22,41-46,140-152
1klf d1klfl1 L:1-6,8-13,15-22,41-46,140-152
1klf d1klfp1 P:1-6,8-13,15-22,41-46,140-152
1klf d1klfj1 J:1-6,8-13,15-22,41-46,140-152
2. 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
1ng9 d1ng9a2 A:576-584,598-605,608-614,643-649,721-727
1wb9 d1wb9a2 A:576-584,598-605,608-614,643-649,721-727
1wbb d1wbba2 A:576-584,598-605,608-614,643-649,721-727
1ewr d1ewra2 A:549-557,569-575,576-583,612-617,689-695
1ewr d1ewrb2 B:1549-1557,1569-1575,1576-1583,1612-1617,1689-1695
1wbd d1wbda2 A:576-584,598-605,608-614,643-649,721-727
1oh5 d1oh5a2 A:576-584,598-605,608-614,643-649,721-727
1nne d1nneb2 B:1549-1557,1569-1575,1576-1583,1612-1617,1689-1695
1ewq d1ewqb2 B:1549-1557,1569-1575,1576-1583,1612-1617,1689-1695
1fw6 d1fw6b2 B:1549-1557,1569-1575,1576-1583,1612-1617,1689-1695
1nne d1nnea2 A:549-557,569-575,576-583,612-617,689-695
1ewq d1ewqa2 A:548-557,569-575,576-583,612-617,689-695
1fw6 d1fw6a2 A:550-557,569-575,576-583,612-617,689-695
1r0y d1r0yb_ B:389-396,438-450,451-459,478-486,598-604
3. b.17.1 PEBP-like
PEBP-like sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
1kn3 d1kn3a_ A:25-30,31-35,37-41,50-55,163-172
1bd9 d1bd9a_ A:25-30,31-35,37-41,51-55,163-172
1beh d1behb_ B:25-30,31-35,37-41,51-55,163-172
2qyq d2qyqa1 A:25-30,31-35,37-41,50-55,163-172
4. 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
2ayn d2aynb1 B:245-257,264-272,273-277,308-321,322-328
2ayn d2aync1 C:245-257,264-272,273-277,308-321,322-328
1nbf d1nbfe_ E:323-334,339-348,349-353,388-400,400-407
2ayn d2ayna1 A:247-257,264-272,273-277,306-320,322-328
1nb8 d1nb8b_ B:323-335,339-347,349-353,388-400,400-407
5. 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
1p4v d1p4vc_ C:305-311,452-460,564-572,576-582,590-594
9gaa d9gaac_ C:305-311,452-460,564-572,576-582,590-594
9gaf d9gafc_ C:305-311,452-460,564-572,576-582,590-594
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 307 (enumeration index: query2379) of S5
3rfz A:1-6,9-13,14-23,41-46,140-152
3rfz D:1-6,8-13,15-23,41-46,140-152
3m99 A:280-289,295-304,305-309,345-355,356-363
2vtc B:3-10,11-16,69-74,74-83,173-186
2vtc A:3-10,11-16,69-74,74-83,173-186
3mtn C:375-386,387-398,399-403,444-456,457-464
3mp2 A:94-104,105-114,115-119,134-148,148-153
2o8c B:1088-1095,1110-1116,1128-1134,1163-1168,1241-1247
3n3k A:925-938,939-951,951-955,993-1005,1005-1012
3mhs A:280-289,296-303,305-309,344-355,356-363
3gd7 C:1208-1214,1225-1236,1237-1244,1265-1270,1395-1401
3gd7 D:1208-1214,1229-1236,1237-1244,1265-1270,1395-1401
3owr D:38-50,61-67,77-86,103-113,146-158
2o8f B:1088-1095,1110-1116,1128-1133,1163-1168,1241-1247
2y6e D:452-461,467-475,476-480,808-818,819-826
2y6e B:450-463,464-475,476-480,808-819,819-826
2y6e E:452-463,464-475,476-480,808-818,819-826
2y6e F:452-463,464-475,476-480,808-818,819-826
3k0s A:576-584,598-605,608-614,643-649,721-727
2pjz A:1-12,16-29,31-37,57-63,176-183
3zud A:3-10,11-16,66-71,72-80,172-185
3i3t A:375-386,387-398,399-403,445-456,457-464
3i3t C:375-386,387-398,399-403,445-456,457-464
3i3t G:374-386,387-398,399-403,445-457,457-464
3i3t E:374-386,387-398,399-403,445-457,457-464
2o8b B:1088-1095,1110-1116,1128-1134,1163-1168,1240-1247
2yet A:3-10,11-16,66-71,72-80,172-185
2yet B:3-10,11-16,66-71,72-80,172-185
2o8e B:1088-1095,1110-1116,1128-1134,1163-1168,1240-1248
3mcy B:1-6,8-13,14-23,41-46,141-152
3mcy D:1-6,8-13,15-23,41-46,140-152
3mcy C:1-6,8-13,15-23,41-46,141-152
3mcy A:1-6,8-13,14-23,41-46,141-152
2o8d B:1088-1095,1110-1116,1128-1134,1163-1168,1240-1247
3mhh A:280-288,296-304,305-309,346-355,356-363
2ghi B:15-25,38-46,47-53,73-79,205-211
3p69 B:38-50,61-67,77-86,103-113,146-158
3p69 A:38-50,61-67,77-86,103-113,146-158