1. 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
1iqp d1iqpb2 B:58-72,71-80,89-104,111-118,123-138
2fna d2fnaa2 A:72-92,91-101,122-135,137-144,155-168
2fna d2fnab2 B:72-92,91-101,122-135,137-144,155-168
1ak2 d1ak2a1 A:46-58,59-72,76-91,95-101,105-120
2ak2 d2ak2a1 A:46-58,59-72,76-91,95-101,105-120
2dy1 d2dy1a2 A:194-217,216-226,230-245,247-253,260-272
1efg d1efga2 A:202-221,224-234,238-253,255-264,268-280
1wdt d1wdta2 A:194-217,216-226,230-245,247-253,260-272
1dvr d1dvra1 A:34-46,47-60,64-79,84-89,94-109
1dar d1dara2 A:202-225,224-234,238-253,255-264,268-280
2efg d2efga2 A:202-225,224-234,238-253,255-264,268-280
1ktv d1ktvb2 B:205-225,224-234,238-253,255-264,268-280
1fnm d1fnma2 A:202-222,224-234,238-253,255-264,267-280
1ktv d1ktva2 A:205-225,224-234,238-253,255-264,268-280
2bm1 d2bm1a2 A:202-222,224-234,238-253,255-264,267-280
2bm0 d2bm0a2 A:202-221,224-234,238-253,255-264,267-280
1elo d1eloa2 A:205-225,224-234,238-253,255-264,268-280
2bv3 d2bv3a2 A:202-225,224-234,238-253,255-264,267-280
2. c.1.8 (Trans)glycosidases
TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
1ieq d1ieqa1 A:111-119,120-139,374-389,538-545,549-559
1lq2 d1lq2a1 A:111-119,120-139,374-389,538-545,549-559
1j8v d1j8va1 A:111-119,120-139,374-389,538-545,549-559
1iev d1ieva1 A:111-119,120-139,374-389,538-545,549-559
1iew d1iewa1 A:111-119,120-139,374-389,538-544,549-559
1x38 d1x38a1 A:111-119,120-139,374-389,538-544,549-559
1x39 d1x39a1 A:111-119,120-139,374-389,538-544,549-559
1ex1 d1ex1a1 A:111-119,120-139,374-389,538-544,549-559
1iex d1iexa1 A:111-119,120-139,374-389,538-544,549-559
3. 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
1h81 d1h81a1 A:267-274,283-294,411-420,424-428,439-461
1h84 d1h84a1 A:267-274,283-294,411-420,424-428,439-461
1b37 d1b37a1 A:267-274,283-294,411-420,424-428,439-461
1h81 d1h81c1 C:267-274,283-294,411-420,424-428,439-461
1h83 d1h83a1 A:267-274,283-294,411-420,424-428,439-461
1b5q d1b5qa1 A:267-274,283-294,411-420,424-428,439-461
1h82 d1h82a1 A:267-274,283-294,411-420,424-428,439-461
1b5q d1b5qc1 C:267-274,283-294,411-420,424-428,439-461
1h82 d1h82c1 C:267-274,283-294,411-420,424-428,439-461
1h83 d1h83c1 C:267-274,283-294,411-420,424-428,439-461
1b37 d1b37c1 C:267-274,283-294,411-420,424-428,439-461
1h84 d1h84c1 C:267-274,283-294,411-420,424-428,439-461
1h86 d1h86a1 A:267-274,283-294,411-420,424-428,439-461
4. c.1.10 Aldolase Common fold covers whole protein structure !
TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
1ucw d1ucwa_ A:35-46,45-64,65-90,91-96,104-123
1ucw d1ucwb_ B:35-46,45-64,65-90,91-96,104-123
1onr d1onrb_ B:35-46,45-64,65-90,91-97,104-123
1onr d1onra_ A:35-46,45-64,65-90,91-97,104-123
1i2n d1i2nb_ B:35-46,45-64,65-90,91-97,104-123
1i2o d1i2ob_ B:35-46,45-64,65-90,91-97,104-123
1i2n d1i2na_ A:35-46,45-64,65-90,91-97,104-123
1i2r d1i2rb_ B:35-46,45-64,65-90,91-97,104-123
1i2o d1i2oa_ A:35-46,45-64,65-90,91-97,104-123
1i2r d1i2ra_ A:35-46,45-64,65-90,91-97,104-123
1i2q d1i2qb_ B:35-46,45-64,65-90,91-97,104-123
1i2q d1i2qa_ A:35-46,45-64,65-90,91-97,104-123
1i2p d1i2pb_ B:35-46,45-64,65-90,91-97,104-123
1i2p d1i2pa_ A:35-46,45-64,65-90,91-97,104-123
1f05 d1f05b_ B:45-56,55-73,75-100,101-106,114-133
2cwn d2cwna1 A:45-56,55-73,75-100,101-106,114-133
2cwn d2cwnb1 B:45-56,58-73,75-100,101-107,114-133
2e1d d2e1db1 B:45-56,55-73,75-100,101-107,114-133
2e1d d2e1da1 A:45-56,55-73,75-100,101-107,114-133
5. 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
2bkq d2bkqd1 D:28-45,55-66,67-79,84-93,123-141
2bkq d2bkqc1 C:28-45,55-66,67-79,84-92,123-141
2bkq d2bkqb1 B:28-45,55-66,67-79,84-92,123-141
2bkq d2bkqa1 A:28-45,55-66,67-79,84-93,123-141
2iy0 d2iy0a1 A:467-485,494-505,505-514,522-531,556-576
6. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
1pn6 d1pn6a_ A:202-225,224-234,238-253,255-264,267-280
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1168 (enumeration index: query223.1165) of S5
3sqm D:105-117,116-139,362-377,498-503,506-519
3sqm B:105-117,116-139,362-377,498-503,506-519
3sqm C:105-117,116-139,362-377,498-503,506-518
3sqm A:105-117,116-139,362-377,498-503,506-518
3cnp A:254-264,279-290,458-469,473-477,488-510
3cnp B:254-264,279-290,458-469,473-477,488-511
2jb3 B:294-302,306-316,441-450,453-457,467-488
2jb3 A:294-302,306-316,441-450,453-457,467-488
3l86 A:66-93,99-106,127-138,139-145,158-171
2rgx A:12-25,30-42,60-72,77-82,86-101
2x42 A:83-91,92-111,320-336,492-499,524-535
2x42 A:83-91,92-111,320-336,513-519,524-535
3nvd B:140-148,149-168,420-435,575-581,593-605
3nvd A:140-148,149-168,420-436,575-581,593-605
3qf7 B:35-49,130-139,768-788,792-798,804-821
3qf7 A:35-49,130-139,768-788,792-798,804-822
3ku9 A:267-274,283-294,411-420,424-428,439-461
3ku9 B:267-274,283-294,411-420,424-428,439-461
3cn8 B:254-264,279-289,458-469,473-477,488-511
3cn8 A:254-264,279-290,458-469,473-477,488-510
3igx B:36-47,46-65,68-93,94-100,107-126
3go4 A:51-77,166-173,177-190,192-201,227-236
2wri Y:205-225,224-234,238-253,255-264,267-280
3cwn B:35-46,45-64,65-90,91-97,104-123
3cwn A:35-46,45-64,65-90,91-97,104-123
3bnu B:254-264,279-289,458-469,473-477,488-511
3bnu A:254-264,279-290,458-469,473-477,488-512
2xsy Y:205-225,224-234,238-253,255-264,267-280
3bmx B:140-148,149-168,420-435,575-581,593-605
3bmx A:140-148,149-168,420-435,575-581,593-605
2xex A:200-223,222-232,236-251,253-262,265-278
2xex B:200-223,222-232,236-251,253-262,265-278
3cnt A:254-264,279-290,458-469,473-477,488-512
3cnt B:254-263,279-289,458-469,473-477,488-511
3bq9 A:24-44,90-112,120-136,226-231,233-245
3bq9 B:24-44,90-112,120-136,226-231,233-245
3kpf B:267-274,283-294,411-420,424-428,439-461
2bac A:255-263,266-276,382-391,395-399,407-424
2yr6 B:411-423,457-471,621-641,646-651,660-681
2yr6 A:411-423,457-471,621-641,646-651,660-681
2ba9 A:255-263,266-276,382-391,395-399,407-424
3gh1 C:30-46,92-113,123-139,229-234,236-248
3gh1 A:30-46,92-115,122-139,229-234,236-248
3gh1 D:30-46,92-113,122-139,229-234,236-248
3gh1 B:30-46,92-113,122-139,229-234,236-248
3f93 A:125-133,134-153,382-397,544-550,555-564
3f93 C:125-133,134-153,382-397,523-530,555-564
3f93 B:125-133,134-153,382-397,544-550,555-564
3f93 D:125-133,134-153,382-397,544-550,555-564
3f93 B:125-133,134-153,382-397,523-530,555-564
3f93 A:125-133,134-153,382-397,523-530,555-564
3f93 C:125-133,134-153,382-397,544-550,555-564
2dkd B:36-55,86-99,113-126,132-140,142-160
2j7k A:202-221,224-234,238-253,255-264,268-280
3ayl B:411-423,457-471,621-641,646-651,660-681
3ayl A:411-423,457-471,621-641,646-651,660-681
3f94 A:125-133,134-153,382-397,544-550,555-564
3iuq A:38-60,59-75,470-480,612-620,661-682
3iuq A:38-60,59-75,470-480,646-653,661-682
3bnm A:254-264,279-290,458-469,473-477,488-512
3bnm B:254-264,279-289,458-469,473-477,488-511
3iur A:38-60,59-75,470-480,612-620,662-682
3iur A:38-60,59-75,470-480,646-653,662-682
3dl0 B:12-25,30-42,60-74,80-85,89-104
2x40 A:83-91,92-111,320-336,513-519,524-535
3ivm A:38-60,59-75,470-480,612-620,662-682
3ivm A:38-60,59-75,470-480,646-653,662-682
3adv B:251-263,264-271,276-304,345-349,356-378
3rxy A:73-89,91-100,206-217,219-225,227-238
3rxy D:67-89,91-100,205-217,219-225,227-238
3rxy B:70-89,91-100,206-217,219-225,227-238
3rxy F:67-89,91-100,205-217,219-225,227-238
3rxy C:73-89,91-100,206-217,219-225,227-238
3rxy E:67-89,91-100,205-217,219-225,227-238
3tho A:35-49,130-139,768-788,792-798,804-822
2yr4 A:411-423,457-471,621-641,646-651,660-681
2yr4 B:411-423,457-471,621-641,646-651,660-681
1z6l B:254-263,279-290,460-469,473-477,488-509
1z6l A:254-264,279-290,460-469,473-477,488-509
1xpq C:254-264,279-290,460-469,473-477,488-510
1xpq D:254-264,279-290,460-469,473-477,488-507
1xpq B:254-263,279-289,460-469,473-477,488-509
1xpq A:254-264,279-289,460-469,473-477,488-510
3bi4 B:254-264,279-290,458-469,473-477,488-511
3bi4 A:254-264,279-290,458-469,473-477,488-512
3l1r B:267-274,283-294,411-420,424-428,439-461
3l1r A:267-274,283-294,411-420,424-428,439-461
3iun A:38-60,59-75,470-480,612-620,662-682
3iun A:38-60,59-75,470-480,646-653,662-682
2hko A:626-633,644-655,769-778,794-799,810-832
3lk6 B:140-148,149-168,420-435,575-581,593-605
3lk6 C:140-148,149-168,420-435,575-581,593-605
3lk6 A:140-148,149-168,420-435,575-581,593-605
3lk6 D:140-148,149-168,420-435,575-581,593-605
3giw A:51-77,166-173,177-190,192-201,227-236
2x41 A:83-91,92-111,320-336,513-519,524-535
2jb1 B:294-302,306-316,441-450,453-457,467-488
2jb1 A:294-302,306-316,441-450,453-457,467-488
3ac0 B:66-74,75-94,306-322,636-642,647-658
3ac0 C:66-74,75-94,306-322,636-642,647-658
3ac0 A:66-74,75-94,306-322,636-642,647-658
3ac0 D:66-74,75-94,306-322,636-642,647-658
1yy5 B:254-263,279-290,460-469,473-477,488-509
1yy5 A:254-264,279-290,460-469,473-477,488-510
2xuy Y:205-225,224-234,238-253,255-264,267-280
3tk7 A:36-47,46-65,68-93,94-99,107-126
3ty0 B:751-763,764-773,776-804,845-849,857-878
3cnd B:254-263,279-289,458-469,473-477,488-511
3cnd A:254-264,279-290,458-469,473-477,488-510
2jb2 B:294-302,306-316,441-450,453-457,467-488
2jb2 A:294-302,306-316,441-450,453-457,467-488
3sql B:105-117,116-139,362-377,498-503,506-520
3sql A:105-117,116-139,362-377,498-503,506-519
3lov A:285-294,298-305,415-432,433-437,445-464
3tno A:36-47,46-65,68-93,94-99,107-126
2c9y A:45-57,58-71,75-90,95-99,104-119
3kof B:35-46,45-64,65-90,91-97,104-123
3kof A:35-46,45-64,65-90,91-96,104-123
2dkc B:36-55,86-100,113-126,132-140,142-160
2chg B:50-64,63-72,81-96,103-110,115-130
2chg D:50-64,63-72,81-96,103-110,115-130
2b9w A:255-263,266-276,382-391,395-399,407-424
3ayj B:411-423,457-471,621-641,646-651,660-681
3ayj A:411-423,457-471,621-641,646-651,660-681
3ayi B:411-423,457-471,621-641,646-651,660-681
3ayi A:411-423,457-471,621-641,646-651,660-681
3euj A:70-84,219-236,1394-1422,1429-1435,1440-1455
3bi2 B:254-264,279-289,458-469,473-477,488-511
3bi2 A:254-264,279-290,458-469,473-477,488-510
2osb B:12-25,30-42,60-74,80-85,89-104
2dka A:36-55,86-100,113-126,132-140,142-160
3abz A:66-74,75-94,306-322,636-642,647-658
3abz B:66-74,75-94,306-322,636-642,647-658
3abz C:66-74,75-94,306-322,636-642,647-658
3abz D:66-74,75-94,306-322,636-642,647-658
3m16 A:39-49,49-68,72-96,98-104,111-130
3euk F:70-84,219-236,1394-1422,1429-1435,1440-1455
3euk H:70-84,219-236,1394-1422,1429-1436,1440-1455
3euk A:70-84,219-236,1394-1418,1429-1435,1440-1455
3euk C:70-84,219-236,1394-1422,1429-1435,1440-1455
2rh5 B:30-42,43-56,60-72,77-82,86-101
2bab A:255-263,266-276,382-391,395-399,407-424
2wrk Y:202-220,224-234,238-253,255-260,266-280
1rsg B:254-264,279-289,460-469,473-477,488-511
1rsg A:254-264,279-289,460-469,473-477,488-512
1xpg B:65-75,149-156,170-192,195-201,208-223
2yr5 B:411-423,457-471,621-641,646-651,660-681
2yr5 A:411-423,457-471,621-641,646-651,660-681
2pmb D:33-49,95-116,126-142,232-237,239-251
2pmb B:32-49,95-116,126-142,232-237,239-251
2pmb C:33-49,95-116,126-142,232-237,239-251
2pmb A:33-49,95-116,126-142,232-237,239-251
2jae B:294-302,306-316,441-450,453-457,467-488
2jae A:294-302,306-316,441-450,453-457,467-488
3ium A:38-60,59-75,470-480,645-653,662-682
3ium A:38-60,59-75,470-480,612-620,662-682
2b9y A:255-263,266-276,382-391,395-399,407-424
3cns A:254-264,279-290,458-469,473-477,488-509
3cns B:254-264,279-290,458-469,473-477,488-509
3iuj A:38-60,59-75,470-480,612-620,661-682
3upb A:36-47,46-65,68-93,94-99,107-126
3iul A:38-60,59-75,470-480,612-620,662-682
3iul A:38-60,59-75,470-480,646-653,662-682
2b9x A:255-263,266-276,382-391,395-399,407-424
3bi5 A:254-264,279-290,458-469,473-477,488-512
3bi5 B:254-264,279-289,458-469,473-477,488-511
2rdo 7:208-231,230-240,244-259,261-270,273-286
1zn0 B:202-225,224-234,238-253,255-264,267-280
2om7 L:202-222,224-234,238-253,255-264,267-280