1. e.29.1 beta and beta-prime subunits of DNA dependent RNA-polymerase The catalytic site is formed by the association of two double-psi beta-barrel domains, one from each subunit !
beta and beta-prime subunits of DNA dependent RNA-polymerase Multidomain subunits of complex domain organization
2vum d2vumb1 B:550-562,577-583,613-620,621-628,694-701
1twg d1twgb_ B:550-562,577-583,613-620,621-628,694-702
2ja6 d2ja6b1 B:550-562,577-583,613-620,621-628,694-701
2ja7 d2ja7n1 N:550-562,577-583,613-620,621-628,694-701
2ja5 d2ja5b1 B:550-562,577-583,613-620,621-628,694-701
2ja7 d2ja7b1 B:550-562,577-583,613-620,621-628,694-701
2ja8 d2ja8b1 B:550-562,577-583,613-620,621-628,694-701
2r7z d2r7zb1 B:550-562,577-583,613-620,621-628,694-701
2r92 d2r92b1 B:550-562,577-583,613-620,621-628,694-701
2nvx d2nvxb1 B:550-562,577-583,613-620,621-628,694-701
1twf d1twfb_ B:550-562,577-583,613-620,621-628,694-701
2b63 d2b63b1 B:550-562,577-583,613-620,621-628,694-701
2nvy d2nvyb1 B:550-562,577-583,613-620,621-628,694-701
3cqz d3cqzb1 B:550-562,577-583,613-620,621-628,694-701
1i50 d1i50b_ B:550-562,577-583,613-620,621-628,694-701
2nvt d2nvtb1 B:550-562,577-583,613-620,621-628,694-701
2r93 d2r93b1 B:550-562,577-583,613-620,621-628,694-701
1k83 d1k83b_ B:550-562,577-583,613-620,621-628,694-701
2b8k d2b8kb1 B:550-562,577-583,613-620,621-628,694-701
1twh d1twhb_ B:550-562,577-583,613-620,621-628,694-701
2e2h d2e2hb1 B:550-562,577-583,613-620,621-628,694-701
2nvq d2nvqb1 B:550-562,577-583,613-620,621-628,694-701
1twa d1twab_ B:550-562,577-583,613-620,621-628,694-701
1twc d1twcb_ B:550-562,577-583,613-620,621-628,694-701
2e2i d2e2ib1 B:550-562,577-583,613-620,621-628,694-701
1i6h d1i6hb_ B:550-562,577-583,613-620,621-628,694-701
1i3q d1i3qb_ B:550-562,577-583,613-620,621-628,694-701
2yu9 d2yu9b1 B:550-562,577-583,613-620,621-628,694-701
2e2j d2e2jb1 B:550-562,577-583,613-620,621-628,694-701
2nvz d2nvzb1 B:550-562,577-583,614-620,621-627,694-701
2. i.8.1 RNA polymerase
RNA polymerase
1y1v d1y1vb_ B:550-562,577-583,613-620,621-628,694-701
1y1y d1y1yb_ B:550-562,577-583,613-620,621-628,694-701
1r9t d1r9tb_ B:550-562,577-583,613-620,621-628,694-701
1y77 d1y77b_ B:550-562,577-583,613-620,621-628,694-701
1wcm d1wcmb_ B:550-562,577-583,613-620,621-628,694-701
1y1w d1y1wb_ B:550-562,577-583,613-620,621-628,694-701
1r9s d1r9sb_ B:550-562,577-583,613-620,621-628,694-701
1nik d1nikb_ B:550-562,577-583,613-620,621-628,694-701
1nt9 d1nt9b_ B:550-562,577-583,613-620,621-628,694-701
1pqv d1pqvb_ B:550-562,577-583,613-620,621-628,694-701
1r5u d1r5ub_ B:550-562,577-583,613-620,621-628,694-701
1sfo d1sfob_ B:550-562,577-583,614-620,621-627,694-701
3. 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
1jal d1jalb2 B:48-59,61-66,278-287,288-297,300-310
4. c.56.2 Purine and uridine phosphorylases complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8 !
Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
1i80 d1i80c_ C:7-24,29-36,70-78,79-87,253-268
1lv8 d1lv8f_ F:2006-2022,2026-2032,2066-2074,2075-2083,2265-2282
1lvu d1lvuc_ C:2006-2022,2026-2032,2066-2074,2075-2083,2264-2282
1vmk d1vmkc_ C:1-17,21-27,61-69,70-78,246-265
1lvu d1lvud_ D:6-22,26-32,66-74,75-83,257-283
1lvu d1lvub_ B:1006-1022,1026-1032,1066-1074,1075-1083,1257-1282
1vmk d1vmka_ A:1-17,21-27,61-69,70-78,239-265
1vmk d1vmkb_ B:1-17,21-27,61-69,70-78,239-265
5. 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
1dg3 d1dg3a2 A:24-35,37-45,76-85,91-100,259-277
1f5n d1f5na2 A:24-35,37-45,77-85,91-99,259-277
6. d.114.1 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
3c9f d3c9fa1 A:360-374,380-387,413-421,512-520,519-534
3c9f d3c9fb1 B:360-374,380-387,413-421,512-520,519-534
7. c.1.4 FMN-linked oxidoreductases
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
2vdc d2vdcd2 D:310-325,422-426,522-527,541-547,551-563
2vdc d2vdcb2 B:310-325,422-426,522-527,541-547,551-563
1ea0 d1ea0b2 B:310-325,422-426,522-527,541-547,551-563
2vdc d2vdcf2 F:310-325,422-426,522-527,541-547,551-563
2vdc d2vdca2 A:310-325,422-426,522-527,541-547,551-563
2vdc d2vdce2 E:310-325,422-426,522-527,541-547,551-563
1ea0 d1ea0a2 A:310-325,422-426,522-527,541-547,551-563
2vdc d2vdcc2 C:310-325,422-426,522-527,541-547,551-563
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 983 (enumeration index: query741.752.1827) of S5
3pz6 C:310-324,328-337,355-361,364-370,370-381
3pz6 B:310-324,328-337,355-361,364-370,370-381
3pz6 E:310-324,328-337,355-361,364-370,370-379
3pz6 D:310-324,328-336,355-361,364-370,370-381
3pz6 A:310-324,328-337,355-361,364-370,370-381
3pz6 F:310-324,328-337,355-361,364-370,370-379
3fqd B:71-83,89-93,178-190,191-200,250-268
3fqd B:71-83,89-93,178-190,191-200,308-331
3e35 A:11-26,29-37,94-102,104-114,213-229
2xrf A:51-59,60-66,101-107,108-114,290-314
2xrf B:51-59,60-66,101-107,108-114,290-314
2xrf C:51-59,60-66,101-107,108-114,290-314
2waq B:484-496,520-526,556-564,565-573,620-627
3hoy B:550-562,577-583,613-620,621-628,694-701
3s2h B:550-562,577-583,613-620,621-628,694-701
3i4n B:550-562,577-583,613-620,621-628,694-701
3j0k B:550-562,577-583,613-620,621-628,694-701
3po3 B:550-562,577-583,613-620,621-628,694-701
3e0q B:8-24,28-34,68-76,77-85,268-284
3s17 B:550-562,577-583,613-620,621-628,694-701
3fki B:550-562,577-583,613-620,621-628,694-701
3s14 B:550-562,577-583,613-620,621-628,694-701
3fqj A:103-114,127-131,213-225,226-235,272-285
3fqj A:103-114,127-131,213-225,226-235,323-343
3p0f A:51-59,60-66,101-107,108-114,290-314
3rzd B:550-562,577-583,613-620,621-628,694-701
3e0d A:850-865,867-871,879-884,885-891,898-913
3e0d B:850-865,867-871,879-884,885-891,898-913
2wfd A:276-283,286-294,311-319,321-327,327-338
2wfd B:276-283,286-294,311-319,321-327,327-338
3fqi A:103-114,127-131,213-225,226-235,323-343
3fqi A:103-114,127-131,213-225,226-235,272-285
3kuk A:44-52,53-59,94-100,101-107,283-308
3kuk B:44-52,53-59,94-100,101-107,283-308
3po2 B:550-562,577-583,613-620,621-628,694-701
3hox B:550-562,577-583,613-620,621-628,694-701
3s1n B:550-562,577-583,613-620,621-628,694-701
2b8w B:24-35,37-45,77-85,91-99,259-277
2b8w A:24-35,37-45,77-85,91-99,259-277
3gtp B:550-562,577-583,614-620,621-627,694-701
3m3y B:550-562,577-583,613-620,621-628,694-701
3kvr B:44-52,53-59,94-100,101-107,283-309
3kvr A:44-52,53-59,94-100,101-107,283-309
3hoz B:550-562,577-583,613-620,621-628,694-701
3kvy A:44-52,53-59,94-100,101-107,283-308
3khs D:2-18,23-30,63-71,72-80,260-281
3khs C:2-18,23-30,63-71,72-80,260-283
3khs B:2-18,23-30,63-71,72-80,256-283
3khs A:2-18,23-29,63-71,72-80,260-282
3o6x D:64-83,85-91,155-160,161-169,300-323
3o6x B:64-83,85-91,155-160,161-169,300-323
3o6x C:64-83,85-91,155-160,161-169,300-323
3o6x E:64-83,85-91,155-160,161-169,300-323
3o6x F:64-83,85-91,155-160,161-169,300-323
3o6x A:64-83,85-91,155-160,161-169,300-323
3rzo B:550-562,577-583,613-620,621-628,694-701
3hkz B:481-493,517-523,553-561,562-570,617-625
3hkz J:481-493,517-523,553-561,562-570,617-625
2bc9 A:24-35,36-45,77-85,90-99,259-277
3gtl B:550-562,577-583,613-620,621-628,694-701
3hov B:550-562,577-583,613-620,621-628,694-701
3gb9 C:6-22,26-32,66-74,75-83,260-282
3b8h E:5-16,18-26,73-81,96-104,329-342
3hou B:550-562,577-583,613-620,621-628,694-701
3hou N:550-562,577-583,613-620,621-628,694-701
3fqg A:71-83,89-93,178-190,191-200,250-268
3fqg A:71-83,89-93,178-190,191-200,308-331
3gtk B:550-562,577-583,613-620,621-628,694-701
3qt1 B:550-562,578-583,613-620,621-628,694-701
3gtm B:550-562,577-583,613-620,621-628,694-701
3how B:550-562,577-583,613-620,621-628,694-701
3s15 B:550-562,577-583,613-620,621-628,694-701
2wb1 R:484-496,520-526,556-564,565-573,620-628
2wb1 B:484-496,520-526,556-564,565-573,620-628
4a3c B:550-562,577-583,613-620,621-628,694-701
3h0g B:536-549,563-569,599-606,607-614,678-686
3h0g N:536-549,563-569,599-606,607-614,678-686
2d4h A:24-35,37-45,77-85,91-99,259-277
2d4h B:24-35,36-45,77-85,90-99,259-277
2b92 A:24-35,37-45,76-85,91-99,259-277
2b92 B:24-35,37-45,77-85,91-99,259-277
3gtg B:550-562,577-583,613-620,621-628,694-701
3s1m B:550-562,577-583,613-620,621-628,694-701
3fnq C:8-24,28-33,68-76,77-85,269-284
1tcu B:8-24,28-34,68-76,77-85,267-284
2dby A:47-58,64-69,283-291,293-302,305-315
3k7a B:550-562,577-583,613-620,621-628,694-701
2wdc A:390-405,408-414,442-449,512-518,520-527
3m4o B:550-562,577-583,614-620,621-627,694-701
3p0e C:51-59,60-66,101-107,108-114,290-314
3p0e B:51-59,60-66,101-107,108-114,299-314
3k8o S:6-22,26-33,66-74,75-83,267-282
3k8o E:6-22,26-33,66-74,75-83,267-282
3fbt A:161-169,169-173,183-189,190-196,328-346
3fbt A:136-151,169-173,183-189,190-196,328-346
3nbq A:45-53,54-60,95-101,102-108,284-308
3s1r B:550-562,577-583,613-620,621-628,694-701
3ggs A:6-22,26-32,66-74,75-83,264-282
3ggs C:6-22,26-32,66-74,75-83,259-282
3s2d B:550-562,577-583,613-620,621-628,694-701
1td1 B:8-24,28-34,68-76,77-85,267-284
3h3v C:550-562,577-583,613-620,621-628,694-701
3iex B:8-24,28-34,68-76,77-85,266-284
2hpi A:850-865,867-871,879-884,885-891,898-913
2hpi A:622-640,867-871,879-884,885-891,898-913
2y0s R:484-496,520-526,556-564,565-573,620-627
2y0s B:484-496,520-526,556-564,565-573,620-627
2pmz B:481-493,517-523,553-561,562-570,617-625
2pmz R:481-493,517-523,553-561,562-570,617-625
3gto B:550-562,577-583,614-620,621-627,694-701
3gtj B:550-562,577-583,613-620,621-628,694-701
3i4m B:550-562,577-583,613-620,621-628,694-701
2hpm A:850-865,867-871,879-884,885-891,898-913
2hpm A:622-640,867-871,879-884,885-891,898-913
2dwq A:47-58,64-69,283-291,293-302,305-315
3k1f B:550-562,577-583,613-620,621-628,694-701
3s1q B:550-562,577-583,613-620,621-628,694-701
3s16 B:550-562,577-583,613-620,621-628,694-701
3gtq B:550-562,577-583,614-620,621-627,694-701
2zit E:5-16,18-26,73-81,96-104,329-342