7. d.140.1 Ribosomal protein S8 Ribosomal protein S8 consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a 1i94 d1i94h_ H:4-20,22-28,29-43,82-86 2hgr d2hgrk1 K:4-20,22-28,29-43,82-86 1hnx d1hnxh_ H:4-20,22-28,29-43,82-86 1hnz d1hnzh_ H:4-20,22-28,29-43,82-86 1i96 d1i96h_ H:4-20,22-28,29-43,82-86 1yl4 d1yl4k1 K:4-20,22-28,29-43,82-86 2uxb d2uxbh1 H:4-20,22-28,29-43,82-86 1i95 d1i95h_ H:4-20,22-28,29-43,82-86 1xnr d1xnrh_ H:4-20,22-28,29-43,82-86 2hhh d2hhhh1 H:4-20,22-28,29-43,82-86 1an7 d1an7a_ A:4-20,22-28,29-43,82-86 2uuc d2uuch1 H:4-20,22-28,29-43,82-86 1n36 d1n36h_ H:4-20,22-28,29-43,82-86 2v48 d2v48h1 H:4-20,22-28,29-43,82-86 1n32 d1n32h_ H:4-20,22-28,29-43,82-86 2v46 d2v46h1 H:4-20,22-28,29-43,82-86 1hnw d1hnwh_ H:4-20,22-28,29-43,82-86 1j5e d1j5eh_ H:4-20,22-28,29-43,82-86 1hr0 d1hr0h_ H:4-20,22-28,29-43,82-86 1xnq d1xnqh_ H:4-20,22-28,29-43,82-86 2uu9 d2uu9h1 H:4-20,22-28,29-43,82-86 2hgi d2hgik1 K:4-20,22-28,29-43,82-86 2vqe d2vqeh1 H:4-20,22-28,29-43,82-86 2uub d2uubh1 H:4-20,22-28,29-43,82-86 2j00 d2j00h1 H:4-20,22-28,29-43,82-86 2j02 d2j02h1 H:4-20,22-28,29-43,82-86 1fjg d1fjgh_ H:4-20,22-28,29-43,82-86 2vqf d2vqfh1 H:4-20,22-28,29-43,82-86 1xmo d1xmoh_ H:4-20,22-28,29-43,82-86 1n33 d1n33h_ H:4-20,22-28,29-43,82-86 1n34 d1n34h_ H:4-20,22-28,29-43,82-86 2uxc d2uxch1 H:4-20,22-28,29-43,82-86 1i97 d1i97h_ H:4-20,23-28,29-43,82-86 1xmq d1xmqh_ H:4-20,22-28,29-43,82-86 2uua d2uuah1 H:4-20,22-28,29-43,82-86 2uxd d2uxdh1 H:4-20,22-28,29-43,82-86 1an7 d1an7b_ B:4-20,22-28,29-43,82-86 2e5l d2e5lh1 H:4-20,22-28,29-43,82-86 2f4v d2f4vh1 H:4-20,22-28,29-43,82-86 1s03 d1s03h_ H:4-20,22-28,29-43,73-77 3d5c d3d5ch1 H:4-20,22-28,29-43,82-86 3d5a d3d5ah1 H:4-20,22-28,29-43,82-86 1s03 d1s03g_ G:4-20,22-28,29-43,73-77 1sei d1seia_ A:2-20,22-28,29-43,74-78 1sei d1seib_ B:2-20,22-28,29-43,74-78 10. e.23.1 Acetyl-CoA synthetase-like Acetyl-CoA synthetase-like 4 domains: (1&2) duplication: share the same alpha/beta fold; (3) beta-barrel; (4) alpha+beta 3cw9 d3cw9b1 B:64-78,79-84,207-222,223-228 1t5d d1t5dx_ X:64-78,78-84,207-222,223-228 3cw9 d3cw9a1 A:64-78,79-84,207-222,223-228 1t5h d1t5hx_ X:64-78,78-84,207-222,223-228 1amu d1amub_ B:99-113,113-119,234-248,249-254 1amu d1amua_ A:99-113,113-119,234-248,249-254 1amu d1amub_ B:99-113,183-190,234-248,249-254 1pg4 d1pg4a_ A:142-156,156-162,309-324,326-332 1pg4 d1pg4b_ B:142-156,156-162,309-324,326-332 1pg3 d1pg3b_ B:142-156,156-162,309-324,326-332 1pg3 d1pg3a_ A:142-156,156-162,309-324,326-332 1ry2 d1ry2a_ A:199-213,213-219,365-380,381-388 1lci d1lcia_ A:85-99,100-105,245-259,260-265 1ba3 d1ba3a_ A:85-99,100-105,245-259,260-265 1lci d1lcia_ A:85-99,191-198,245-259,260-265 1ba3 d1ba3a_ A:85-99,191-198,245-259,260-265 1pg3 d1pg3a_ A:142-156,255-265,309-324,326-332 1pg4 d1pg4b_ B:142-156,257-265,309-324,326-332 1pg4 d1pg4a_ A:142-156,257-265,309-324,326-332 1pg3 d1pg3b_ B:142-156,257-265,309-324,326-332 1t5d d1t5dx_ X:64-78,154-162,207-222,223-228 3cw9 d3cw9b1 B:64-78,154-162,207-222,223-228 1t5h d1t5hx_ X:64-78,154-162,207-222,223-228 1ry2 d1ry2a_ A:199-213,313-321,365-380,381-388 3cw9 d3cw9a1 A:64-78,154-162,207-222,223-228 1amu d1amua_ A:99-113,183-191,234-248,249-254 1mdb d1mdba_ A:85-99,99-105,234-241,250-256 1mdf d1mdfa_ A:85-99,99-105,234-241,250-256 1mdf d1mdfa_ A:85-99,184-190,234-241,250-256 1mdb d1mdba_ A:85-99,184-191,234-241,250-256 1mdf d1mdfa_ A:279-294,301-306,311-323,454-465 1md9 d1md9a_ A:279-294,301-306,311-323,454-465 1mdb d1mdba_ A:279-294,301-306,311-323,454-465 14. c.145.1 NadA-like NadA-like duplication; consists of three similar domains related by pseudo threefold symmetry; 3 layers, a/b/a; parallel beta sheet, order: 2134 1wzu d1wzua1 A:37-48,51-57,58-70,121-125 16. c.56.7 AF0625-like contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134 ! 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 2gfq d2gfqa1 A:113-128,132-138,201-211,212-221 2gfq d2gfqc1 C:113-128,132-138,201-212,212-221 2gfq d2gfqb1 B:113-128,132-138,201-211,212-221 1yqe d1yqea1 A:109-124,130-139,196-206,207-216 18. c.85.1 FucI/AraA N-terminal and middle domains FucI/AraA N-terminal and middle domains consists of two domains of similar topology, 3 layers (a/b/a) each ! Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345 ! Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134 2hxg d2hxgb2 B:289-300,301-305,308-323,327-331 2hxg d2hxga2 A:289-300,301-305,308-323,327-331 2ajt d2ajta2 A:289-300,301-306,308-323,326-331 2ajt d2ajtc2 C:289-300,301-305,308-323,326-331 1fui d1fuid2 D:311-322,333-337,339-354,357-367 1fui d1fuif2 F:311-322,333-337,339-354,357-367 1fui d1fuie2 E:311-322,333-337,339-354,357-367 1fui d1fuia2 A:311-322,333-337,339-354,357-367 1fui d1fuib2 B:311-322,333-337,339-354,357-367 1fui d1fuic2 C:311-322,333-337,339-354,357-367 20. c.1.5 Inosine monophosphate dehydrogenase (IMPDH) The phosphate moiety of substrate binds in the 'common' phosphate-binding site ! 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 1meh d1meha1 A:330-350,354-359,363-374,474-478 1me9 d1me9a1 A:330-350,354-359,363-374,474-478 1ak5 d1ak5a1 A:330-350,354-359,363-374,474-478 1mew d1mewa1 A:330-350,354-359,363-374,474-478 1me7 d1me7a1 A:330-350,354-359,363-374,474-478 1mei d1meia1 A:330-350,354-359,363-374,474-478 1me8 d1me8a1 A:330-350,354-359,363-374,474-478 1vrd d1vrda1 A:312-328,330-334,339-350,452-456 1lrt d1lrtc1 C:330-350,354-359,363-374,474-479 1eep d1eepb_ B:240-253,257-263,267-278,383-387 1lrt d1lrta1 A:330-350,354-359,363-374,474-479 1pvn d1pvnc1 C:330-350,354-359,363-374,474-479 1pvn d1pvna1 A:330-350,354-359,363-374,474-479 1pvn d1pvnb1 B:330-350,354-359,363-374,474-479 1pvn d1pvnd1 D:330-350,354-359,363-374,474-479 1lrt d1lrtb1 B:330-350,354-359,363-374,473-479 1lrt d1lrtd1 D:330-350,354-359,363-374,473-479 1zfj d1zfja1 A:321-337,339-343,348-359,464-468 1eep d1eepa_ A:240-253,257-262,267-278,383-387 32. c.83.1 Aconitase iron-sulfur domain Aconitase iron-sulfur domain consists of three similar domains with 3 layers (a/b/a) each; duplication ! core: parallel beta-sheet of 5 strands, order 32145 2b3y d2b3ya2 A:36-50,200-204,222-232,234-239 2b3y d2b3yb2 B:36-50,200-204,222-232,234-239 2b3x d2b3xa2 A:36-50,200-204,222-232,234-239 5acn d5acna2 A:216-229,235-242,249-264,458-464 6acn d6acna2 A:216-229,235-242,249-264,458-464 1nit d1nita2 A:216-229,235-242,249-264,458-464 1b0m d1b0ma2 A:216-229,235-242,249-264,458-464 1nis d1nisa2 A:216-229,235-242,249-264,458-464 1aco d1acoa2 A:216-229,235-242,249-264,458-464 7acn d7acna2 A:216-229,235-242,249-264,458-464 8acn d8acna2 A:216-229,235-242,249-264,458-464 1fgh d1fgha2 A:216-229,235-242,249-264,458-464 2b3y d2b3ya2 A:36-50,81-87,222-232,234-239 1amj d1amja2 A:216-229,235-242,249-263,458-464 2b3x d2b3xa2 A:36-50,81-87,222-232,234-239 1b0j d1b0ja2 A:216-229,235-242,249-264,458-464 2b3y d2b3yb2 B:36-50,81-87,222-232,234-239 1c96 d1c96a2 A:216-229,235-242,249-263,458-464 1c97 d1c97a2 A:216-229,235-242,249-263,458-464 1ami d1amia2 A:216-229,235-242,249-263,458-464