1. d.339.1 ORC1-binding domain ORC1-binding domain complex fold, composed of an alpha hairpin, meander beta-sheet and a five-stranded barrel of unusual topology 1zhi d1zhib1 B:493-498,499-504,522-533,551-558 1zbx d1zbxb1 B:493-498,499-505,522-533,551-558 1z1a d1z1ab1 B:493-498,499-505,522-533,551-558 1z1a d1z1aa1 A:493-498,499-505,522-533,551-558 2. c.45.1 (Phosphotyrosine protein) phosphatases II share with the family I the common active site structure with a circularly permuted topology ! (Phosphotyrosine protein) phosphatases II core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423 1zsq d1zsqa2 A:266-276,277-286,296-311,441-456 1zvr d1zvra2 A:266-276,277-286,296-311,441-456 1lw3 d1lw3a2 A:268-275,278-286,296-311,441-456 1m7r d1m7rb2 B:268-276,277-286,296-311,441-456 1m7r d1m7ra2 A:268-276,277-286,296-311,441-456 2oz5 d2oz5b1 B:11-15,26-32,37-48,181-196 2q47 d2q47a1 A:57-63,65-71,73-84,171-184 1lar d1lara1 A:1381-1386,1393-1398,1401-1416,1549-1562 1p15 d1p15b_ B:582-587,594-600,602-617,751-764 1p15 d1p15a_ A:582-587,594-600,602-617,751-764 1lar d1larb1 B:1381-1386,1393-1398,1401-1416,1549-1562 2q47 d2q47b1 B:57-63,65-71,73-84,171-184 1xri d1xria_ A:57-63,65-71,73-84,171-184 1xri d1xrib_ B:57-63,65-71,73-84,171-184 1rpm d1rpmb_ B:955-960,967-973,975-990,1122-1135 1rpm d1rpma_ A:955-960,967-973,975-990,1122-1135 1jln d1jlna_ A:340-345,353-358,361-376,507-520 1aax d1aaxa_ A:68-76,77-86,88-103,245-258 1i57 d1i57a_ A:68-76,77-86,88-103,245-258 1c86 d1c86a_ A:68-76,77-86,88-103,245-258 1lyv d1lyva_ A:245-252,253-260,263-278,428-441 1ohe d1ohea2 A:215-220,223-228,244-256,336-349 1pa9 d1pa9a_ A:83-90,91-98,101-116,266-279 2i42 d2i42a1 A:245-252,253-260,263-278,428-441 1wax d1waxa1 A:68-76,77-85,88-103,245-258 2b4s d2b4sa1 A:68-76,77-85,88-103,245-258 1bzh d1bzha_ A:68-76,77-85,88-103,245-258 3blu d3blua1 A:245-252,253-260,263-278,428-441 2h4k d2h4ka1 A:68-76,77-85,88-103,245-258 2f6v d2f6va1 A:68-76,77-85,88-103,245-258 2f71 d2f71a1 A:68-76,77-85,88-103,245-258 2f6z d2f6za1 A:68-76,77-85,88-103,245-258 1kak d1kaka_ A:68-75,78-85,88-103,245-258 2f6t d2f6ta1 A:68-76,77-85,88-103,245-258 1bzj d1bzja_ A:68-76,77-85,88-103,245-258 1ytw d1ytwa_ A:245-252,253-260,263-278,428-441 1pa1 d1pa1a_ A:568-576,577-585,588-603,745-758 1sug d1suga_ A:68-76,77-85,88-103,245-258 2b07 d2b07a1 A:68-76,77-85,88-103,245-258 2f6y d2f6ya1 A:68-76,77-85,88-103,245-258 2hb1 d2hb1a1 A:68-76,77-85,88-103,245-258 2azr d2azra1 A:68-76,77-85,88-103,245-258 1q1m d1q1ma_ A:68-76,77-85,88-103,245-258 1gfy d1gfya_ A:68-76,77-85,88-103,245-258 2f6w d2f6wa1 A:68-76,77-85,88-103,245-258 2hnq d2hnqa_ A:68-76,77-85,88-103,245-258 1eeo d1eeoa_ A:68-75,78-85,88-103,245-258 1qxk d1qxka_ A:68-76,77-85,88-103,245-258 1pty d1ptya_ A:68-76,77-85,88-103,245-258 1ypt d1ypta_ A:245-252,253-260,263-278,428-441 2bgd d2bgda1 A:68-76,77-85,88-103,245-258 2cm8 d2cm8a1 A:68-76,77-85,88-103,245-258 1yts d1ytsa_ A:245-252,253-260,263-278,428-441 1onz d1onza_ A:68-76,77-85,88-103,245-258 2cnh d2cnha1 A:68-76,77-85,88-103,245-258 1ptu d1ptua_ A:68-76,77-85,88-103,245-258 1c83 d1c83a_ A:68-76,77-85,88-103,245-258 1pxh d1pxha_ A:68-76,77-85,88-103,245-258 1ptv d1ptva_ A:68-76,77-85,88-103,245-258 1qz0 d1qz0a_ A:245-252,253-260,263-278,428-441 2f70 d2f70a1 A:68-76,77-85,88-103,245-258 1t4j d1t4ja_ A:68-76,77-85,88-103,245-258 1qz0 d1qz0b_ B:245-252,253-260,263-278,428-441 1c87 d1c87a_ A:68-76,77-85,88-103,245-258 1ypt d1yptb_ B:245-252,253-260,263-278,428-441 1q6s d1q6sb_ B:1068-1076,1077-1085,1088-1103,1245-1258 1ecv d1ecva_ A:68-76,77-85,88-103,245-258 1nwe d1nwea_ A:68-76,77-85,88-103,245-258 1nwl d1nwla_ A:68-76,77-85,88-103,245-258 2cma d2cmaa1 A:68-76,77-85,88-103,245-258 1no6 d1no6a_ A:68-76,77-85,88-103,245-258 2cm3 d2cm3b1 B:68-76,77-85,88-103,245-258 1a5y d1a5ya_ A:68-76,77-85,88-103,245-258 1xbo d1xboa_ A:68-76,77-85,88-103,245-258 1oes d1oesa_ A:68-76,77-85,88-103,245-258 2h4g d2h4ga1 A:68-76,77-85,88-103,245-258 1c84 d1c84a_ A:68-76,77-85,88-103,245-258 2cnf d2cnfa1 A:68-76,77-85,88-103,245-258 1ptt d1ptta_ A:68-76,77-85,88-103,245-258 1xxv d1xxvb1 B:245-252,253-260,263-278,428-441 1oev d1oeva_ A:68-76,77-85,88-103,245-258 2cng d2cnga1 A:68-76,77-85,88-103,245-258 1gwz d1gwza_ A:305-310,322-327,330-345,485-498 1l8g d1l8ga_ A:68-76,77-85,88-103,245-258 1c85 d1c85a_ A:68-76,77-85,88-103,245-258 1xxv d1xxva1 A:245-252,253-260,263-278,428-441 2cmc d2cmca1 A:68-76,77-85,88-103,245-258 1pyn d1pyna_ A:68-76,77-85,88-103,245-258 1ony d1onya_ A:68-76,77-85,88-103,245-258 1een d1eena_ A:68-76,77-85,88-103,245-258 2cm7 d2cm7a1 A:68-75,78-85,88-103,245-258 1r6h d1r6ha_ A:12-18,19-26,32-44,127-140 1t49 d1t49a_ A:68-76,77-85,88-103,245-258 1c88 d1c88a_ A:68-76,77-85,88-103,245-258 1oet d1oeta_ A:68-76,77-85,88-103,245-258 1g7f d1g7fa_ A:68-76,77-85,88-103,245-258 1g7g d1g7ga_ A:68-76,77-85,88-103,245-258 1ytn d1ytna_ A:245-252,253-260,263-278,428-441 1oeo d1oeox_ X:68-76,77-85,88-103,245-258 2bge d2bgea1 A:68-76,77-85,88-103,245-258 1q6n d1q6na_ A:568-576,577-585,588-603,745-758 1ph0 d1ph0a_ A:68-76,77-85,88-103,245-258 1nl9 d1nl9a_ A:68-76,77-85,88-103,245-258 2cne d2cnea1 A:68-76,77-85,88-103,245-258 1q6s d1q6sa_ A:568-576,577-585,588-603,745-758 2cni d2cnia1 A:68-76,77-85,88-103,245-258 2cm3 d2cm3a1 A:68-76,77-85,88-103,245-258 1nny d1nnya_ A:68-76,77-85,88-103,245-258 2cmb d2cmba1 A:68-76,77-85,88-103,245-258 1q6t d1q6tb_ B:1068-1076,1077-1085,1088-1103,1245-1258 1jf7 d1jf7a_ A:68-75,78-85,88-103,245-258 1nz7 d1nz7a_ A:68-76,77-85,88-103,245-258 1oeu d1oeua_ A:68-76,77-85,88-103,245-258 1lqf d1lqfd_ D:568-576,577-585,588-603,745-758 1lar d1larb2 B:1670-1675,1682-1687,1690-1705,1840-1853 1g1f d1g1fa_ A:68-76,77-85,88-103,245-258 1lqf d1lqfa_ A:568-576,577-585,588-603,745-758 1bzc d1bzca_ A:68-76,77-85,88-103,245-258 1xxp d1xxpa1 A:245-252,253-260,263-278,428-441 1q6n d1q6nb_ B:1068-1076,1077-1085,1088-1103,1245-1258 1xxp d1xxpb1 B:245-252,253-260,263-278,428-441 1q6p d1q6pb_ B:1068-1076,1077-1085,1088-1103,1245-1258 1fpr d1fpra_ A:305-310,322-328,333-345,485-498 2cm2 d2cm2a1 A:68-76,77-85,88-103,245-258 1q6m d1q6ma_ A:68-76,77-85,88-103,245-258 1lqf d1lqfc_ C:568-576,577-585,588-603,745-758 1q6p d1q6pa_ A:568-576,577-585,588-603,745-758 1kav d1kava_ A:68-76,77-85,88-103,245-258 1t48 d1t48a_ A:68-76,77-85,88-103,245-258 1lqf d1lqfb_ B:568-576,577-585,588-603,745-758 1q6j d1q6ja_ A:68-76,77-85,88-103,245-258 1g1g d1g1ga_ A:68-76,77-85,88-103,245-258 1q6t d1q6ta_ A:568-576,577-585,588-603,745-758 1jf7 d1jf7b_ B:68-76,77-85,88-103,245-258 2shp d2shpb1 B:306-311,326-332,334-349,489-502 2shp d2shpa1 A:306-311,326-332,334-349,489-502 1l8k d1l8ka_ A:70-78,79-87,90-105,243-256 1u26 d1u26a_ A:57-62,90-96,98-110,264-276 1g1h d1g1ha_ A:68-76,77-85,88-103,245-258 1lar d1lara2 A:1670-1675,1682-1688,1690-1705,1840-1853 1wch d1wcha_ A:2264-2273,2274-2283,2286-2301,2435-2448 1rxd d1rxdb_ B:8-14,15-21,25-40,124-137 1rxd d1rxdc_ C:8-14,15-21,25-40,124-137 1rxd d1rxda_ A:8-14,15-21,25-40,124-137 1vhr d1vhra_ A:29-33,36-41,47-55,146-159 3. d.154.1 DmpA/ArgJ-like convergent similarity to the Ntn amidohydrolases ! DmpA/ArgJ-like duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha 1vz7 d1vz7d_ D:28-34,67-74,81-100,138-147 1vz8 d1vz8a_ A:28-35,67-74,80-100,138-147 1vz7 d1vz7a_ A:28-35,67-74,80-100,138-147 1vz6 d1vz6a_ A:28-35,67-74,80-100,138-147 1vz6 d1vz6b_ B:28-35,67-74,80-100,138-147 1vz7 d1vz7b_ B:28-35,67-74,81-100,138-147 1vz8 d1vz8b_ B:28-35,67-74,81-100,138-147 1vz8 d1vz8d_ D:28-35,67-74,81-100,138-147 1vz8 d1vz8c_ C:28-35,67-74,81-100,139-147 1vz7 d1vz7c_ C:28-35,67-74,81-98,140-147 7. e.41.1 Adenylylcyclase toxin (the edema factor) Domain 1 has topological and active site similarity to the Nucleotidyltransferases (eg. 1kny N-domain); domain 3 binds calmodulin ! Adenylylcyclase toxin (the edema factor) 3 domains: (1&2) alpha+beta, with domain 2 being inserted in domain 1; (3) all-alpha 1lvc d1lvca_ A:323-329,493-500,550-568,607-623 1lvc d1lvcc_ C:323-329,493-500,550-568,607-623 1k90 d1k90c_ C:323-329,493-500,550-568,607-623 1sk6 d1sk6c_ C:323-329,493-500,550-568,607-623 1k90 d1k90a_ A:323-329,493-500,550-568,607-623 1k8t d1k8ta_ A:323-329,493-500,550-568,607-623 1pk0 d1pk0a_ A:323-329,493-500,550-568,607-623 1pk0 d1pk0b_ B:323-329,493-500,550-568,607-623 1k93 d1k93a_ A:323-329,493-500,550-568,607-623 1pk0 d1pk0c_ C:323-329,493-500,550-568,607-623 1k90 d1k90b_ B:323-329,493-500,550-568,607-623 1s26 d1s26a_ A:323-329,493-500,550-568,607-623 1k93 d1k93c_ C:323-329,493-500,550-568,607-623 1s26 d1s26c_ C:323-329,493-500,550-568,607-623 1sk6 d1sk6a_ A:323-329,493-500,550-568,607-623 1k93 d1k93b_ B:323-329,493-500,550-568,607-623 1s26 d1s26b_ B:323-329,493-500,550-568,607-623 1sk6 d1sk6b_ B:323-329,493-500,550-568,607-623 1lvc d1lvcb_ B:323-329,493-500,550-568,607-623 8. d.172.1 gp120 core gp120 core unusual fold 1g9m d1g9mg_ G:269-274,283-289,334-354,474-486 2ny0 d2ny0a1 A:269-274,283-289,334-354,474-486 2ny1 d2ny1a1 A:269-274,283-289,334-354,474-486 1rzj d1rzjg_ G:269-274,283-289,334-354,474-486 2ny6 d2ny6a1 A:269-274,283-289,334-354,474-486 1g9n d1g9ng_ G:269-274,283-289,334-354,474-486 2ny5 d2ny5g1 G:269-274,283-289,334-354,474-486 2nxz d2nxza1 A:269-274,283-289,334-354,474-486 2i5y d2i5yp1 P:269-274,283-289,334-354,474-486 2ny3 d2ny3a1 A:269-274,283-289,334-354,474-486 2nxy d2nxya1 A:269-274,283-289,334-354,474-486 2ny4 d2ny4a1 A:269-274,283-289,334-354,474-486 2ny2 d2ny2a1 A:269-274,283-289,334-354,474-486 2i60 d2i60p1 P:269-274,283-289,334-354,474-486 2b4c d2b4cg1 G:269-274,283-289,334-354,474-486 2i60 d2i60g1 G:269-274,283-289,334-354,474-486 1yyl d1yylp1 P:1269-1274,1283-1289,1334-1354,1474-1486 1yym d1yymp1 P:1269-1274,1283-1289,1334-1354,1474-1486 2i5y d2i5yg1 G:269-274,283-289,334-354,474-486 1yym d1yymg1 G:269-274,283-289,334-354,474-486 1yyl d1yylg1 G:269-274,283-289,334-354,474-486 1rzk d1rzkg_ G:269-274,283-289,334-354,474-484 2ny7 d2ny7g1 G:269-274,283-289,334-354,474-486 1gc1 d1gc1g_ G:269-274,283-289,334-349,474-486 11. d.165.1 Ribosome inactivating proteins (RIP) Ribosome inactivating proteins (RIP) contains mixed beta-sheet 1abr d1abra_ A:72-81,82-88,91-100,147-169 1cf5 d1cf5a_ A:68-77,78-84,87-94,141-163 1hwn d1hwna_ A:75-84,85-91,94-101,150-162 1lp8 d1lp8a_ A:50-59,60-70,96-105,160-182 1cf5 d1cf5b_ B:68-77,78-84,87-94,141-163 1lpd d1lpda_ A:50-59,60-70,96-105,160-182 1lpc d1lpca_ A:50-59,60-70,96-105,160-182 2r3d d2r3da1 A:78-87,88-94,97-109,160-182 1rl0 d1rl0a_ A:50-59,60-70,96-105,160-182 2q3n d2q3na1 A:72-80,81-87,90-97,146-168 1puu d1puua_ A:74-83,84-91,95-102,148-170 1uq4 d1uq4a_ A:78-87,88-94,97-109,160-182 1sz6 d1sz6a_ A:74-83,84-91,95-102,148-170 1uq5 d1uq5a_ A:78-87,88-94,97-109,160-182 1br5 d1br5a_ A:78-87,88-94,97-109,160-182 2p8n d2p8na1 A:78-87,88-94,97-109,160-182 2r2x d2r2xa1 A:78-87,88-94,97-109,160-182 1rzo d1rzoa_ A:1078-1087,1088-1094,1097-1109,1159-1181 2aai d2aaia_ A:78-87,88-94,97-109,160-182 1ifu d1ifua_ A:78-87,88-94,97-109,160-182 2pjo d2pjoa1 A:78-87,88-94,97-109,160-182 1j1m d1j1ma_ A:78-87,88-94,97-109,160-182 1il5 d1il5a_ A:78-87,88-94,97-109,160-182 1rzo d1rzoc_ C:1078-1087,1088-1094,1097-1109,1159-1181 1ifs d1ifsa_ A:78-87,88-94,97-109,160-182 1rtc d1rtca_ A:78-87,88-94,97-109,160-182 1ift d1ifta_ A:78-87,88-94,97-109,160-182 1il4 d1il4a_ A:78-87,88-94,97-107,160-182 1br6 d1br6a_ A:78-87,88-94,97-109,160-182 1obt d1obta_ A:78-87,88-94,97-109,160-182 1il3 d1il3a_ A:78-87,88-94,97-107,160-182 2jdl d2jdla1 A:68-77,78-83,85-95,146-159 1obs d1obsa_ A:78-87,88-94,97-109,160-182 1il9 d1il9a_ A:78-87,88-94,97-107,160-182 1il5 d1il5b_ B:78-87,88-94,97-107,160-182 1d8v d1d8va_ A:68-77,78-83,83-96,141-163 1mrg d1mrga_ A:68-77,78-84,85-95,143-165 1mom d1moma_ A:68-77,78-84,85-95,143-165 1f8q d1f8qa_ A:68-77,78-84,85-95,143-165 1nio d1nioa_ A:69-78,79-84,86-96,146-158 1giu d1giua_ A:68-77,78-85,85-95,143-165 1j4g d1j4ga_ A:68-77,78-83,85-95,143-165 1mrj d1mrja_ A:68-77,78-85,85-95,143-165 1qcj d1qcja_ A:70-80,84-92,94-107,159-181 1j4g d1j4gd_ D:68-77,78-85,85-95,143-165 1nli d1nlia_ A:68-77,78-85,85-95,143-165 1mrk d1mrka_ A:68-77,78-85,85-95,143-165 2jdl d2jdlb1 B:68-77,78-85,85-95,143-165 1qcj d1qcjb_ B:70-80,84-92,94-107,159-181 1tcs d1tcsa_ A:68-77,78-85,85-95,143-165 1ahb d1ahba_ A:68-77,78-85,85-95,143-165 1gis d1gisa_ A:69-78,79-84,86-96,144-166 1bry d1bryy_ Y:68-77,78-85,85-95,143-165 1bry d1bryz_ Z:68-77,78-85,85-95,143-165 1j4g d1j4gb_ B:68-77,78-85,85-95,143-165 1mri d1mria_ A:68-77,78-85,85-95,143-165 1ahc d1ahca_ A:68-77,78-85,85-95,143-165 1hwo d1hwoa_ A:75-84,85-91,94-101,150-167 1j4g d1j4gc_ C:68-77,78-85,85-95,143-165 1lln d1llna_ A:67-78,79-86,90-99,151-177 1hwp d1hwpa_ A:75-84,85-91,94-101,150-168 1hwm d1hwma_ A:75-84,85-91,94-101,149-168 1j1q d1j1qa_ A:70-81,82-90,93-106,158-180 1j1s d1j1sa_ A:70-81,82-90,93-106,158-180 1j1r d1j1ra_ A:70-81,82-90,93-106,158-180 1gik d1gika_ A:70-81,82-90,93-106,158-180 1qcg d1qcga_ A:70-81,83-92,94-107,159-181 1qcg d1qcgb_ B:70-81,83-92,94-107,159-181 1qci d1qcib_ B:70-81,83-92,94-107,159-181 1qci d1qcia_ A:70-81,83-92,94-107,159-181 3ctk d3ctka1 A:68-79,80-89,91-98,148-170 1d6a d1d6ab_ B:70-81,83-92,94-107,159-181 1d6a d1d6aa_ A:70-81,83-92,94-107,159-181 1apa d1apaa_ A:75-86,87-96,99-112,163-185 1paf d1pafa_ A:70-81,83-92,94-107,159-181 1pag d1paga_ A:70-81,83-92,94-107,159-181 1pag d1pagb_ B:70-81,83-92,94-107,159-181 1paf d1pafb_ B:70-81,83-92,94-107,159-181 12. d.250.1 Folate-binding domain some topological similarity to Formylmethanofuran:tetrahydromethanopterin formyltransferase ! Folate-binding domain duplication: consists of two beta(2)-alpha-beta(3)-alpha subdomains swapped with the first strands 1woo d1wooa2 A:42-49,140-149,149-159,223-235 1vlo d1vloa2 A:43-50,141-150,150-160,220-232 1v5v d1v5va2 A:46-53,150-159,159-170,247-259 1wop d1wopa2 A:42-49,140-149,149-159,223-235 1v5v d1v5vb2 B:46-53,150-159,159-170,247-259 1wor d1wora2 A:42-49,140-149,149-159,223-235 1wos d1wosa2 A:42-49,140-149,149-159,223-235 1pj7 d1pj7a4 A:499-506,601-610,610-621,686-698 1pj6 d1pj6a4 A:499-506,601-610,610-621,686-698 1pj5 d1pj5a4 A:499-506,601-610,610-621,686-698