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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURAL BASIS FOR INTERACTION OF THE RIBOSOME WITH THE SW REGIONS OF GTP-BOUND ELONGATION FACTORS
Keywords RNA-PROTEIN COMPLEX, RIBOSOME
Experiment ELECTRON MICROSCOPY
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2OM7     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  RNA    A 12 256 0
2  RNA    B 10 214 0
3  RNA    C 96 2069 0
4  RNA    D 13 278 0
5  RNA    F 29 624 0
6  RNA    G 54 1172 0
7  RNA    H 42 898 0
8  RNA    I 58 1241 0
9  RNA    J 73 1569 0
10  RNA    M 74 1448 122
11  Protein   30S RIBOSOMAL PROTEIN S12  E 125 971 0
12  Protein   50S RIBOSOMAL PROTEIN L1  K 191 1142 0
13  Protein   ELONGATION FACTOR G  L 655 5126 0
14  Protein   30S RIBOSOMAL PROTEIN S2  N 235 1901 0
total       1667 18909 122
Proteins
Unit 11 PRO5 THR6 ILE7 ASN8 GLN9 LEU10 VAL11 ARG12 LYS13 GLY14 ARG15 GLU16 LYS17 VAL18 ARG19 LYS20 LYS21 SER22 LYS23 VAL24 PRO25 ALA26 LEU27 LYS28 GLY29 ALA30 PRO31 PHE32 ARG33 ARG34 GLY35 VAL36 CYS37 THR38 VAL39 VAL40 ARG41 THR42 VAL43 THR44 PRO45 LYS46 LYS47 PRO48 ASN49 SER50 ALA51 LEU52 ARG53 LYS54 VAL55 ALA56 LYS57 VAL58 ARG59 LEU60 THR61 SER62 GLY63 TYR64 GLU65 VAL66 THR67 ALA68 TYR69 ILE70 PRO71 GLY72 GLU73 GLY74 HIS75 ASN76 LEU77 GLN78 GLU79 HIS80 SER81 VAL82 VAL83 LEU84 ILE85 ARG86 GLY87 GLY88 ARG89 VAL90 LYS91 ASP92 LEU93 PRO94 GLY95 VAL96 ARG97 TYR98 HIS99 ILE100 VAL101 ARG102 GLY103 VAL104 TYR105 ASP106 ALA107 ALA108 GLY109 VAL110 LYS111 ASP112 ARG113 LYS114 LYS115 SER116 ARG117 SER118 LYS119 TYR120 GLY121 THR122 LYS123 LYS124 PRO125 LYS126 GLU127 ALA128 ALA129
Unit 12 LYS18 VAL19 TYR20 THR21 ILE22 ASP23 GLU24 ALA25 ALA26 ARG27 THR34 ALA35 LYS36 PHE37 ASP38 GLU39 THR40 VAL41 GLU42 VAL43 HIS44 ALA45 LYS46 LEU47 GLY48 ILE49 ASP50 PRO51 ARG52 ARG53 SER54 ASP55 GLN56 ASN57 VAL58 ARG59 GLY60 THR61 VAL62 SER63 LEU64 PRO65 HIS66 GLY67 LEU68 GLY69 LYS70 GLN71 VAL72 ARG73 VAL74 LEU75 ALA76 ILE77 ALA78 LYS79 GLY80 GLU81 LYS82 ILE83 LYS84 GLU85 ALA86 GLU87 GLU88 ALA89 GLY90 ALA91 ASP92 TYR93 VAL94 GLY95 GLY96 GLU97 GLU98 ILE99 ILE100 GLN101 LYS102 ILE103 LEU104 ASP105 GLY106 TRP107 MET108 ASP109 PHE110 VAL119 MET120 GLY121 ALA122 VAL123 GLY124 SER125 LYS126 LEU127 GLY128 ARG129 ILE130 LEU131 GLY132 PRO133 ARG134 GLY135 LEU136 ASN139 PRO140 LYS141 ALA142 GLY143 THR144 VAL145 GLY146 PHE147 ASN148 ILE149 GLY150 GLU151 ILE152 ILE153 ARG154 GLU155 ILE156 LYS157 ALA158 GLY159 ARG160 ILE161 GLU162 PHE163 ARG164 ASN165 ASP166 LYS167 THR168 GLY169 ALA170 ILE171 HIS172 ALA173 PRO174 VAL175 GLY176 LYS177 ALA178 SER179 PHE180 PRO181 PRO182 GLU183 LYS184 LEU185 ALA186 ASP187 ASN188 ILE189 ARG190 ALA191 PHE192 ILE193 ARG194 ALA195 LEU196 GLU197 ALA198 HIS199 LYS200 PRO201 GLU202 GLY203 ALA204 LYS205 GLY206 THR207 PHE208 LEU209 ARG210 SER211 VAL212 TYR213 VAL214 THR215 THR216 THR217 MET218 GLY219 PRO220 SER221 VAL222 ARG223 ILE224
Unit 13 GLU6 TYR7 ASP8 LEU9 LYS10 ARG11 LEU12 ARG13 ASN14 ILE15 GLY16 ILE17 ALA18 ALA19 HIS20 ILE21 ASP22 ALA23 GLY24 LYS25 THR26 THR27 THR28 THR29 GLU30 ARG31 ILE32 LEU33 TYR34 TYR35 THR36 GLY37 ARG38 ILE39 ALA68 VAL69 THR70 THR71 CYS72 PHE73 TRP74 LYS75 ASP76 HIS77 ARG78 ILE79 ASN80 ILE81 ILE82 ASP83 THR84 PRO85 GLY86 HIS87 VAL88 ASP89 PHE90 THR91 ILE92 GLU93 VAL94 GLU95 ARG96 SER97 MET98 ARG99 VAL100 LEU101 ASP102 GLY103 ALA104 ILE105 VAL106 VAL107 PHE108 ASP109 SER110 SER111 GLN112 GLY113 VAL114 GLU115 PRO116 GLN117 SER118 GLU119 THR120 VAL121 TRP122 ARG123 GLN124 ALA125 GLU126 LYS127 TYR128 LYS129 VAL130 PRO131 ARG132 ILE133 ALA134 PHE135 ALA136 ASN137 LYS138 MET139 ASP140 LYS141 THR142 GLY143 ALA144 ASP145 LEU146 TRP147 LEU148 VAL149 ILE150 ARG151 THR152 MET153 GLN154 GLU155 ARG156 LEU157 GLY158 ALA159 ARG160 PRO161 VAL162 VAL163 MET164 GLN165 LEU166 PRO167 ILE168 GLY169 ARG170 GLU171 ASP172 THR173 PHE174 SER175 GLY176 ILE177 ILE178 ASP179 VAL180 LEU181 ARG182 MET183 LYS184 ALA185 TYR186 THR187 TYR188 GLY189 ASN190 ASP191 LEU192 GLY193 THR194 ASP195 ILE196 ARG197 GLU198 ILE199 PRO200 ILE201 PRO202 GLU203 GLU204 TYR205 LEU206 ASP207 GLN208 ALA209 ARG210 GLU211 TYR212 HIS213 GLU214 LYS215 LEU216 VAL217 GLU218 VAL219 ALA220 ALA221 ASP222 PHE223 ASP224 GLU225 ASN226 ILE227 MET228 LEU229 LYS230 TYR231 LEU232 GLU233 GLY234 GLU235 GLU236 PRO237 THR238 GLU239 GLU240 GLU241 LEU242 VAL243 ALA244 ALA245 ILE246 ARG247 LYS248 GLY249 THR250 ILE251 ASP252 LEU253 LYS254 ILE255 THR256 PRO257 VAL258 PHE259 LEU260 GLY261 SER262 ALA263 LEU264 LYS265 ASN266 LYS267 GLY268 VAL269 GLN270 LEU271 LEU272 LEU273 ASP274 ALA275 VAL276 VAL277 ASP278 TYR279 LEU280 PRO281 SER282 PRO283 LEU284 ASP285 ILE286 PRO287 PRO288 ILE289 LYS290 GLY291 THR292 THR293 PRO294 GLU295 GLY296 GLU297 VAL298 VAL299 GLU300 ILE301 HIS302 PRO303 ASP304 PRO305 ASN306 GLY307 PRO308 LEU309 ALA310 ALA311 LEU312 ALA313 PHE314 LYS315 ILE316 MET317 ALA318 ASP319 PRO320 TYR321 VAL322 GLY323 ARG324 LEU325 THR326 PHE327 ILE328 ARG329 VAL330 TYR331 SER332 GLY333 THR334 LEU335 THR336 SER337 GLY338 SER339 TYR340 VAL341 TYR342 ASN343 THR344 THR345 LYS346 GLY347 ARG348 LYS349 GLU350 ARG351 VAL352 ALA353 ARG354 LEU355 LEU356 ARG357 MET358 HIS359 ALA360 ASN361 HIS362 ARG363 GLU364 GLU365 VAL366 GLU367 GLU368 LEU369 LYS370 ALA371 GLY372 ASP373 LEU374 GLY375 ALA376 VAL377 VAL378 GLY379 LEU380 LYS381 GLU382 THR383 ILE384 THR385 GLY386 ASP387 THR388 LEU389 VAL390 GLY391 GLU392 ASP393 ALA394 PRO395 ARG396 VAL397 ILE398 LEU399 GLU400 SER401 ILE402 GLU403 VAL404 PRO405 GLU406 PRO407 VAL408 ILE409 ASP410 VAL411 ALA412 ILE413 GLU414 PRO415 LYS416 THR417 LYS418 ALA419 ASP420 GLN421 GLU422 LYS423 LEU424 SER425 GLN426 ALA427 LEU428 ALA429 ARG430 LEU431 ALA432 GLU433 GLU434 ASP435 PRO436 THR437 PHE438 ARG439 VAL440 SER441 THR442 HIS443 PRO444 GLU445 THR446 GLY447 GLN448 THR449 ILE450 ILE451 SER452 GLY453 MET454 GLY455 GLU456 LEU457 HIS458 LEU459 GLU460 ILE461 ILE462 VAL463 ASP464 ARG465 LEU466 LYS467 ARG468 GLU469 PHE470 LYS471 VAL472 ASP473 ALA474 ASN475 VAL476 GLY477 LYS478 PRO479 GLN480 VAL481 ALA482 TYR483 ARG484 GLU485 THR486 ILE487 THR488 LYS489 PRO490 VAL491 ASP492 VAL493 GLU494 GLY495 LYS496 PHE497 ILE498 ARG499 GLN500 THR501 GLY502 GLY503 ARG504 GLY505 GLN506 TYR507 GLY508 HIS509 VAL510 LYS511 ILE512 LYS513 VAL514 GLU515 PRO516 LEU517 PRO518 ARG519 GLY520 SER521 GLY522 PHE523 GLU524 PHE525 VAL526 ASN527 ALA528 ILE529 VAL530 GLY531 GLY532 VAL533 ILE534 PRO535 LYS536 GLU537 TYR538 ILE539 PRO540 ALA541 VAL542 GLN543 LYS544 GLY545 ILE546 GLU547 GLU548 ALA549 MET550 GLN551 SER552 GLY553 PRO554 LEU555 ILE556 GLY557 PHE558 PRO559 VAL560 VAL561 ASP562 ILE563 LYS564 VAL565 THR566 LEU567 TYR568 ASP569 GLY570 SER571 TYR572 HIS573 GLU574 VAL575 ASP576 SER577 SER578 GLU579 MET580 ALA581 PHE582 LYS583 ILE584 ALA585 GLY586 SER587 MET588 ALA589 ILE590 LYS591 GLU592 ALA593 VAL594 GLN595 LYS596 GLY597 ASP598 PRO599 VAL600 ILE601 LEU602 GLU603 PRO604 ILE605 MET606 ARG607 VAL608 GLU609 VAL610 THR611 THR612 PRO613 GLU614 GLU615 TYR616 MET617 GLY618 ASP619 VAL620 ILE621 GLY622 ASP623 LEU624 ASN625 ALA626 ARG627 ARG628 GLY629 GLN630 ILE631 LEU632 GLY633 MET634 GLU635 PRO636 ARG637 GLY638 ASN639 ALA640 GLN641 VAL642 ILE643 ARG644 ALA645 PHE646 VAL647 PRO648 LEU649 ALA650 GLU651 MET652 PHE653 GLY654 TYR655 ALA656 THR657 ASP658 LEU659 ARG660 SER661 LYS662 THR663 GLN664 GLY665 ARG666 GLY667 SER668 PHE669 VAL670 MET671 PHE672 PHE673 ASP674 HIS675 TYR676 GLN677 GLU678 VAL679 PRO680 LYS681 GLN682 VAL683 GLN684 GLU685 LYS686 LEU687 ILE688
Unit 14 VAL7 LYS8 GLU9 LEU10 LEU11 GLU12 ALA13 GLY14 VAL15 HIS16 PHE17 GLY18 HIS19 GLU20 ARG21 LYS22 ARG23 TRP24 ASN25 PRO26 LYS27 PHE28 ALA29 ARG30 TYR31 ILE32 TYR33 ALA34 GLU35 ARG36 ASN37 GLY38 ILE39 HIS40 ILE41 ILE42 ASP43 LEU44 GLN45 LYS46 THR47 MET48 GLU49 GLU50 LEU51 GLU52 ARG53 THR54 PHE55 ARG56 PHE57 ILE58 GLU59 ASP60 LEU61 ALA62 MET63 ARG64 GLY65 GLY66 THR67 ILE68 LEU69 PHE70 VAL71 GLY72 THR73 LYS74 LYS75 GLN76 ALA77 GLN78 ASP79 ILE80 VAL81 ARG82 MET83 GLU84 ALA85 GLU86 ARG87 ALA88 GLY89 MET90 PRO91 TYR92 VAL93 ASN94 GLN95 ARG96 TRP97 LEU98 GLY99 GLY100 MET101 LEU102 THR103 ASN104 PHE105 LYS106 THR107 ILE108 SER109 GLN110 ARG111 VAL112 HIS113 ARG114 LEU115 GLU116 GLU117 LEU118 GLU119 ALA120 LEU121 PHE122 ALA123 SER124 PRO125 GLU126 ILE127 GLU128 GLU129 ARG130 PRO131 LYS132 LYS133 GLU134 GLN135 VAL136 ARG137 LEU138 LYS139 HIS140 GLU141 LEU142 GLU143 ARG144 LEU145 GLN146 LYS147 TYR148 LEU149 SER150 GLY151 PHE152 ARG153 LEU154 LEU155 LYS156 ARG157 LEU158 PRO159 ASP160 ALA161 ILE162 PHE163 VAL164 VAL165 ASP166 PRO167 THR168 LYS169 GLU170 ALA171 ILE172 ALA173 VAL174 ARG175 GLU176 ALA177 ARG178 LYS179 LEU180 PHE181 ILE182 PRO183 VAL184 ILE185 ALA186 LEU187 ALA188 ASP189 THR190 ASP191 SER192 ASP193 PRO194 ASP195 LEU196 VAL197 ASP198 TYR199 ILE200 ILE201 PRO202 GLY203 ASN204 ASP205 ASP206 ALA207 ILE208 ARG209 SER210 ILE211 GLN212 LEU213 ILE214 LEU215 SER216 ARG217 ALA218 VAL219 ASP220 LEU221 ILE222 ILE223 GLN224 ALA225 ARG226 GLY227 GLY228 VAL229 VAL230 GLU231 PRO232 SER233 PRO234 SER235 TYR236 ALA237 LEU238 VAL239 GLN240 GLU241
Nucleic acids
Unit 1 C339 U340 C341 C342 U343 A344 C345 G346 G347 G348 A349 G350
Unit 2 U367 U368 C369 C370 G371 C390 G391 G392 A393 G394
Unit 3 G1401 C1402 C1403 C1404 G1405 U1406 C1407 A1408 C1409 G1410 C1411 C1412 A1413 U1414 G1415 G1416 G1417 A1418 G1419 C1420 G1421 G1422 G1423 C1424 U1425 C1426 U1427 A1428 C1429 C1430 C1431 G1432 A1433 A1434 G1435 U1436 C1437 G1438 C1439 C1440 G1441 G1442 G1442A A1442B G1443 C1444 C1445 U1446 A1447 C1452 G1456 G1457 G1458 C1459 A1460 G1461 G1462 C1463 G1464 C1465 C1466 G1467 A1468 G1469 G1470 G1471 U1472 A1473 G1474 G1475 G1476 C1477 C1478 C1479 G1480 U1481 G1482 A1483 C1484 U1485 G1486 G1487 G1488 G1489 C1490 G1491 A1492 A1493 G1494 U1495 C1496 G1497 U1498 A1499 A1500 C1501
Unit 4 G52 A53 C54 A55 U56 G57 C58 G354 C355 A356 G357 U358 U359
Unit 5 C2646 U2647 C2648 U2649 U2650 C2651 C2652 U2653 A2654 G2655 U2656 A2657 C2658 G2659 A2660 G2661 A2662 G2663 G2664 A2665 C2666 C2667 G2668 G2669 A2670 A2671 G2672 G2673 G2674
Unit 6 G1840 U1841 G1842 C1843 C1844 G1845 G1846 A1847 A1848 G1849 G1850 U1851 C1852 A1853 A1854 G1855 G1856 G1857 G1858 A1859 G1860 G1861 G1862 G1863 U1864 G1865 C1866 A1876 A1877 G1878 C1879 C1880 C1881 C1882 G1883 A1884 A1885 C1886 C1887 G1888 A1889 A1890 G1891 C1892 C1893 C1894 C1895 G1896 G1897 U1898 G1899 A1900 A1901 C1902
Unit 7 G2455 C2456 U2457 G2458 A2459 U2460 C2461 U2462 C2463 C2464 C2465 C2466 C2467 G2468 A2469 G2470 C2471 G2472 U2473 C2474 C2475 A2476 C2477 A2478 G2479 C2480 G2481 G2482 C2483 G2484 G2485 G2486 G2487 A2488 G2489 G2490 U2491 U2492 U2493 G2494 G2495 C2496
Unit 8 G1051 C1052 C1053 A1054 G1055 G1056 A1057 G1058 G1059 U1060 U1061 G1062 G1063 C1064 U1065 U1066 A1067 G1068 A1069 A1070 G1071 C1072 A1073 G1074 C1075 C1076 A1077 U1078 C1079 C1080 U1081 U1082 U1083 A1084 A1085 A1086 G1087 A1088 G1089 U1090 G1091 C1092 G1093 U1094 A1095 A1096 U1097 A1098 G1099 C1100 U1101 C1102 A1103 C1104 U1105 G1106 G1107 U1108
Unit 9 G2094 C2095 U2096 C2097 U2098 U2099 G2100 G2101 U2102 C2103 G2104 C2105 G2106 C2107 C2108 U2109 G2110 C2111 G2112 U2113 A2114 G2115 G2116 A2117 U2118 A2119 G2120 G2121 U2122 G2123 G2124 G2125 A2126 G2127 C2128 C2129 U2130 G2159 G2160 C2161 G2162 C2163 C2164 G2165 G2166 U2167 G2168 A2169 A2170 A2171 U2172 C2174 C2175 A2176 C2177 C2178 C2179 U2180 G2181 G2182 C2183 G2184 C2185 G2186 G2187 C2188 U2189 G2190 G2191 G2192 G2193 G2194 C2195
Unit 10 U1 C2 C3 G4 U5 G6 A7 4SU8 A9 A10 C11 A12 A13 A14 G15 C16 G18 G19 H2U20 H2U21 A22 U23 G24 U25 A26 C27 C28 G29 G30 A31 U32 U33 U34 U35 U36 A37 U38 U39 C40 C41 G42 G43 C44 U45 A46 U48 5MC49 G50 G51 G52 G53 5MU54 PSU55 C56 A57 A58 U59 U60 C61 C62 C63 C64 G65 U66 C67 G68 C69 G70 G71 A72 G73 C74 C75 A76
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany