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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DATP LT(0, 3) COMPLEX
Keywords DNA DAMAGE, DNA REPAIR, DNA-BINDING, DNA-DIRECTED DNA POLYME NUCLEOTIDYLTRANSFERASE, SOS RESPONSE, TRANSFERASE, TRANSFER COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3K5L     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   DNA POLYMERASE II  A 781 6331 0
2  Other macromolecule   DNA (5'-D(*TP*AP*TP*(3DR) P*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')  T 18 346 11
3  DNA    P 13 244 18
4  Ligand   DNA POLYMERASE II  A 3 0 32
5 Water     75 0 75
total       890 6921 136
Proteins
Unit 1 GLY-2 PRO-1 HIS0 MET1 ALA2 GLN3 ALA4 GLY5 PHE6 ILE7 LEU8 THR9 ARG10 HIS11 TRP12 ARG13 ASP14 THR15 PRO16 GLN17 GLY18 THR19 GLU20 VAL21 SER22 PHE23 TRP24 LEU25 ALA26 THR27 ASP28 ASN29 GLY30 PRO31 LEU32 GLN33 VAL34 THR35 LEU36 ALA37 PRO38 GLN39 GLU40 SER41 VAL42 ALA43 PHE44 ILE45 PRO46 ALA47 ASP48 GLN49 VAL50 PRO51 ARG52 ALA53 GLN54 HIS55 ILE56 LEU57 GLN58 GLY59 GLU60 GLN61 GLY62 PHE63 ARG64 LEU65 THR66 PRO67 LEU68 ALA69 LEU70 LYS71 ASP72 PHE73 HIS74 ARG75 GLN76 PRO77 VAL78 TYR79 GLY80 LEU81 TYR82 CYS83 ARG84 ALA85 HIS86 ARG87 GLN88 LEU89 MET90 ASN91 TYR92 GLU93 LYS94 ARG95 LEU96 ARG97 GLU98 GLY99 GLY100 VAL101 THR102 VAL103 TYR104 GLU105 ALA106 ASP107 VAL108 ARG109 PRO110 PRO111 GLU112 ARG113 TYR114 LEU115 MET116 GLU117 ARG118 PHE119 ILE120 THR121 SER122 PRO123 VAL124 TRP125 VAL126 GLU127 GLY128 ASP129 MET130 HIS131 ASN132 GLY133 THR134 ILE135 VAL136 ASN137 ALA138 ARG139 LEU140 LYS141 PRO142 HIS143 PRO144 ASP145 TYR146 ARG147 PRO148 PRO149 LEU150 LYS151 TRP152 VAL153 SER154 ILE155 ASP156 ILE157 GLU158 THR159 THR160 ARG161 HIS162 GLY163 GLU164 LEU165 TYR166 CYS167 ILE168 GLY169 LEU170 GLU171 GLY172 CYS173 GLY174 GLN175 ARG176 ILE177 VAL178 TYR179 MET180 LEU181 GLY182 PRO183 GLU184 ASN185 GLY186 ASP187 ALA188 SER189 SER190 LEU191 ASP192 PHE193 GLU194 LEU195 GLU196 TYR197 VAL198 ALA199 SER200 ARG201 PRO202 GLN203 LEU204 LEU205 GLU206 LYS207 LEU208 ASN209 ALA210 TRP211 PHE212 ALA213 ASN214 TYR215 ASP216 PRO217 ASP218 VAL219 ILE220 ILE221 GLY222 TRP223 ASN224 VAL225 VAL226 GLN227 PHE228 ASP229 LEU230 ARG231 MET232 LEU233 GLN234 LYS235 HIS236 ALA237 GLU238 ARG239 TYR240 ARG241 LEU242 PRO243 LEU244 ARG245 LEU246 GLY247 ARG248 ASP249 ASN250 SER251 GLU252 LEU253 GLU254 TRP255 ARG256 GLU257 HIS258 GLY259 PHE260 LYS261 ASN262 GLY263 VAL264 PHE265 PHE266 ALA267 GLN268 ALA269 LYS270 GLY271 ARG272 LEU273 ILE274 ILE275 ASP276 GLY277 ILE278 GLU279 ALA280 LEU281 LYS282 SER283 ALA284 PHE285 TRP286 ASN287 PHE288 SER289 SER290 PHE291 SER292 LEU293 GLU294 THR295 VAL296 ALA297 GLN298 GLU299 LEU300 LEU301 GLY302 GLU303 GLY304 LYS305 SER306 ILE307 ASP308 ASN309 PRO310 TRP311 ASP312 ARG313 MET314 ASP315 GLU316 ILE317 ASP318 ARG319 ARG320 PHE321 ALA322 GLU323 ASP324 LYS325 PRO326 ALA327 LEU328 ALA329 THR330 TYR331 ASN332 LEU333 LYS334 ASN335 CYS336 GLU337 LEU338 VAL339 THR340 GLN341 ILE342 PHE343 HIS344 LYS345 THR346 GLU347 ILE348 MET349 PRO350 PHE351 LEU352 LEU353 GLU354 ARG355 ALA356 THR357 VAL358 ASN359 GLY360 LEU361 PRO362 VAL363 ASP364 ARG365 HIS366 GLY367 GLY368 SER369 VAL370 ALA371 ALA372 PHE373 GLY374 HIS375 LEU376 TYR377 PHE378 PRO379 ARG380 MET381 HIS382 ARG383 ALA384 GLY385 TYR386 VAL387 ALA388 PRO389 ASN390 LEU391 GLY392 GLU393 VAL394 PRO395 PRO396 HIS397 ALA398 SER399 PRO400 GLY401 GLY402 TYR403 VAL404 MET405 ASP406 SER407 ARG408 PRO409 GLY410 LEU411 TYR412 ASP413 SER414 VAL415 LEU416 VAL417 LEU418 ASP419 TYR420 LYS421 SER422 LEU423 TYR424 PRO425 SER426 ILE427 ILE428 ARG429 THR430 PHE431 LEU432 ILE433 ASP434 PRO435 VAL436 GLY437 LEU438 VAL439 GLU440 GLY441 MET442 ALA443 GLN444 PRO445 ASP446 PRO447 GLU448 HIS449 SER450 THR451 GLU452 GLY453 PHE454 LEU455 ASP456 ALA457 TRP458 PHE459 SER460 ARG461 GLU462 LYS463 HIS464 CYS465 LEU466 PRO467 GLU468 ILE469 VAL470 THR471 ASN472 ILE473 TRP474 HIS475 GLY476 ARG477 ASP478 GLU479 ALA480 LYS481 ARG482 GLN483 GLY484 ASN485 LYS486 PRO487 LEU488 SER489 GLN490 ALA491 LEU492 LYS493 ILE494 ILE495 MET496 ASN497 ALA498 PHE499 TYR500 GLY501 VAL502 LEU503 GLY504 THR505 THR506 ALA507 CYS508 ARG509 PHE510 PHE511 ASP512 PRO513 ARG514 LEU515 ALA516 SER517 SER518 ILE519 THR520 MET521 ARG522 GLY523 HIS524 GLN525 ILE526 MET527 ARG528 GLN529 THR530 LYS531 ALA532 LEU533 ILE534 GLU535 ALA536 GLN537 GLY538 TYR539 ASP540 VAL541 ILE542 TYR543 GLY544 ASP545 THR546 ASP547 SER548 THR549 PHE550 VAL551 TRP552 LEU553 LYS554 GLY555 ALA556 HIS557 SER558 GLU559 GLU560 GLU561 ALA562 ALA563 LYS564 ILE565 GLY566 ARG567 ALA568 LEU569 VAL570 GLN571 HIS572 VAL573 ASN574 ALA575 TRP576 TRP577 ALA578 GLU579 THR580 LEU581 GLN582 LYS583 GLN584 ARG585 LEU586 THR587 SER588 ALA589 LEU590 GLU591 LEU592 GLU593 TYR594 GLU595 THR596 HIS597 PHE598 CYS599 ARG600 PHE601 LEU602 MET603 PRO604 THR605 ILE606 ARG607 GLY608 ALA609 ASP610 THR611 GLY612 SER613 LYS614 LYS615 ARG616 TYR617 ALA618 GLY619 LEU620 ILE621 GLN622 GLU623 GLY624 ASP625 LYS626 GLN627 ARG628 MET629 VAL630 PHE631 LYS632 GLY633 LEU634 GLU635 THR636 VAL637 ARG638 THR639 ASP640 TRP641 THR642 PRO643 LEU644 ALA645 GLN646 GLN647 PHE648 GLN649 GLN650 GLU651 LEU652 TYR653 LEU654 ARG655 ILE656 PHE657 ARG658 ASN659 GLU660 PRO661 TYR662 GLN663 GLU664 TYR665 VAL666 ARG667 GLU668 THR669 ILE670 ASP671 LYS672 LEU673 MET674 ALA675 GLY676 GLU677 LEU678 ASP679 ALA680 ARG681 LEU682 VAL683 TYR684 ARG685 LYS686 ARG687 LEU688 ARG689 ARG690 PRO691 LEU692 SER693 GLU694 TYR695 GLN696 ARG697 ASN698 VAL699 PRO700 PRO701 HIS702 VAL703 ARG704 ALA705 ALA706 ARG707 LEU708 ALA709 ASP710 GLU711 GLU712 ASN713 GLN714 LYS715 ARG716 GLY717 ARG718 PRO719 LEU720 GLN721 TYR722 GLN723 ASN724 ARG725 GLY726 THR727 ILE728 LYS729 TYR730 VAL731 TRP732 THR733 THR734 ASN735 GLY736 PRO737 GLU738 PRO739 LEU740 ASP741 TYR742 GLN743 ARG744 SER745 PRO746 LEU747 ASP748 TYR749 GLU750 HIS751 TYR752 LEU753 THR754 ARG755 GLN756 LEU757 GLN758 PRO759 VAL760 ALA761 GLU762 GLY763 ILE764 LEU765 PRO766 PHE767 ILE768 GLU769 ASP770 ASN771 PHE772 ALA773 THR774 LEU775 MET776 THR777 GLY778
Nucleic acids
Unit 3 DG901 DT902 DG903 DC904 DC905 DT906 DA907 DG908 DC909 DG910 DT911 DA912 DOC913
Other macromolecules
Unit 2 DT801 DA802 DT803 3DR804 DG805 DT806 DA807 DC808 DG809 DC810 DT811 DA812 DG813 DG814 DC815 DA816 DC817 DA818
Ligands
Unit 4 DTP914 MG1001 MG1002
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