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Sequence, Chains, Asymmetric and Biological Units

Title T7 DNA POLYMERASE TERNARY COMPLEX WITH 8 OXO GUANOSINE AND DCMP AT THE ELONGATION SITE
Keywords 8-OXOGUANOSINE DNA POLYMERASE, TRANSFERASE/ELECTRON TRANSPORT/DNA COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   1TKD     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  DNA    P 16 307 18
2  Other macromolecule   DNA (5'-D(*CP*CP*CP*AP*(8OG) P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP* CP*G)-3')  T 19 368 23
3  Protein   DNA POLYMERASE  A 698 5534 0
4  Protein   THIOREDOXIN 1  B 105 802 0
5  Ligand   DNA POLYMERASE  A 9 0 74
6 Water     716 0 716
total       1563 7011 831
Proteins
Unit 3 MET1 ILE2 VAL3 SER4 ASP5 ILE6 GLU7 ALA8 ASN9 ALA10 LEU11 LEU12 GLU13 SER14 VAL15 THR16 LYS17 PHE18 HIS19 CYS20 GLY21 VAL22 ILE23 TYR24 ASP25 TYR26 SER27 THR28 ALA29 GLU30 TYR31 VAL32 SER33 TYR34 ARG35 PRO36 SER37 ASP38 PHE39 GLY40 ALA41 TYR42 LEU43 ASP44 ALA45 LEU46 GLU47 ALA48 GLU49 VAL50 ALA51 ARG52 GLY53 GLY54 LEU55 ILE56 VAL57 PHE58 HIS59 ASN60 GLY61 HIS62 LYS63 TYR64 ASP65 VAL66 PRO67 ALA68 LEU69 THR70 LYS71 LEU72 ALA73 LYS74 LEU75 GLN76 LEU77 ASN78 ARG79 GLU80 PHE81 HIS82 LEU83 PRO84 ARG85 GLU86 ASN87 CYS88 ILE89 ASP90 THR91 LEU92 VAL93 LEU94 SER95 ARG96 LEU97 ILE98 HIS99 SER100 ASN101 LEU102 LYS103 ASP104 THR105 ASP106 MET107 GLY108 LEU109 LEU110 ARG111 SER112 GLY113 LYS114 LEU115 PRO116 GLY117 ALA124 LEU125 GLU126 ALA127 TRP128 GLY129 TYR130 ARG131 LEU132 GLY133 GLU134 MET135 LYS136 GLY137 GLU138 TYR139 LYS140 ASP141 ASP142 PHE143 LYS144 ARG145 MET146 LEU147 GLU148 GLU149 GLN150 GLY151 GLU152 GLU153 TYR154 VAL155 ASP156 GLY157 MET158 GLU159 TRP160 TRP161 ASN162 PHE163 ASN164 GLU165 GLU166 MET167 MET168 ASP169 TYR170 ASN171 VAL172 GLN173 ASP174 VAL175 VAL176 VAL177 THR178 LYS179 ALA180 LEU181 LEU182 GLU183 LYS184 LEU185 LEU186 SER187 ASP188 LYS189 HIS190 TYR191 PHE192 PRO193 PRO194 GLU195 ILE196 ASP197 PHE198 THR199 ASP200 VAL201 GLY202 TYR203 THR204 THR205 PHE206 TRP207 SER208 GLU209 SER210 LEU211 GLU212 ALA213 VAL214 ASP215 ILE216 GLU217 HIS218 ARG219 ALA220 ALA221 TRP222 LEU223 LEU224 ALA225 LYS226 GLN227 GLU228 ARG229 ASN230 GLY231 PHE232 PRO233 PHE234 ASP235 THR236 LYS237 ALA238 ILE239 GLU240 GLU241 LEU242 TYR243 VAL244 GLU245 LEU246 ALA247 ALA248 ARG249 ARG250 SER251 GLU252 LEU253 LEU254 ARG255 LYS256 LEU257 THR258 GLU259 THR260 PHE261 GLY262 SER263 TRP264 TYR265 GLN266 PRO267 LYS268 GLY269 GLY270 THR271 GLU272 MET273 PHE274 CYS275 HIS276 PRO277 ARG278 THR279 GLY280 LYS281 PRO282 LEU283 PRO284 LYS285 TYR286 PRO287 ARG288 ILE289 LYS290 THR291 PRO292 LYS293 VAL294 GLY295 GLY296 ILE297 PHE298 LYS299 LYS300 PRO301 LYS302 ASN303 LYS304 ALA305 GLN306 ARG307 GLU308 GLY309 ARG310 GLU311 PRO312 CYS313 GLU314 LEU315 ASP316 THR317 ARG318 GLU319 TYR320 VAL321 ALA322 GLY323 ALA324 PRO325 TYR326 THR327 PRO328 VAL329 GLU330 HIS331 VAL332 VAL333 PHE334 ASN335 PRO336 SER337 SER338 ARG339 ASP340 HIS341 ILE342 GLN343 LYS344 LYS345 LEU346 GLN347 GLU348 ALA349 GLY350 TRP351 VAL352 PRO353 THR354 LYS355 TYR356 THR357 ASP358 LYS359 GLY360 ALA361 PRO362 VAL363 VAL364 ASP365 ASP366 GLU367 VAL368 LEU369 GLU370 GLY371 VAL372 ARG373 VAL374 ASP375 ASP376 PRO377 GLU378 LYS379 GLN380 ALA381 ALA382 ILE383 ASP384 LEU385 ILE386 LYS387 GLU388 TYR389 LEU390 MET391 ILE392 GLN393 LYS394 ARG395 ILE396 GLY397 GLN398 SER399 ALA400 GLU401 GLY402 ASP403 LYS404 ALA405 TRP406 LEU407 ARG408 TYR409 VAL410 ALA411 GLU412 ASP413 GLY414 LYS415 ILE416 HIS417 GLY418 SER419 VAL420 ASN421 PRO422 ASN423 GLY424 ALA425 VAL426 THR427 GLY428 ARG429 ALA430 THR431 HIS432 ALA433 PHE434 PRO435 ASN436 LEU437 ALA438 GLN439 ILE440 PRO441 GLY442 VAL443 ARG444 SER445 PRO446 TYR447 GLY448 GLU449 GLN450 CYS451 ARG452 ALA453 ALA454 PHE455 GLY456 ALA457 GLU458 HIS459 HIS460 LEU461 ASP462 GLY463 ILE464 THR465 GLY466 LYS467 PRO468 TRP469 VAL470 GLN471 ALA472 GLY473 ILE474 ASP475 ALA476 SER477 GLY478 LEU479 GLU480 LEU481 ARG482 CYS483 LEU484 ALA485 HIS486 PHE487 MET488 ALA489 ARG490 PHE491 ASP492 ASN493 GLY494 GLU495 TYR496 ALA497 HIS498 GLU499 ILE500 LEU501 ASN502 GLY503 ASP504 ILE505 HIS506 THR507 LYS508 ASN509 GLN510 ILE511 ALA512 ALA513 GLU514 LEU515 PRO516 THR517 ARG518 ASP519 ASN520 ALA521 LYS522 THR523 PHE524 ILE525 TYR526 GLY527 PHE528 LEU529 TYR530 GLY531 ALA532 GLY533 ASP534 GLU535 LYS536 ILE537 GLY538 GLN539 ILE540 VAL541 GLY542 ALA543 GLY544 LYS545 GLU546 ARG547 GLY548 LYS549 GLU550 LEU551 LYS552 LYS553 LYS554 PHE555 LEU556 GLU557 ASN558 THR559 PRO560 ALA561 ILE562 ALA563 ALA564 LEU565 ARG566 GLU567 SER568 ILE569 GLN570 GLN571 THR572 LEU573 VAL574 GLU575 SER576 SER577 GLN578 TRP579 VAL580 ALA581 GLY582 GLU583 GLN584 GLN585 VAL586 LYS587 TRP588 LYS589 ARG590 ARG591 TRP592 ILE593 LYS594 GLY595 LEU596 ASP597 GLY598 ARG599 LYS600 VAL601 HIS602 VAL603 ARG604 SER605 PRO606 HIS607 ALA608 ALA609 LEU610 ASN611 THR612 LEU613 LEU614 GLN615 SER616 ALA617 GLY618 ALA619 LEU620 ILE621 CYS622 LYS623 LEU624 TRP625 ILE626 ILE627 LYS628 THR629 GLU630 GLU631 MET632 LEU633 VAL634 GLU635 LYS636 GLY637 LEU638 LYS639 HIS640 GLY641 TRP642 ASP643 GLY644 ASP645 PHE646 ALA647 TYR648 MET649 ALA650 TRP651 VAL652 HIS653 ASP654 GLU655 ILE656 GLN657 VAL658 GLY659 CYS660 ARG661 THR662 GLU663 GLU664 ILE665 ALA666 GLN667 VAL668 VAL669 ILE670 GLU671 THR672 ALA673 GLN674 GLU675 ALA676 MET677 ARG678 TRP679 VAL680 GLY681 ASP682 HIS683 TRP684 ASN685 PHE686 ARG687 CYS688 LEU689 LEU690 ASP691 THR692 GLU693 GLY694 LYS695 MET696 GLY697 PRO698 ASN699 TRP700 ALA701 ILE702 CYS703 HIS704
Unit 4 LYS3 ILE4 ILE5 HIS6 LEU7 THR8 ASP9 ASP10 SER11 PHE12 ASP13 THR14 ASP15 VAL16 LEU17 LYS18 ALA19 ASP20 GLY21 ALA22 ILE23 LEU24 VAL25 ASP26 PHE27 TRP28 ALA29 GLU30 TRP31 CYS32 GLY33 PRO34 CYS35 LYS36 MET37 ILE38 ALA39 PRO40 ILE41 LEU42 ASP43 GLU44 ILE45 ALA46 ASP47 GLU48 TYR49 GLN50 GLY51 LYS52 LEU53 THR54 VAL55 ALA56 LYS57 LEU58 ASN59 ILE60 ASP61 GLN62 ASN63 PRO64 GLY65 THR66 ALA67 PRO68 LYS69 TYR70 GLY71 ILE72 ARG73 GLY74 ILE75 PRO76 THR77 LEU78 LEU79 LEU80 PHE81 LYS82 ASN83 GLY84 GLU85 VAL86 ALA87 ALA88 THR89 LYS90 VAL91 GLY92 ALA93 LEU94 SER95 LYS96 GLY97 GLN98 LEU99 LYS100 GLU101 PHE102 LEU103 ASP104 ALA105 ASN106 LEU107
Nucleic acids
Unit 1 DC807 DG808 DA809 DC810 DG811 DG812 DC813 DC814 DA815 DG816 DT817 DG818 DC819 DC820 DA821 DOC822
Other macromolecules
Unit 2 DC853 DA854 8OG855 DT856 DG857 DG858 DC859 DA860 DC861 DT862 DG863 DG864 DC865 DC866 DG867 DT868 DC869 DG870 DT871
Ligands
Unit 5 D3T823 MG901 MG902 MG903 SO4904 SO4905 SO4906 MES991 1PE992
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