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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMEN DNA AND DDATP-DT IN CLOSED CONFORMATION
Keywords DNA POLYMERASE I, PROTEIN-DNA COMPLEX, TRANSFERASE-DNA COMPL
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3THV     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   DNA POLYMERASE I  A 579 9363 0
2  Protein   DNA POLYMERASE I  D 579 9364 0
3  DNA    B 9 247 30
4  Other macromolecule   5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'  C 12 384 0
5  DNA    E 9 247 30
6  Other macromolecule   5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'  F 12 384 0
7  Ligand   DNA POLYMERASE I  A 3 0 47
8  Ligand   DNA POLYMERASE I  D 4 0 52
9 Water     1696 0 1696
total       2903 19989 1855
Proteins
Unit 1 LYS298 MET299 ALA300 PHE301 THR302 LEU303 ALA304 ASP305 ARG306 VAL307 THR308 GLU309 GLU310 MET311 LEU312 ALA313 ASP314 LYS315 ALA316 ALA317 LEU318 VAL319 VAL320 GLU321 VAL322 VAL323 GLU324 GLU325 ASN326 TYR327 HIS328 ASP329 ALA330 PRO331 ILE332 VAL333 GLY334 ILE335 ALA336 VAL337 VAL338 ASN339 GLU340 HIS341 GLY342 ARG343 PHE344 PHE345 LEU346 ARG347 PRO348 GLU349 THR350 ALA351 LEU352 ALA353 ASP354 PRO355 GLN356 PHE357 VAL358 ALA359 TRP360 LEU361 GLY362 ASP363 GLU364 THR365 LYS366 LYS367 LYS368 SER369 MET370 PHE371 ASP372 SER373 LYS374 ARG375 ALA376 ALA377 VAL378 ALA379 LEU380 LYS381 TRP382 LYS383 GLY384 ILE385 GLU386 LEU387 CYS388 GLY389 VAL390 SER391 PHE392 ASP393 LEU394 LEU395 LEU396 ALA397 ALA398 TYR399 LEU400 LEU401 ASP402 PRO403 ALA404 GLN405 GLY406 VAL407 ASP408 ASP409 VAL410 ALA411 ALA412 ALA413 ALA414 LYS415 MET416 LYS417 GLN418 TYR419 GLU420 ALA421 VAL422 ARG423 PRO424 ASP425 GLU426 ALA427 VAL428 TYR429 GLY430 LYS431 GLY432 ALA433 LYS434 ARG435 ALA436 VAL437 PRO438 ASP439 GLU440 PRO441 VAL442 LEU443 ALA444 GLU445 HIS446 LEU447 VAL448 ARG449 LYS450 ALA451 ALA452 ALA453 ILE454 TRP455 GLU456 LEU457 GLU458 ARG459 PRO460 PHE461 LEU462 ASP463 GLU464 LEU465 ARG466 ARG467 ASN468 GLU469 GLN470 ASP471 ARG472 LEU473 LEU474 VAL475 GLU476 LEU477 GLU478 GLN479 PRO480 LEU481 SER482 SER483 ILE484 LEU485 ALA486 GLU487 MET488 GLU489 PHE490 ALA491 GLY492 VAL493 LYS494 VAL495 ASP496 THR497 LYS498 ARG499 LEU500 GLU501 GLN502 MET503 GLY504 LYS505 GLU506 LEU507 ALA508 GLU509 GLN510 LEU511 GLY512 THR513 VAL514 GLU515 GLN516 ARG517 ILE518 TYR519 GLU520 LEU521 ALA522 GLY523 GLN524 GLU525 PHE526 ASN527 ILE528 ASN529 SER530 PRO531 LYS532 GLN533 LEU534 GLY535 VAL536 ILE537 LEU538 PHE539 GLU540 LYS541 LEU542 GLN543 LEU544 PRO545 VAL546 LEU547 LYS548 LYS549 THR550 LYS551 THR552 GLY553 TYR554 SER555 THR556 SER557 ALA558 ASP559 VAL560 LEU561 GLU562 LYS563 LEU564 ALA565 PRO566 TYR567 HIS568 GLU569 ILE570 VAL571 GLU572 ASN573 ILE574 LEU575 HIS576 TYR577 ARG578 GLN579 LEU580 GLY581 LYS582 LEU583 GLN584 SER585 THR586 TYR587 ILE588 GLU589 GLY590 LEU591 LEU592 LYS593 VAL594 VAL595 ARG596 PRO597 ALA598 THR599 LYS600 LYS601 VAL602 HIS603 THR604 ILE605 PHE606 ASN607 GLN608 ALA609 LEU610 THR611 GLN612 THR613 GLY614 ARG615 LEU616 SER617 SER618 THR619 GLU620 PRO621 ASN622 LEU623 GLN624 ASN625 ILE626 PRO627 ILE628 ARG629 LEU630 GLU631 GLU632 GLY633 ARG634 LYS635 ILE636 ARG637 GLN638 ALA639 PHE640 VAL641 PRO642 SER643 GLU644 SER645 ASP646 TRP647 LEU648 ILE649 PHE650 ALA651 ALA652 ASP653 TYR654 SER655 GLN656 ILE657 GLU658 LEU659 ARG660 VAL661 LEU662 ALA663 HIS664 ILE665 ALA666 GLU667 ASP668 ASP669 ASN670 LEU671 MET672 GLU673 ALA674 PHE675 ARG676 ARG677 ASP678 LEU679 ASP680 ILE681 HIS682 THR683 LYS684 THR685 ALA686 MET687 ASP688 ILE689 PHE690 GLN691 VAL692 SER693 GLU694 ASP695 GLU696 VAL697 THR698 PRO699 ASN700 MET701 ARG702 ARG703 GLN704 ALA705 LYS706 ALA707 VAL708 ASN709 TYR710 GLY711 ILE712 VAL713 TYR714 GLY715 ILE716 SER717 ASP718 TYR719 GLY720 LEU721 ALA722 GLN723 ASN724 LEU725 ASN726 ILE727 SER728 ARG729 LYS730 GLU731 ALA732 ALA733 GLU734 PHE735 ILE736 GLU737 ARG738 TYR739 PHE740 GLU741 SER742 PHE743 PRO744 GLY745 VAL746 LYS747 ARG748 TYR749 MET750 GLU751 ASN752 ILE753 VAL754 GLN755 GLU756 ALA757 LYS758 GLN759 LYS760 GLY761 TYR762 VAL763 THR764 THR765 LEU766 LEU767 HIS768 ARG769 ARG770 ARG771 TYR772 LEU773 PRO774 ASP775 ILE776 THR777 SER778 ARG779 ASN780 PHE781 ASN782 VAL783 ARG784 SER785 PHE786 ALA787 GLU788 ARG789 MET790 ALA791 MET792 ASN793 THR794 PRO795 ILE796 GLN797 GLY798 SER799 ALA800 ALA801 ASP802 ILE803 ILE804 LYS805 LYS806 ALA807 MET808 ILE809 ASP810 LEU811 ASN812 ALA813 ARG814 LEU815 LYS816 GLU817 GLU818 ARG819 LEU820 GLN821 ALA822 HIS823 LEU824 LEU825 LEU826 GLN827 VAL828 HIS829 ASP830 GLU831 LEU832 ILE833 LEU834 GLU835 ALA836 PRO837 LYS838 GLU839 GLU840 MET841 GLU842 ARG843 LEU844 CYS845 ARG846 LEU847 VAL848 PRO849 GLU850 VAL851 MET852 GLU853 GLN854 ALA855 VAL856 THR857 LEU858 ARG859 VAL860 PRO861 LEU862 LYS863 VAL864 ASP865 TYR866 HIS867 TYR868 GLY869 SER870 THR871 TRP872 TYR873 ASP874 ALA875 LYS876
Unit 2 LYS298 MET299 ALA300 PHE301 THR302 LEU303 ALA304 ASP305 ARG306 VAL307 THR308 GLU309 GLU310 MET311 LEU312 ALA313 ASP314 LYS315 ALA316 ALA317 LEU318 VAL319 VAL320 GLU321 VAL322 VAL323 GLU324 GLU325 ASN326 TYR327 HIS328 ASP329 ALA330 PRO331 ILE332 VAL333 GLY334 ILE335 ALA336 VAL337 VAL338 ASN339 GLU340 HIS341 GLY342 ARG343 PHE344 PHE345 LEU346 ARG347 PRO348 GLU349 THR350 ALA351 LEU352 ALA353 ASP354 PRO355 GLN356 PHE357 VAL358 ALA359 TRP360 LEU361 GLY362 ASP363 GLU364 THR365 LYS366 LYS367 LYS368 SER369 MET370 PHE371 ASP372 SER373 LYS374 ARG375 ALA376 ALA377 VAL378 ALA379 LEU380 LYS381 TRP382 LYS383 GLY384 ILE385 GLU386 LEU387 CYS388 GLY389 VAL390 SER391 PHE392 ASP393 LEU394 LEU395 LEU396 ALA397 ALA398 TYR399 LEU400 LEU401 ASP402 PRO403 ALA404 GLN405 GLY406 VAL407 ASP408 ASP409 VAL410 ALA411 ALA412 ALA413 ALA414 LYS415 MET416 LYS417 GLN418 TYR419 GLU420 ALA421 VAL422 ARG423 PRO424 ASP425 GLU426 ALA427 VAL428 TYR429 GLY430 LYS431 GLY432 ALA433 LYS434 ARG435 ALA436 VAL437 PRO438 ASP439 GLU440 PRO441 VAL442 LEU443 ALA444 GLU445 HIS446 LEU447 VAL448 ARG449 LYS450 ALA451 ALA452 ALA453 ILE454 TRP455 GLU456 LEU457 GLU458 ARG459 PRO460 PHE461 LEU462 ASP463 GLU464 LEU465 ARG466 ARG467 ASN468 GLU469 GLN470 ASP471 ARG472 LEU473 LEU474 VAL475 GLU476 LEU477 GLU478 GLN479 PRO480 LEU481 SER482 SER483 ILE484 LEU485 ALA486 GLU487 MET488 GLU489 PHE490 ALA491 GLY492 VAL493 LYS494 VAL495 ASP496 THR497 LYS498 ARG499 LEU500 GLU501 GLN502 MET503 GLY504 LYS505 GLU506 LEU507 ALA508 GLU509 GLN510 LEU511 GLY512 THR513 VAL514 GLU515 GLN516 ARG517 ILE518 TYR519 GLU520 LEU521 ALA522 GLY523 GLN524 GLU525 PHE526 ASN527 ILE528 ASN529 SER530 PRO531 LYS532 GLN533 LEU534 GLY535 VAL536 ILE537 LEU538 PHE539 GLU540 LYS541 LEU542 GLN543 LEU544 PRO545 VAL546 LEU547 LYS548 LYS549 THR550 LYS551 THR552 GLY553 TYR554 SER555 THR556 SER557 ALA558 ASP559 VAL560 LEU561 GLU562 LYS563 LEU564 ALA565 PRO566 TYR567 HIS568 GLU569 ILE570 VAL571 GLU572 ASN573 ILE574 LEU575 HIS576 TYR577 ARG578 GLN579 LEU580 GLY581 LYS582 LEU583 GLN584 SER585 THR586 TYR587 ILE588 GLU589 GLY590 LEU591 LEU592 LYS593 VAL594 VAL595 ARG596 PRO597 ALA598 THR599 LYS600 LYS601 VAL602 HIS603 THR604 ILE605 PHE606 ASN607 GLN608 ALA609 LEU610 THR611 GLN612 THR613 GLY614 ARG615 LEU616 SER617 SER618 THR619 GLU620 PRO621 ASN622 LEU623 GLN624 ASN625 ILE626 PRO627 ILE628 ARG629 LEU630 GLU631 GLU632 GLY633 ARG634 LYS635 ILE636 ARG637 GLN638 ALA639 PHE640 VAL641 PRO642 SER643 GLU644 SER645 ASP646 TRP647 LEU648 ILE649 PHE650 ALA651 ALA652 ASP653 TYR654 SER655 GLN656 ILE657 GLU658 LEU659 ARG660 VAL661 LEU662 ALA663 HIS664 ILE665 ALA666 GLU667 ASP668 ASP669 ASN670 LEU671 MET672 GLU673 ALA674 PHE675 ARG676 ARG677 ASP678 LEU679 ASP680 ILE681 HIS682 THR683 LYS684 THR685 ALA686 MET687 ASP688 ILE689 PHE690 GLN691 VAL692 SER693 GLU694 ASP695 GLU696 VAL697 THR698 PRO699 ASN700 MET701 ARG702 ARG703 GLN704 ALA705 LYS706 ALA707 VAL708 ASN709 TYR710 GLY711 ILE712 VAL713 TYR714 GLY715 ILE716 SER717 ASP718 TYR719 GLY720 LEU721 ALA722 GLN723 ASN724 LEU725 ASN726 ILE727 SER728 ARG729 LYS730 GLU731 ALA732 ALA733 GLU734 PHE735 ILE736 GLU737 ARG738 TYR739 PHE740 GLU741 SER742 PHE743 PRO744 GLY745 VAL746 LYS747 ARG748 TYR749 MET750 GLU751 ASN752 ILE753 VAL754 GLN755 GLU756 ALA757 LYS758 GLN759 LYS760 GLY761 TYR762 VAL763 THR764 THR765 LEU766 LEU767 HIS768 ARG769 ARG770 ARG771 TYR772 LEU773 PRO774 ASP775 ILE776 THR777 SER778 ARG779 ASN780 PHE781 ASN782 VAL783 ARG784 SER785 PHE786 ALA787 GLU788 ARG789 MET790 ALA791 MET792 ASN793 THR794 PRO795 ILE796 GLN797 GLY798 SER799 ALA800 ALA801 ASP802 ILE803 ILE804 LYS805 LYS806 ALA807 MET808 ILE809 ASP810 LEU811 ASN812 ALA813 ARG814 LEU815 LYS816 GLU817 GLU818 ARG819 LEU820 GLN821 ALA822 HIS823 LEU824 LEU825 LEU826 GLN827 VAL828 HIS829 ASP830 GLU831 LEU832 ILE833 LEU834 GLU835 ALA836 PRO837 LYS838 GLU839 GLU840 MET841 GLU842 ARG843 LEU844 CYS845 ARG846 LEU847 VAL848 PRO849 GLU850 VAL851 MET852 GLU853 GLN854 ALA855 VAL856 THR857 LEU858 ARG859 VAL860 PRO861 LEU862 LYS863 VAL864 ASP865 TYR866 HIS867 TYR868 GLY869 SER870 THR871 TRP872 TYR873 ASP874 ALA875 LYS876
Nucleic acids
Unit 3 DC21 DC22 DT23 DG24 DA25 DC26 DT27 DC28 2DA29
Unit 5 DC21 DC22 DT23 DG24 DA25 DC26 DT27 DC28 2DA29
Other macromolecules
Unit 4 DA1 DT2 DT3 DT4 DG5 DA6 DG7 DT8 DC9 DA10 DG11 DG12
Unit 6 DA1 DT2 DT3 DT4 DG5 DA6 DG7 DT8 DC9 DA10 DG11 DG12
Ligands
Unit 7 MG1 SO42 DDS201
Unit 8 SO41 MG2 SO43 DDS202
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