0.010020 0.000000 0.000000 0.000000 0.019342 0.000000 0.000000 0.000000 0.019342 0.00000 0.00000 0.00000 Knox, J.R. Moews, P.C. Fan, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 99.800 51.700 51.700 C10 H15 N5 O10 P2 427.201 n ADENOSINE-5'-DIPHOSPHATE non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Mg 2 24.305 MAGNESIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C6 H15 N O7 P2 275.133 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 36 2531 2538 10.1021/bi962431t 9054558 D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. 1997 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 92 1172 A Common Fold for Peptide Synthetases Cleaving ATP to Adp 1995 US Science SCIEAS 0038 0036-8075 266 439 Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 A Resolution 1994 10.2210/pdb1iow/pdb pdb_00001iow 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 295 1 AREA DETECTOR 1995 SIEMENS M x-ray 1 1.5418 1.0 1.5418 32851.594 D-ALA\:D-ALA LIGASE 6.3.2.4 Y216F 1 man polymer 24.305 MAGNESIUM ION 2 syn non-polymer 427.201 ADENOSINE-5'-DIPHOSPHATE 1 syn non-polymer 275.133 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID 1 syn non-polymer 18.015 water 250 nat water DD-LIGASE, DDLB no no MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMG LPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAE NALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKFLSDETQYFCPAGLEASQEANLQAL VLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMG LPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAE NALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKFLSDETQYFCPAGLEASQEANLQAL VLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Escherichia Escherichia Escherichia coli sample ENZYME PROVIDED BY C.T. WALSH, HARVARD MED SCHOOL. SEE SHI AND WALSH, BIOCHEM. 34, P. 2768, 1995. 562 Escherichia coli DDLB 316407 Escherichia coli str. K12 substr. W3110 W3110 PTB2 1 2.0 39.38 6.5 AMMONIUM SULFATE, pH 6.5 database_2 pdbx_database_status pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1997-02-12 1 1 2008-03-24 1 2 2011-07-13 1 3 2021-11-03 1 4 2023-08-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1996-09-20 REL MG MAGNESIUM ION ADP ADENOSINE-5'-DIPHOSPHATE PHY 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID HOH water 2DLN PDB experimental model MG 330 2 MG MG 330 A MG 331 2 MG MG 331 A ADP 310 3 ADP ADP 310 A PHY 320 4 PHY PHY 320 A HOH 401 5 HOH HOH 401 A HOH 402 5 HOH HOH 402 A HOH 403 5 HOH HOH 403 A HOH 404 5 HOH HOH 404 A HOH 405 5 HOH HOH 405 A HOH 406 5 HOH HOH 406 A HOH 407 5 HOH HOH 407 A HOH 408 5 HOH HOH 408 A HOH 409 5 HOH HOH 409 A HOH 410 5 HOH HOH 410 A HOH 411 5 HOH HOH 411 A HOH 412 5 HOH HOH 412 A HOH 413 5 HOH HOH 413 A HOH 414 5 HOH HOH 414 A HOH 415 5 HOH HOH 415 A HOH 416 5 HOH HOH 416 A HOH 417 5 HOH HOH 417 A HOH 418 5 HOH HOH 418 A HOH 419 5 HOH HOH 419 A HOH 420 5 HOH HOH 420 A HOH 421 5 HOH HOH 421 A HOH 422 5 HOH HOH 422 A HOH 423 5 HOH HOH 423 A HOH 424 5 HOH HOH 424 A HOH 425 5 HOH HOH 425 A HOH 426 5 HOH HOH 426 A HOH 427 5 HOH HOH 427 A HOH 428 5 HOH HOH 428 A HOH 429 5 HOH HOH 429 A HOH 430 5 HOH HOH 430 A HOH 431 5 HOH HOH 431 A HOH 432 5 HOH HOH 432 A HOH 433 5 HOH HOH 433 A HOH 434 5 HOH HOH 434 A HOH 435 5 HOH HOH 435 A HOH 436 5 HOH HOH 436 A HOH 437 5 HOH HOH 437 A HOH 438 5 HOH HOH 438 A HOH 439 5 HOH HOH 439 A HOH 440 5 HOH HOH 440 A HOH 441 5 HOH HOH 441 A HOH 442 5 HOH HOH 442 A HOH 443 5 HOH HOH 443 A HOH 444 5 HOH HOH 444 A HOH 445 5 HOH HOH 445 A HOH 446 5 HOH HOH 446 A HOH 447 5 HOH HOH 447 A HOH 448 5 HOH HOH 448 A HOH 449 5 HOH HOH 449 A HOH 450 5 HOH HOH 450 A HOH 451 5 HOH HOH 451 A HOH 452 5 HOH HOH 452 A HOH 453 5 HOH HOH 453 A HOH 454 5 HOH HOH 454 A HOH 455 5 HOH HOH 455 A HOH 456 5 HOH HOH 456 A HOH 457 5 HOH HOH 457 A HOH 458 5 HOH HOH 458 A HOH 459 5 HOH HOH 459 A HOH 460 5 HOH HOH 460 A HOH 461 5 HOH HOH 461 A HOH 462 5 HOH HOH 462 A HOH 463 5 HOH HOH 463 A HOH 464 5 HOH HOH 464 A HOH 465 5 HOH HOH 465 A HOH 466 5 HOH HOH 466 A HOH 467 5 HOH HOH 467 A HOH 468 5 HOH HOH 468 A HOH 469 5 HOH HOH 469 A HOH 470 5 HOH HOH 470 A HOH 471 5 HOH HOH 471 A HOH 472 5 HOH HOH 472 A HOH 473 5 HOH HOH 473 A HOH 474 5 HOH HOH 474 A HOH 475 5 HOH HOH 475 A HOH 476 5 HOH HOH 476 A HOH 477 5 HOH HOH 477 A HOH 478 5 HOH HOH 478 A HOH 479 5 HOH HOH 479 A HOH 480 5 HOH HOH 480 A HOH 481 5 HOH HOH 481 A HOH 482 5 HOH HOH 482 A HOH 483 5 HOH HOH 483 A HOH 484 5 HOH HOH 484 A HOH 485 5 HOH HOH 485 A HOH 486 5 HOH HOH 486 A HOH 487 5 HOH HOH 487 A HOH 488 5 HOH HOH 488 A HOH 489 5 HOH HOH 489 A HOH 490 5 HOH HOH 490 A HOH 491 5 HOH HOH 491 A HOH 492 5 HOH HOH 492 A HOH 493 5 HOH HOH 493 A HOH 494 5 HOH HOH 494 A HOH 495 5 HOH HOH 495 A HOH 496 5 HOH HOH 496 A HOH 497 5 HOH HOH 497 A HOH 498 5 HOH HOH 498 A HOH 499 5 HOH HOH 499 A HOH 500 5 HOH HOH 500 A HOH 501 5 HOH HOH 501 A HOH 502 5 HOH HOH 502 A HOH 503 5 HOH HOH 503 A HOH 504 5 HOH HOH 504 A HOH 505 5 HOH HOH 505 A HOH 506 5 HOH HOH 506 A HOH 507 5 HOH HOH 507 A HOH 508 5 HOH HOH 508 A HOH 509 5 HOH HOH 509 A HOH 510 5 HOH HOH 510 A HOH 511 5 HOH HOH 511 A HOH 512 5 HOH HOH 512 A HOH 513 5 HOH HOH 513 A HOH 514 5 HOH HOH 514 A HOH 515 5 HOH HOH 515 A HOH 516 5 HOH HOH 516 A HOH 517 5 HOH HOH 517 A HOH 518 5 HOH HOH 518 A HOH 519 5 HOH HOH 519 A HOH 520 5 HOH HOH 520 A HOH 521 5 HOH HOH 521 A HOH 522 5 HOH HOH 522 A HOH 523 5 HOH HOH 523 A HOH 524 5 HOH HOH 524 A HOH 525 5 HOH HOH 525 A HOH 526 5 HOH HOH 526 A HOH 527 5 HOH HOH 527 A HOH 528 5 HOH HOH 528 A HOH 529 5 HOH HOH 529 A HOH 530 5 HOH HOH 530 A HOH 531 5 HOH HOH 531 A HOH 532 5 HOH HOH 532 A HOH 533 5 HOH HOH 533 A HOH 534 5 HOH HOH 534 A HOH 535 5 HOH HOH 535 A HOH 536 5 HOH HOH 536 A HOH 537 5 HOH HOH 537 A HOH 538 5 HOH HOH 538 A HOH 539 5 HOH HOH 539 A HOH 540 5 HOH HOH 540 A HOH 541 5 HOH HOH 541 A HOH 542 5 HOH HOH 542 A HOH 543 5 HOH HOH 543 A HOH 544 5 HOH HOH 544 A HOH 545 5 HOH HOH 545 A HOH 546 5 HOH HOH 546 A HOH 547 5 HOH HOH 547 A HOH 548 5 HOH HOH 548 A HOH 549 5 HOH HOH 549 A HOH 550 5 HOH HOH 550 A HOH 551 5 HOH HOH 551 A HOH 552 5 HOH HOH 552 A HOH 553 5 HOH HOH 553 A HOH 554 5 HOH HOH 554 A HOH 555 5 HOH HOH 555 A HOH 556 5 HOH HOH 556 A HOH 557 5 HOH HOH 557 A HOH 558 5 HOH HOH 558 A HOH 559 5 HOH HOH 559 A HOH 560 5 HOH HOH 560 A HOH 561 5 HOH HOH 561 A HOH 562 5 HOH HOH 562 A HOH 563 5 HOH HOH 563 A HOH 564 5 HOH HOH 564 A HOH 565 5 HOH HOH 565 A HOH 566 5 HOH HOH 566 A HOH 567 5 HOH HOH 567 A HOH 568 5 HOH HOH 568 A HOH 569 5 HOH HOH 569 A HOH 570 5 HOH HOH 570 A HOH 571 5 HOH HOH 571 A HOH 572 5 HOH HOH 572 A HOH 573 5 HOH HOH 573 A HOH 574 5 HOH HOH 574 A HOH 575 5 HOH HOH 575 A HOH 576 5 HOH HOH 576 A HOH 577 5 HOH HOH 577 A HOH 578 5 HOH HOH 578 A HOH 579 5 HOH HOH 579 A HOH 580 5 HOH HOH 580 A HOH 581 5 HOH HOH 581 A HOH 582 5 HOH HOH 582 A HOH 583 5 HOH HOH 583 A HOH 584 5 HOH HOH 584 A HOH 585 5 HOH HOH 585 A HOH 586 5 HOH HOH 586 A HOH 587 5 HOH HOH 587 A HOH 588 5 HOH HOH 588 A HOH 589 5 HOH HOH 589 A HOH 590 5 HOH HOH 590 A HOH 591 5 HOH HOH 591 A HOH 592 5 HOH HOH 592 A HOH 593 5 HOH HOH 593 A HOH 594 5 HOH HOH 594 A HOH 595 5 HOH HOH 595 A HOH 596 5 HOH HOH 596 A HOH 597 5 HOH HOH 597 A HOH 598 5 HOH HOH 598 A HOH 599 5 HOH HOH 599 A HOH 600 5 HOH HOH 600 A HOH 601 5 HOH HOH 601 A HOH 602 5 HOH HOH 602 A HOH 603 5 HOH HOH 603 A HOH 604 5 HOH HOH 604 A HOH 605 5 HOH HOH 605 A HOH 606 5 HOH HOH 606 A HOH 607 5 HOH HOH 607 A HOH 608 5 HOH HOH 608 A HOH 609 5 HOH HOH 609 A HOH 610 5 HOH HOH 610 A HOH 611 5 HOH HOH 611 A HOH 612 5 HOH HOH 612 A HOH 613 5 HOH HOH 613 A HOH 614 5 HOH HOH 614 A HOH 615 5 HOH HOH 615 A HOH 616 5 HOH HOH 616 A HOH 617 5 HOH HOH 617 A HOH 618 5 HOH HOH 618 A HOH 619 5 HOH HOH 619 A HOH 620 5 HOH HOH 620 A HOH 621 5 HOH HOH 621 A HOH 622 5 HOH HOH 622 A HOH 623 5 HOH HOH 623 A HOH 624 5 HOH HOH 624 A HOH 625 5 HOH HOH 625 A HOH 626 5 HOH HOH 626 A HOH 627 5 HOH HOH 627 A HOH 628 5 HOH HOH 628 A HOH 629 5 HOH HOH 629 A HOH 630 5 HOH HOH 630 A HOH 631 5 HOH HOH 631 A HOH 632 5 HOH HOH 632 A HOH 633 5 HOH HOH 633 A HOH 634 5 HOH HOH 634 A HOH 635 5 HOH HOH 635 A HOH 636 5 HOH HOH 636 A HOH 637 5 HOH HOH 637 A HOH 638 5 HOH HOH 638 A HOH 639 5 HOH HOH 639 A HOH 640 5 HOH HOH 640 A HOH 641 5 HOH HOH 641 A HOH 642 5 HOH HOH 642 A HOH 643 5 HOH HOH 643 A HOH 644 5 HOH HOH 644 A HOH 645 5 HOH HOH 645 A HOH 646 5 HOH HOH 646 A HOH 647 5 HOH HOH 647 A HOH 648 5 HOH HOH 648 A HOH 649 5 HOH HOH 649 A HOH 650 5 HOH HOH 650 A MET 1 n 1 MET 1 A THR 2 n 2 THR 2 A ASP 3 n 3 ASP 3 A LYS 4 n 4 LYS 4 A ILE 5 n 5 ILE 5 A ALA 6 n 6 ALA 6 A VAL 7 n 7 VAL 7 A LEU 8 n 8 LEU 8 A LEU 9 n 9 LEU 9 A GLY 10 n 10 GLY 10 A GLY 11 n 11 GLY 11 A THR 12 n 12 THR 12 A SER 13 n 13 SER 13 A ALA 14 n 14 ALA 14 A GLU 15 n 15 GLU 15 A ARG 16 n 16 ARG 16 A GLU 17 n 17 GLU 17 A VAL 18 n 18 VAL 18 A SER 19 n 19 SER 19 A LEU 20 n 20 LEU 20 A ASN 21 n 21 ASN 21 A SER 22 n 22 SER 22 A GLY 23 n 23 GLY 23 A ALA 24 n 24 ALA 24 A ALA 25 n 25 ALA 25 A VAL 26 n 26 VAL 26 A LEU 27 n 27 LEU 27 A ALA 28 n 28 ALA 28 A GLY 29 n 29 GLY 29 A LEU 30 n 30 LEU 30 A ARG 31 n 31 ARG 31 A GLU 32 n 32 GLU 32 A GLY 33 n 33 GLY 33 A GLY 34 n 34 GLY 34 A ILE 35 n 35 ILE 35 A ASP 36 n 36 ASP 36 A ALA 37 n 37 ALA 37 A TYR 38 n 38 TYR 38 A PRO 39 n 39 PRO 39 A VAL 40 n 40 VAL 40 A ASP 41 n 41 ASP 41 A PRO 42 n 42 PRO 42 A LYS 43 n 43 LYS 43 A GLU 44 n 44 GLU 44 A VAL 45 n 45 VAL 45 A ASP 46 n 46 ASP 46 A VAL 47 n 47 VAL 47 A THR 48 n 48 THR 48 A GLN 49 n 49 GLN 49 A LEU 50 n 50 LEU 50 A LYS 51 n 51 LYS 51 A SER 52 n 52 SER 52 A MET 53 n 53 MET 53 A GLY 54 n 54 GLY 54 A PHE 55 n 55 PHE 55 A GLN 56 n 56 GLN 56 A LYS 57 n 57 LYS 57 A VAL 58 n 58 VAL 58 A PHE 59 n 59 PHE 59 A ILE 60 n 60 ILE 60 A ALA 61 n 61 ALA 61 A LEU 62 n 62 LEU 62 A HIS 63 n 63 HIS 63 A GLY 64 n 64 GLY 64 A ARG 65 n 65 ARG 65 A GLY 66 n 66 GLY 66 A GLY 67 n 67 GLY 67 A GLU 68 n 68 GLU 68 A ASP 69 n 69 ASP 69 A GLY 70 n 70 GLY 70 A THR 71 n 71 THR 71 A LEU 72 n 72 LEU 72 A GLN 73 n 73 GLN 73 A GLY 74 n 74 GLY 74 A MET 75 n 75 MET 75 A LEU 76 n 76 LEU 76 A GLU 77 n 77 GLU 77 A LEU 78 n 78 LEU 78 A MET 79 n 79 MET 79 A GLY 80 n 80 GLY 80 A LEU 81 n 81 LEU 81 A PRO 82 n 82 PRO 82 A TYR 83 n 83 TYR 83 A THR 84 n 84 THR 84 A GLY 85 n 85 GLY 85 A SER 86 n 86 SER 86 A GLY 87 n 87 GLY 87 A VAL 88 n 88 VAL 88 A MET 89 n 89 MET 89 A ALA 90 n 90 ALA 90 A SER 91 n 91 SER 91 A ALA 92 n 92 ALA 92 A LEU 93 n 93 LEU 93 A SER 94 n 94 SER 94 A MET 95 n 95 MET 95 A ASP 96 n 96 ASP 96 A LYS 97 n 97 LYS 97 A LEU 98 n 98 LEU 98 A ARG 99 n 99 ARG 99 A SER 100 n 100 SER 100 A LYS 101 n 101 LYS 101 A LEU 102 n 102 LEU 102 A LEU 103 n 103 LEU 103 A TRP 104 n 104 TRP 104 A GLN 105 n 105 GLN 105 A GLY 106 n 106 GLY 106 A ALA 107 n 107 ALA 107 A GLY 108 n 108 GLY 108 A LEU 109 n 109 LEU 109 A PRO 110 n 110 PRO 110 A VAL 111 n 111 VAL 111 A ALA 112 n 112 ALA 112 A PRO 113 n 113 PRO 113 A TRP 114 n 114 TRP 114 A VAL 115 n 115 VAL 115 A ALA 116 n 116 ALA 116 A LEU 117 n 117 LEU 117 A THR 118 n 118 THR 118 A ARG 119 n 119 ARG 119 A ALA 120 n 120 ALA 120 A GLU 121 n 121 GLU 121 A PHE 122 n 122 PHE 122 A GLU 123 n 123 GLU 123 A LYS 124 n 124 LYS 124 A GLY 125 n 125 GLY 125 A LEU 126 n 126 LEU 126 A SER 127 n 127 SER 127 A ASP 128 n 128 ASP 128 A LYS 129 n 129 LYS 129 A GLN 130 n 130 GLN 130 A LEU 131 n 131 LEU 131 A ALA 132 n 132 ALA 132 A GLU 133 n 133 GLU 133 A ILE 134 n 134 ILE 134 A SER 135 n 135 SER 135 A ALA 136 n 136 ALA 136 A LEU 137 n 137 LEU 137 A GLY 138 n 138 GLY 138 A LEU 139 n 139 LEU 139 A PRO 140 n 140 PRO 140 A VAL 141 n 141 VAL 141 A ILE 142 n 142 ILE 142 A VAL 143 n 143 VAL 143 A LYS 144 n 144 LYS 144 A PRO 145 n 145 PRO 145 A SER 146 n 146 SER 146 A ARG 147 n 147 ARG 147 A GLU 148 n 148 GLU 148 A GLY 149 n 149 GLY 149 A SER 150 n 150 SER 150 A SER 151 n 151 SER 151 A VAL 152 n 152 VAL 152 A GLY 153 n 153 GLY 153 A MET 154 n 154 MET 154 A SER 155 n 155 SER 155 A LYS 156 n 156 LYS 156 A VAL 157 n 157 VAL 157 A VAL 158 n 158 VAL 158 A ALA 159 n 159 ALA 159 A GLU 160 n 160 GLU 160 A ASN 161 n 161 ASN 161 A ALA 162 n 162 ALA 162 A LEU 163 n 163 LEU 163 A GLN 164 n 164 GLN 164 A ASP 165 n 165 ASP 165 A ALA 166 n 166 ALA 166 A LEU 167 n 167 LEU 167 A ARG 168 n 168 ARG 168 A LEU 169 n 169 LEU 169 A ALA 170 n 170 ALA 170 A PHE 171 n 171 PHE 171 A GLN 172 n 172 GLN 172 A HIS 173 n 173 HIS 173 A ASP 174 n 174 ASP 174 A GLU 175 n 175 GLU 175 A GLU 176 n 176 GLU 176 A VAL 177 n 177 VAL 177 A LEU 178 n 178 LEU 178 A ILE 179 n 179 ILE 179 A GLU 180 n 180 GLU 180 A LYS 181 n 181 LYS 181 A TRP 182 n 182 TRP 182 A LEU 183 n 183 LEU 183 A SER 184 n 184 SER 184 A GLY 185 n 185 GLY 185 A PRO 186 n 186 PRO 186 A GLU 187 n 187 GLU 187 A PHE 188 n 188 PHE 188 A THR 189 n 189 THR 189 A VAL 190 n 190 VAL 190 A ALA 191 n 191 ALA 191 A ILE 192 n 192 ILE 192 A LEU 193 n 193 LEU 193 A GLY 194 n 194 GLY 194 A GLU 195 n 195 GLU 195 A GLU 196 n 196 GLU 196 A ILE 197 n 197 ILE 197 A LEU 198 n 198 LEU 198 A PRO 199 n 199 PRO 199 A SER 200 n 200 SER 200 A ILE 201 n 201 ILE 201 A ARG 202 n 202 ARG 202 A ILE 203 n 203 ILE 203 A GLN 204 n 204 GLN 204 A PRO 205 n 205 PRO 205 A SER 206 n 206 SER 206 A GLY 207 n 207 GLY 207 A THR 208 n 208 THR 208 A PHE 209 n 209 PHE 209 A TYR 210 n 210 TYR 210 A ASP 211 n 211 ASP 211 A TYR 212 n 212 TYR 212 A GLU 213 n 213 GLU 213 A ALA 214 n 214 ALA 214 A LYS 215 n 215 LYS 215 A PHE 216 n 216 PHE 216 A LEU 217 n 217 LEU 217 A SER 218 n 218 SER 218 A ASP 219 n 219 ASP 219 A GLU 220 n 220 GLU 220 A THR 221 n 221 THR 221 A GLN 222 n 222 GLN 222 A TYR 223 n 223 TYR 223 A PHE 224 n 224 PHE 224 A CYS 225 n 225 CYS 225 A PRO 226 n 226 PRO 226 A ALA 227 n 227 ALA 227 A GLY 228 n 228 GLY 228 A LEU 229 n 229 LEU 229 A GLU 230 n 230 GLU 230 A ALA 231 n 231 ALA 231 A SER 232 n 232 SER 232 A GLN 233 n 233 GLN 233 A GLU 234 n 234 GLU 234 A ALA 235 n 235 ALA 235 A ASN 236 n 236 ASN 236 A LEU 237 n 237 LEU 237 A GLN 238 n 238 GLN 238 A ALA 239 n 239 ALA 239 A LEU 240 n 240 LEU 240 A VAL 241 n 241 VAL 241 A LEU 242 n 242 LEU 242 A LYS 243 n 243 LYS 243 A ALA 244 n 244 ALA 244 A TRP 245 n 245 TRP 245 A THR 246 n 246 THR 246 A THR 247 n 247 THR 247 A LEU 248 n 248 LEU 248 A GLY 249 n 249 GLY 249 A CYS 250 n 250 CYS 250 A LYS 251 n 251 LYS 251 A GLY 252 n 252 GLY 252 A TRP 253 n 253 TRP 253 A GLY 254 n 254 GLY 254 A ARG 255 n 255 ARG 255 A ILE 256 n 256 ILE 256 A ASP 257 n 257 ASP 257 A VAL 258 n 258 VAL 258 A MET 259 n 259 MET 259 A LEU 260 n 260 LEU 260 A ASP 261 n 261 ASP 261 A SER 262 n 262 SER 262 A ASP 263 n 263 ASP 263 A GLY 264 n 264 GLY 264 A GLN 265 n 265 GLN 265 A PHE 266 n 266 PHE 266 A TYR 267 n 267 TYR 267 A LEU 268 n 268 LEU 268 A LEU 269 n 269 LEU 269 A GLU 270 n 270 GLU 270 A ALA 271 n 271 ALA 271 A ASN 272 n 272 ASN 272 A THR 273 n 273 THR 273 A SER 274 n 274 SER 274 A PRO 275 n 275 PRO 275 A GLY 276 n 276 GLY 276 A MET 277 n 277 MET 277 A THR 278 n 278 THR 278 A SER 279 n 279 SER 279 A HIS 280 n 280 HIS 280 A SER 281 n 281 SER 281 A LEU 282 n 282 LEU 282 A VAL 283 n 283 VAL 283 A PRO 284 n 284 PRO 284 A MET 285 n 285 MET 285 A ALA 286 n 286 ALA 286 A ALA 287 n 287 ALA 287 A ARG 288 n 288 ARG 288 A GLN 289 n 289 GLN 289 A ALA 290 n 290 ALA 290 A GLY 291 n 291 GLY 291 A MET 292 n 292 MET 292 A SER 293 n 293 SER 293 A PHE 294 n 294 PHE 294 A SER 295 n 295 SER 295 A GLN 296 n 296 GLN 296 A LEU 297 n 297 LEU 297 A VAL 298 n 298 VAL 298 A VAL 299 n 299 VAL 299 A ARG 300 n 300 ARG 300 A ILE 301 n 301 ILE 301 A LEU 302 n 302 LEU 302 A GLU 303 n 303 GLU 303 A LEU 304 n 304 LEU 304 A ALA 305 n 305 ALA 305 A ASP 306 n 306 ASP 306 A author_defined_assembly 1 monomeric A ASP 257 A OD2 ASP 257 1_555 A MG 331 C MG MG 1_555 A GLU 270 A OE2 GLU 270 1_555 86.2 A ASP 257 A OD2 ASP 257 1_555 A MG 331 C MG MG 1_555 A ADP 310 D O2B ADP 1_555 172.0 A GLU 270 A OE2 GLU 270 1_555 A MG 331 C MG MG 1_555 A ADP 310 D O2B ADP 1_555 86.3 A ASP 257 A OD2 ASP 257 1_555 A MG 331 C MG MG 1_555 A ADP 310 D O2A ADP 1_555 99.1 A GLU 270 A OE2 GLU 270 1_555 A MG 331 C MG MG 1_555 A ADP 310 D O2A ADP 1_555 87.7 A ADP 310 D O2B ADP 1_555 A MG 331 C MG MG 1_555 A ADP 310 D O2A ADP 1_555 83.3 A ASP 257 A OD2 ASP 257 1_555 A MG 331 C MG MG 1_555 A PHY 320 E O4P PHY 1_555 95.4 A GLU 270 A OE2 GLU 270 1_555 A MG 331 C MG MG 1_555 A PHY 320 E O4P PHY 1_555 101.0 A ADP 310 D O2B ADP 1_555 A MG 331 C MG MG 1_555 A PHY 320 E O4P PHY 1_555 83.3 A ADP 310 D O2A ADP 1_555 A MG 331 C MG MG 1_555 A PHY 320 E O4P PHY 1_555 163.5 A ASP 257 A OD2 ASP 257 1_555 A MG 331 C MG MG 1_555 A HOH 407 F O HOH 1_555 89.5 A GLU 270 A OE2 GLU 270 1_555 A MG 331 C MG MG 1_555 A HOH 407 F O HOH 1_555 170.8 A ADP 310 D O2B ADP 1_555 A MG 331 C MG MG 1_555 A HOH 407 F O HOH 1_555 98.3 A ADP 310 D O2A ADP 1_555 A MG 331 C MG MG 1_555 A HOH 407 F O HOH 1_555 85.0 A PHY 320 E O4P PHY 1_555 A MG 331 C MG MG 1_555 A HOH 407 F O HOH 1_555 87.4 A GLU 270 A OE2 GLU 270 1_555 A MG 330 B MG MG 1_555 A GLU 270 A OE1 GLU 270 1_555 57.3 A GLU 270 A OE2 GLU 270 1_555 A MG 330 B MG MG 1_555 A ASN 272 A OD1 ASN 272 1_555 102.2 A GLU 270 A OE1 GLU 270 1_555 A MG 330 B MG MG 1_555 A ASN 272 A OD1 ASN 272 1_555 90.2 A GLU 270 A OE2 GLU 270 1_555 A MG 330 B MG MG 1_555 A ADP 310 D O3B ADP 1_555 88.7 A GLU 270 A OE1 GLU 270 1_555 A MG 330 B MG MG 1_555 A ADP 310 D O3B ADP 1_555 97.3 A ASN 272 A OD1 ASN 272 1_555 A MG 330 B MG MG 1_555 A ADP 310 D O3B ADP 1_555 168.9 A GLU 270 A OE2 GLU 270 1_555 A MG 330 B MG MG 1_555 A PHY 320 E O5P PHY 1_555 110.2 A GLU 270 A OE1 GLU 270 1_555 A MG 330 B MG MG 1_555 A PHY 320 E O5P PHY 1_555 163.4 A ASN 272 A OD1 ASN 272 1_555 A MG 330 B MG MG 1_555 A PHY 320 E O5P PHY 1_555 81.5 A ADP 310 D O3B ADP 1_555 A MG 330 B MG MG 1_555 A PHY 320 E O5P PHY 1_555 93.1 A GLU 270 A OE2 GLU 270 1_555 A MG 330 B MG MG 1_555 A HOH 401 F O HOH 1_555 151.9 A GLU 270 A OE1 GLU 270 1_555 A MG 330 B MG MG 1_555 A HOH 401 F O HOH 1_555 95.2 A ASN 272 A OD1 ASN 272 1_555 A MG 330 B MG MG 1_555 A HOH 401 F O HOH 1_555 81.7 A ADP 310 D O3B ADP 1_555 A MG 330 B MG MG 1_555 A HOH 401 F O HOH 1_555 89.5 A PHY 320 E O5P PHY 1_555 A MG 330 B MG MG 1_555 A HOH 401 F O HOH 1_555 97.9 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O ASP 36 A O ASP 36 A N ILE 5 A N ILE 5 A O LYS 4 A O LYS 4 A N GLN 56 A N GLN 56 A O VAL 115 A O VAL 115 A N ILE 179 A N ILE 179 A O LEU 178 A O LEU 178 A N LYS 144 A N LYS 144 A O VAL 141 A O VAL 141 A N VAL 157 A N VAL 157 A O TYR 267 A O TYR 267 A N MET 259 A N MET 259 A O GLY 254 A O GLY 254 A N ILE 192 A N ILE 192 A O GLU 187 A O GLU 187 A N ILE 203 A N ILE 203 A O ARG 202 A O ARG 202 A N PHE 224 A N PHE 224 1 14.30 2.30 115.30 129.60 A A A CA CB CG LEU LEU LEU 229 229 229 N 1 9.43 1.50 119.30 128.73 A A A C N CA SER PRO PRO 274 275 275 Y 1 A ASP 3 122.03 73.41 1 A SER 127 -51.72 84.59 1 A ASP 128 0.92 -34.77 1 A ARG 147 -112.81 54.11 1 A ALA 159 72.69 138.86 1 A PRO 186 -59.52 176.81 1 A TYR 210 -69.61 74.95 1 A THR 278 -69.34 -174.16 13.6 0.2340000 0.1580000 0.1580000 1.9 15. 12800 10.0 75. 1 3. MOLECULAR REPLACEMENT 2DLN 0.20 1.9 15. 250 2586 16 27 2293 0.012 1.6 2.14 2735 41. 1.94 1IOW 15352 0. 0.0530000 1 14.2 75. 1.94 2.14 41. model building X-PLOR refinement X-PLOR data reduction XENGEN data scaling XENGEN phasing X-PLOR COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE 1 N N 2 N N 2 N N 3 N N 4 N N 5 N N A ARG 16 A ARG 16 HELX_P A GLU 32 A GLU 32 1 1 17 A VAL 47 A VAL 47 HELX_P A GLN 49 A GLN 49 5 2 3 A THR 71 A THR 71 HELX_P A MET 79 A MET 79 1 3 9 A VAL 88 A VAL 88 HELX_P A MET 95 A MET 95 1 4 8 A LYS 97 A LYS 97 HELX_P A GLY 106 A GLY 106 1 5 10 A ARG 119 A ARG 119 HELX_P A LYS 124 A LYS 124 1 6 6 A LYS 129 A LYS 129 HELX_P A LEU 137 A LEU 137 1 7 9 A GLU 160 A GLU 160 HELX_P A GLN 172 A GLN 172 5 8 13 A TYR 212 A TYR 212 HELX_P A PHE 216 A PHE 216 1 9 5 A ALA 231 A ALA 231 HELX_P A LEU 248 A LEU 248 1 10 18 A LEU 282 A LEU 282 HELX_P A GLN 289 A GLN 289 1 11 8 A PHE 294 A PHE 294 HELX_P A GLU 303 A GLU 303 1 12 10 metalc 2.066 A ASP 257 A OD2 ASP 257 1_555 A MG 331 C MG MG 1_555 metalc 1.867 A GLU 270 A OE2 GLU 270 1_555 A MG 330 B MG MG 1_555 metalc 2.549 A GLU 270 A OE1 GLU 270 1_555 A MG 330 B MG MG 1_555 metalc 2.510 A GLU 270 A OE2 GLU 270 1_555 A MG 331 C MG MG 1_555 metalc 2.257 A ASN 272 A OD1 ASN 272 1_555 A MG 330 B MG MG 1_555 metalc 2.022 A ADP 310 D O3B ADP 1_555 A MG 330 B MG MG 1_555 metalc 2.241 A ADP 310 D O2B ADP 1_555 A MG 331 C MG MG 1_555 metalc 2.327 A ADP 310 D O2A ADP 1_555 A MG 331 C MG MG 1_555 metalc 2.042 A PHY 320 E O5P PHY 1_555 A MG 330 B MG MG 1_555 metalc 2.026 A PHY 320 E O4P PHY 1_555 A MG 331 C MG MG 1_555 metalc 2.163 A MG 330 B MG MG 1_555 A HOH 401 F O HOH 1_555 metalc 1.946 A MG 331 C MG MG 1_555 A HOH 407 F O HOH 1_555 LIGASE GLYCOGEN PHOSPHORYLASE, LIGASE, CELL WALL, PEPTIDOGLYCAN SYNTHESIS, VANCOMYCIN, ADP BINDING A LEU 139 A LEU 139 1 A PRO 140 A PRO 140 -0.48 A GLY 185 A GLY 185 1 A PRO 186 A PRO 186 0.16 A CYS 225 A CYS 225 1 A PRO 226 A PRO 226 0.55 DDLB_ECOLI UNP 1 1 P07862 TDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGL PYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAEN ALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALV LKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 1 305 1IOW 2 306 P07862 A 1 2 306 1 TYR engineered mutation PHE 216 1IOW A P07862 UNP 215 216 3 4 5 parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ASP 36 A ASP 36 A ASP 41 A ASP 41 A LYS 4 A LYS 4 A LEU 9 A LEU 9 A PHE 55 A PHE 55 A ILE 60 A ILE 60 A TRP 114 A TRP 114 A THR 118 A THR 118 A GLU 176 A GLU 176 A LYS 181 A LYS 181 A VAL 141 A VAL 141 A PRO 145 A PRO 145 A SER 155 A SER 155 A VAL 157 A VAL 157 A PHE 266 A PHE 266 A ASN 272 A ASN 272 A TRP 253 A TRP 253 A LEU 260 A LEU 260 A GLU 187 A GLU 187 A LEU 193 A LEU 193 A ILE 201 A ILE 201 A GLN 204 A GLN 204 A GLN 222 A GLN 222 A PHE 224 A PHE 224 ADP BINDING SITE. Unknown 12 LIGAND BINDING SITE. Unknown 7 BINDING SITE FOR RESIDUE MG A 330 A MG 330 Software 6 BINDING SITE FOR RESIDUE MG A 331 A MG 331 Software 6 BINDING SITE FOR RESIDUE ADP A 310 A ADP 310 Software 26 BINDING SITE FOR RESIDUE PHY A 320 A PHY 320 Software 17 A LYS 97 A LYS 97 12 1_555 A LYS 144 A LYS 144 12 1_555 A LYS 215 A LYS 215 12 1_555 A GLU 270 A GLU 270 12 1_555 A ASN 272 A ASN 272 12 1_555 A SER 151 A SER 151 12 1_555 A GLU 180 A GLU 180 12 1_555 A GLU 187 A GLU 187 12 1_555 A TRP 182 A TRP 182 12 1_555 A ALA 159 A ALA 159 12 1_555 A ILE 142 A ILE 142 12 1_555 A PHE 209 A PHE 209 12 1_555 A GLU 15 A GLU 15 7 1_555 A SER 150 A SER 150 7 1_555 A PHE 216 A PHE 216 7 1_555 A VAL 18 A VAL 18 7 1_555 A HIS 63 A HIS 63 7 1_555 A SER 281 A SER 281 7 1_555 A ARG 255 A ARG 255 7 1_555 A GLU 270 A GLU 270 6 1_555 A ASN 272 A ASN 272 6 1_555 A ADP 310 D ADP 6 1_555 A PHY 320 E PHY 6 1_555 A MG 331 C MG 6 1_555 A HOH 401 F HOH 6 1_555 A ASP 257 A ASP 257 6 1_555 A GLU 270 A GLU 270 6 1_555 A ADP 310 D ADP 6 1_555 A PHY 320 E PHY 6 1_555 A MG 330 B MG 6 1_555 A HOH 407 F HOH 6 1_555 A LYS 97 A LYS 97 26 1_555 A ILE 142 A ILE 142 26 1_555 A LYS 144 A LYS 144 26 1_555 A GLU 148 A GLU 148 26 1_555 A GLY 149 A GLY 149 26 1_555 A SER 150 A SER 150 26 1_555 A SER 151 A SER 151 26 1_555 A MET 154 A MET 154 26 1_555 A GLU 180 A GLU 180 26 1_555 A LYS 181 A LYS 181 26 1_555 A TRP 182 A TRP 182 26 1_555 A LEU 183 A LEU 183 26 1_555 A GLU 187 A GLU 187 26 1_555 A PHE 209 A PHE 209 26 1_555 A TYR 210 A TYR 210 26 1_555 A LYS 215 A LYS 215 26 1_555 A ASP 257 A ASP 257 26 1_555 A MET 259 A MET 259 26 1_555 A GLU 270 A GLU 270 26 1_555 A PHY 320 E PHY 26 1_555 A MG 330 B MG 26 1_555 A MG 331 C MG 26 1_555 A HOH 401 F HOH 26 1_555 A HOH 407 F HOH 26 1_555 A HOH 443 F HOH 26 1_555 A HOH 449 F HOH 26 1_555 A GLU 15 A GLU 15 17 1_555 A SER 150 A SER 150 17 1_555 A LYS 215 A LYS 215 17 1_555 A ARG 255 A ARG 255 17 1_555 A ASP 257 A ASP 257 17 1_555 A GLU 270 A GLU 270 17 1_555 A ASN 272 A ASN 272 17 1_555 A PRO 275 A PRO 275 17 1_555 A GLY 276 A GLY 276 17 1_555 A SER 281 A SER 281 17 1_555 A LEU 282 A LEU 282 17 1_555 A ADP 310 D ADP 17 1_555 A MG 330 B MG 17 1_555 A MG 331 C MG 17 1_555 A HOH 405 F HOH 17 1_555 A HOH 407 F HOH 17 1_555 A HOH 410 F HOH 17 1_555 18 P 21 21 2