0.011270 0.000000 0.000000 0.000000 0.011270 0.000000 0.000000 0.000000 0.009718 0.00000 0.00000 0.00000 RESIDUE PRO H 37 IS A CIS PROLINE. Bode, W. Brandstetter, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 88.730 88.730 102.900 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 C27 H31 N5 O4 S 521.631 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine NAPAP peptide-like C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 226 1085 1099 10.1016/0022-2836(92)91054-S 1518046 Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. 1992 To be Published 0353 Crystallographic Determination of Thrombin Complexes with Small Synthetic Inhibitors as a Starting Point for the Receptor-Based Design of Antithrombotics To be Published 0353 X-Ray Crystal Structure of Thrombin in Complex with D-Phe-Pro-Arg and with Small Benzamidine and Arginine-Based "Non-Peptidic" Inhibitors US Protein Sci. PRCIEI 0795 0961-8368 1 426 The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships 1992 NE FEBS Lett. FEBLAL 0165 0014-5793 287 133 Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes 1991 IX Eur.J.Biochem. EJBCAI 0262 0014-2956 193 175 Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin 1990 UK Embo J. EMJODG 0897 0261-4189 8 3467 The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment 1989 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 5735.240 EPSILON-THROMBIN 3.4.21.5 1 man polymer 29772.422 EPSILON-THROMBIN 3.4.21.5 1 man polymer 521.631 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine 1 syn non-polymer 18.015 water 228 nat water no no TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR L polypeptide(L) no no IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISM LDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVL QVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDRLGS IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISM LDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVL QVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDRLGS H 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 n n cow sample 9913 Bos taurus cow sample 9913 Bos taurus 2.85 56.85 repository Initial release Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance Other 1 0 1994-01-31 1 1 2008-03-24 1 2 2011-07-13 1 3 2012-12-12 SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. Y 1992-07-06 REL MID 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine HOH water AMIDINOPHENYLALANINE (OF NAPAP) BINDS TO S1 SPECIFICITY POCKET, PIPERIDINE TO S2 AND NAPHLYL GROUP TO "ARYL BINDING SITE". THE NUMBERING OF THROMBIN RESIDUES IS BASED ON TOPOLOGICAL EQUIVALENCES WITH CHYMOTRYPSINOGEN. Inhibitor N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide Peptide-like NAS 1 3 MID MID 1 H HOH 519 4 HOH HOH 519 L HOH 520 4 HOH HOH 520 L HOH 523 4 HOH HOH 523 L HOH 525 4 HOH HOH 525 L HOH 526 4 HOH HOH 526 L HOH 527 4 HOH HOH 527 L HOH 530 4 HOH HOH 530 L HOH 531 4 HOH HOH 531 L HOH 533 4 HOH HOH 533 L HOH 534 4 HOH HOH 534 L HOH 536 4 HOH HOH 536 L HOH 551 4 HOH HOH 551 L HOH 564 4 HOH HOH 564 L HOH 580 4 HOH HOH 580 L HOH 588 4 HOH HOH 588 L HOH 618 4 HOH HOH 618 L HOH 626 4 HOH HOH 626 L HOH 630 4 HOH HOH 630 L HOH 631 4 HOH HOH 631 L HOH 635 4 HOH HOH 635 L HOH 654 4 HOH HOH 654 L HOH 655 4 HOH HOH 655 L HOH 661 4 HOH HOH 661 L HOH 668 4 HOH HOH 668 L HOH 672 4 HOH HOH 672 L HOH 681 4 HOH HOH 681 L HOH 683 4 HOH HOH 683 L HOH 686 4 HOH HOH 686 L HOH 703 4 HOH HOH 703 L HOH 736 4 HOH HOH 736 L HOH 500 4 HOH HOH 500 H HOH 501 4 HOH HOH 501 H HOH 502 4 HOH HOH 502 H HOH 503 4 HOH HOH 503 H HOH 504 4 HOH HOH 504 H HOH 505 4 HOH HOH 505 H HOH 506 4 HOH HOH 506 H HOH 508 4 HOH HOH 508 H HOH 509 4 HOH HOH 509 H HOH 510 4 HOH HOH 510 H HOH 511 4 HOH HOH 511 H HOH 512 4 HOH HOH 512 H HOH 513 4 HOH HOH 513 H HOH 514 4 HOH HOH 514 H HOH 515 4 HOH HOH 515 H HOH 516 4 HOH HOH 516 H HOH 517 4 HOH HOH 517 H HOH 521 4 HOH HOH 521 H HOH 522 4 HOH HOH 522 H HOH 524 4 HOH HOH 524 H HOH 528 4 HOH HOH 528 H HOH 529 4 HOH HOH 529 H HOH 532 4 HOH HOH 532 H HOH 535 4 HOH HOH 535 H HOH 537 4 HOH HOH 537 H HOH 538 4 HOH HOH 538 H HOH 539 4 HOH HOH 539 H HOH 540 4 HOH HOH 540 H HOH 541 4 HOH HOH 541 H HOH 542 4 HOH HOH 542 H HOH 543 4 HOH HOH 543 H HOH 544 4 HOH HOH 544 H HOH 545 4 HOH HOH 545 H HOH 546 4 HOH HOH 546 H HOH 547 4 HOH HOH 547 H HOH 548 4 HOH HOH 548 H HOH 549 4 HOH HOH 549 H HOH 552 4 HOH HOH 552 H HOH 553 4 HOH HOH 553 H HOH 554 4 HOH HOH 554 H HOH 555 4 HOH HOH 555 H HOH 556 4 HOH HOH 556 H HOH 557 4 HOH HOH 557 H HOH 558 4 HOH HOH 558 H HOH 559 4 HOH HOH 559 H HOH 560 4 HOH HOH 560 H HOH 561 4 HOH HOH 561 H HOH 562 4 HOH HOH 562 H HOH 563 4 HOH HOH 563 H HOH 569 4 HOH HOH 569 H HOH 570 4 HOH HOH 570 H HOH 571 4 HOH HOH 571 H HOH 572 4 HOH HOH 572 H HOH 574 4 HOH HOH 574 H HOH 575 4 HOH HOH 575 H HOH 576 4 HOH HOH 576 H HOH 577 4 HOH HOH 577 H HOH 578 4 HOH HOH 578 H HOH 579 4 HOH HOH 579 H HOH 581 4 HOH HOH 581 H HOH 582 4 HOH HOH 582 H HOH 583 4 HOH HOH 583 H HOH 586 4 HOH HOH 586 H HOH 589 4 HOH HOH 589 H HOH 590 4 HOH HOH 590 H HOH 591 4 HOH HOH 591 H HOH 592 4 HOH HOH 592 H HOH 593 4 HOH HOH 593 H HOH 594 4 HOH HOH 594 H HOH 595 4 HOH HOH 595 H HOH 596 4 HOH HOH 596 H HOH 597 4 HOH HOH 597 H HOH 600 4 HOH HOH 600 H HOH 602 4 HOH HOH 602 H HOH 603 4 HOH HOH 603 H HOH 605 4 HOH HOH 605 H HOH 606 4 HOH HOH 606 H HOH 607 4 HOH HOH 607 H HOH 608 4 HOH HOH 608 H HOH 610 4 HOH HOH 610 H HOH 612 4 HOH HOH 612 H HOH 614 4 HOH HOH 614 H HOH 615 4 HOH HOH 615 H HOH 616 4 HOH HOH 616 H HOH 617 4 HOH HOH 617 H HOH 619 4 HOH HOH 619 H HOH 622 4 HOH HOH 622 H HOH 623 4 HOH HOH 623 H HOH 624 4 HOH HOH 624 H HOH 625 4 HOH HOH 625 H HOH 627 4 HOH HOH 627 H HOH 628 4 HOH HOH 628 H HOH 629 4 HOH HOH 629 H HOH 632 4 HOH HOH 632 H HOH 633 4 HOH HOH 633 H HOH 636 4 HOH HOH 636 H HOH 638 4 HOH HOH 638 H HOH 639 4 HOH HOH 639 H HOH 640 4 HOH HOH 640 H HOH 642 4 HOH HOH 642 H HOH 644 4 HOH HOH 644 H HOH 645 4 HOH HOH 645 H HOH 646 4 HOH HOH 646 H HOH 648 4 HOH HOH 648 H HOH 652 4 HOH HOH 652 H HOH 656 4 HOH HOH 656 H HOH 657 4 HOH HOH 657 H HOH 658 4 HOH HOH 658 H HOH 659 4 HOH HOH 659 H HOH 660 4 HOH HOH 660 H HOH 662 4 HOH HOH 662 H HOH 664 4 HOH HOH 664 H HOH 665 4 HOH HOH 665 H HOH 666 4 HOH HOH 666 H HOH 669 4 HOH HOH 669 H HOH 670 4 HOH HOH 670 H HOH 671 4 HOH HOH 671 H HOH 673 4 HOH HOH 673 H HOH 674 4 HOH HOH 674 H HOH 675 4 HOH HOH 675 H HOH 676 4 HOH HOH 676 H HOH 677 4 HOH HOH 677 H HOH 678 4 HOH HOH 678 H HOH 679 4 HOH HOH 679 H HOH 680 4 HOH HOH 680 H HOH 682 4 HOH HOH 682 H HOH 684 4 HOH HOH 684 H HOH 685 4 HOH HOH 685 H HOH 687 4 HOH HOH 687 H HOH 688 4 HOH HOH 688 H HOH 689 4 HOH HOH 689 H HOH 690 4 HOH HOH 690 H HOH 691 4 HOH HOH 691 H HOH 692 4 HOH HOH 692 H HOH 693 4 HOH HOH 693 H HOH 694 4 HOH HOH 694 H HOH 697 4 HOH HOH 697 H HOH 698 4 HOH HOH 698 H HOH 701 4 HOH HOH 701 H HOH 702 4 HOH HOH 702 H HOH 704 4 HOH HOH 704 H HOH 705 4 HOH HOH 705 H HOH 706 4 HOH HOH 706 H HOH 708 4 HOH HOH 708 H HOH 709 4 HOH HOH 709 H HOH 710 4 HOH HOH 710 H HOH 711 4 HOH HOH 711 H HOH 712 4 HOH HOH 712 H HOH 713 4 HOH HOH 713 H HOH 715 4 HOH HOH 715 H HOH 717 4 HOH HOH 717 H HOH 718 4 HOH HOH 718 H HOH 720 4 HOH HOH 720 H HOH 721 4 HOH HOH 721 H HOH 723 4 HOH HOH 723 H HOH 725 4 HOH HOH 725 H HOH 726 4 HOH HOH 726 H HOH 727 4 HOH HOH 727 H HOH 729 4 HOH HOH 729 H HOH 730 4 HOH HOH 730 H HOH 731 4 HOH HOH 731 H HOH 733 4 HOH HOH 733 H HOH 734 4 HOH HOH 734 H HOH 735 4 HOH HOH 735 H HOH 738 4 HOH HOH 738 H HOH 739 4 HOH HOH 739 H HOH 740 4 HOH HOH 740 H HOH 742 4 HOH HOH 742 H HOH 743 4 HOH HOH 743 H HOH 744 4 HOH HOH 744 H HOH 745 4 HOH HOH 745 H HOH 747 4 HOH HOH 747 H HOH 748 4 HOH HOH 748 H HOH 749 4 HOH HOH 749 H HOH 750 4 HOH HOH 750 H HOH 751 4 HOH HOH 751 H HOH 752 4 HOH HOH 752 H HOH 753 4 HOH HOH 753 H HOH 754 4 HOH HOH 754 H HOH 755 4 HOH HOH 755 H HOH 757 4 HOH HOH 757 H HOH 759 4 HOH HOH 759 H HOH 760 4 HOH HOH 760 H HOH 761 4 HOH HOH 761 H HOH 762 4 HOH HOH 762 H HOH 763 4 HOH HOH 763 H HOH 764 4 HOH HOH 764 H HOH 765 4 HOH HOH 765 H HOH 766 4 HOH HOH 766 H HOH 767 4 HOH HOH 767 H HOH 769 4 HOH HOH 769 H HOH 770 4 HOH HOH 770 H HOH 771 4 HOH HOH 771 H HOH 772 4 HOH HOH 772 H HOH 773 4 HOH HOH 773 H HOH 774 4 HOH HOH 774 H HOH 775 4 HOH HOH 775 H HOH 777 4 HOH HOH 777 H n 1 -12 L n 2 -11 L n 3 -10 L n 4 -9 L n 5 -8 L n 6 -7 L n 7 -6 L n 8 -5 L n 9 -4 L n 10 -3 L n 11 -2 L n 12 -1 L n 13 0 L THR 1 n 14 H THR 1 L PHE 1 n 15 G PHE 1 L GLY 1 n 16 F GLY 1 L ALA 1 n 17 E ALA 1 L GLY 1 n 18 D GLY 1 L GLU 1 n 19 C GLU 1 L ALA 1 n 20 B ALA 1 L ASP 1 n 21 A ASP 1 L CYS 1 n 22 CYS 1 L GLY 2 n 23 GLY 2 L LEU 3 n 24 LEU 3 L ARG 4 n 25 ARG 4 L PRO 5 n 26 PRO 5 L LEU 6 n 27 LEU 6 L PHE 7 n 28 PHE 7 L GLU 8 n 29 GLU 8 L LYS 9 n 30 LYS 9 L LYS 10 n 31 LYS 10 L GLN 11 n 32 GLN 11 L VAL 12 n 33 VAL 12 L GLN 13 n 34 GLN 13 L ASP 14 n 35 ASP 14 L GLN 14 n 36 A GLN 14 L THR 14 n 37 B THR 14 L GLU 14 n 38 C GLU 14 L LYS 14 n 39 D LYS 14 L GLU 14 n 40 E GLU 14 L LEU 14 n 41 F LEU 14 L PHE 14 n 42 G PHE 14 L GLU 14 n 43 H GLU 14 L SER 14 n 44 I SER 14 L TYR 14 n 45 J TYR 14 L ILE 14 n 46 K ILE 14 L GLU 14 n 47 L GLU 14 L GLY 14 n 48 M GLY 14 L ARG 15 n 49 ARG 15 L ILE 16 n 1 ILE 16 H VAL 17 n 2 VAL 17 H GLU 18 n 3 GLU 18 H GLY 19 n 4 GLY 19 H GLN 20 n 5 GLN 20 H ASP 21 n 6 ASP 21 H ALA 22 n 7 ALA 22 H GLU 23 n 8 GLU 23 H VAL 24 n 9 VAL 24 H GLY 25 n 10 GLY 25 H LEU 26 n 11 LEU 26 H SER 27 n 12 SER 27 H PRO 28 n 13 PRO 28 H TRP 29 n 14 TRP 29 H GLN 30 n 15 GLN 30 H VAL 31 n 16 VAL 31 H MET 32 n 17 MET 32 H LEU 33 n 18 LEU 33 H PHE 34 n 19 PHE 34 H ARG 35 n 20 ARG 35 H LYS 36 n 21 LYS 36 H SER 36 n 22 A SER 36 H PRO 37 n 23 PRO 37 H GLN 38 n 24 GLN 38 H GLU 39 n 25 GLU 39 H LEU 40 n 26 LEU 40 H LEU 41 n 27 LEU 41 H CYS 42 n 28 CYS 42 H GLY 43 n 29 GLY 43 H ALA 44 n 30 ALA 44 H SER 45 n 31 SER 45 H LEU 46 n 32 LEU 46 H ILE 47 n 33 ILE 47 H SER 48 n 34 SER 48 H ASP 49 n 35 ASP 49 H ARG 50 n 36 ARG 50 H TRP 51 n 37 TRP 51 H VAL 52 n 38 VAL 52 H LEU 53 n 39 LEU 53 H THR 54 n 40 THR 54 H ALA 55 n 41 ALA 55 H ALA 56 n 42 ALA 56 H HIS 57 n 43 HIS 57 H CYS 58 n 44 CYS 58 H LEU 59 n 45 LEU 59 H LEU 60 n 46 LEU 60 H TYR 60 n 47 A TYR 60 H PRO 60 n 48 B PRO 60 H PRO 60 n 49 C PRO 60 H TRP 60 n 50 D TRP 60 H ASP 60 n 51 E ASP 60 H LYS 60 n 52 F LYS 60 H ASN 60 n 53 G ASN 60 H PHE 60 n 54 H PHE 60 H THR 60 n 55 I THR 60 H VAL 61 n 56 VAL 61 H ASP 62 n 57 ASP 62 H ASP 63 n 58 ASP 63 H LEU 64 n 59 LEU 64 H LEU 65 n 60 LEU 65 H VAL 66 n 61 VAL 66 H ARG 67 n 62 ARG 67 H ILE 68 n 63 ILE 68 H GLY 69 n 64 GLY 69 H LYS 70 n 65 LYS 70 H HIS 71 n 66 HIS 71 H SER 72 n 67 SER 72 H ARG 73 n 68 ARG 73 H THR 74 n 69 THR 74 H ARG 75 n 70 ARG 75 H TYR 76 n 71 TYR 76 H GLU 77 n 72 GLU 77 H ARG 77 n 73 A ARG 77 H LYS 78 n 74 LYS 78 H VAL 79 n 75 VAL 79 H GLU 80 n 76 GLU 80 H LYS 81 n 77 LYS 81 H ILE 82 n 78 ILE 82 H SER 83 n 79 SER 83 H MET 84 n 80 MET 84 H LEU 85 n 81 LEU 85 H ASP 86 n 82 ASP 86 H LYS 87 n 83 LYS 87 H ILE 88 n 84 ILE 88 H TYR 89 n 85 TYR 89 H ILE 90 n 86 ILE 90 H HIS 91 n 87 HIS 91 H PRO 92 n 88 PRO 92 H ARG 93 n 89 ARG 93 H TYR 94 n 90 TYR 94 H ASN 95 n 91 ASN 95 H TRP 96 n 92 TRP 96 H LYS 97 n 93 LYS 97 H GLU 97 n 94 A GLU 97 H ASN 98 n 95 ASN 98 H LEU 99 n 96 LEU 99 H ASP 100 n 97 ASP 100 H ARG 101 n 98 ARG 101 H ASP 102 n 99 ASP 102 H ILE 103 n 100 ILE 103 H ALA 104 n 101 ALA 104 H LEU 105 n 102 LEU 105 H LEU 106 n 103 LEU 106 H LYS 107 n 104 LYS 107 H LEU 108 n 105 LEU 108 H LYS 109 n 106 LYS 109 H ARG 110 n 107 ARG 110 H PRO 111 n 108 PRO 111 H ILE 112 n 109 ILE 112 H GLU 113 n 110 GLU 113 H LEU 114 n 111 LEU 114 H SER 115 n 112 SER 115 H ASP 116 n 113 ASP 116 H TYR 117 n 114 TYR 117 H ILE 118 n 115 ILE 118 H HIS 119 n 116 HIS 119 H PRO 120 n 117 PRO 120 H VAL 121 n 118 VAL 121 H CYS 122 n 119 CYS 122 H LEU 123 n 120 LEU 123 H PRO 124 n 121 PRO 124 H ASP 125 n 122 ASP 125 H LYS 126 n 123 LYS 126 H GLN 127 n 124 GLN 127 H THR 128 n 125 THR 128 H ALA 129 n 126 ALA 129 H ALA 129 n 127 A ALA 129 H LYS 129 n 128 B LYS 129 H LEU 129 n 129 C LEU 129 H LEU 130 n 130 LEU 130 H HIS 131 n 131 HIS 131 H ALA 132 n 132 ALA 132 H GLY 133 n 133 GLY 133 H PHE 134 n 134 PHE 134 H LYS 135 n 135 LYS 135 H GLY 136 n 136 GLY 136 H ARG 137 n 137 ARG 137 H VAL 138 n 138 VAL 138 H THR 139 n 139 THR 139 H GLY 140 n 140 GLY 140 H TRP 141 n 141 TRP 141 H GLY 142 n 142 GLY 142 H ASN 143 n 143 ASN 143 H ARG 144 n 144 ARG 144 H ARG 145 n 145 ARG 145 H GLU 146 n 146 GLU 146 H THR 147 n 147 THR 147 H TRP 148 n 148 TRP 148 H THR 149 n 149 THR 149 H THR 149 n 150 A THR 149 H SER 149 n 151 B SER 149 H VAL 149 n 152 C VAL 149 H ALA 149 n 153 D ALA 149 H GLU 149 n 154 E GLU 149 H VAL 150 n 155 VAL 150 H GLN 151 n 156 GLN 151 H PRO 152 n 157 PRO 152 H SER 153 n 158 SER 153 H VAL 154 n 159 VAL 154 H LEU 155 n 160 LEU 155 H GLN 156 n 161 GLN 156 H VAL 157 n 162 VAL 157 H VAL 158 n 163 VAL 158 H ASN 159 n 164 ASN 159 H LEU 160 n 165 LEU 160 H PRO 161 n 166 PRO 161 H LEU 162 n 167 LEU 162 H VAL 163 n 168 VAL 163 H GLU 164 n 169 GLU 164 H ARG 165 n 170 ARG 165 H PRO 166 n 171 PRO 166 H VAL 167 n 172 VAL 167 H CYS 168 n 173 CYS 168 H LYS 169 n 174 LYS 169 H ALA 170 n 175 ALA 170 H SER 171 n 176 SER 171 H THR 172 n 177 THR 172 H ARG 173 n 178 ARG 173 H ILE 174 n 179 ILE 174 H ARG 175 n 180 ARG 175 H ILE 176 n 181 ILE 176 H THR 177 n 182 THR 177 H ASP 178 n 183 ASP 178 H ASN 179 n 184 ASN 179 H MET 180 n 185 MET 180 H PHE 181 n 186 PHE 181 H CYS 182 n 187 CYS 182 H ALA 183 n 188 ALA 183 H GLY 184 n 189 GLY 184 H TYR 184 n 190 A TYR 184 H LYS 185 n 191 LYS 185 H PRO 186 n 192 PRO 186 H GLY 186 n 193 A GLY 186 H GLU 186 n 194 B GLU 186 H GLY 186 n 195 C GLY 186 H LYS 186 n 196 D LYS 186 H ARG 187 n 197 ARG 187 H GLY 188 n 198 GLY 188 H ASP 189 n 199 ASP 189 H ALA 190 n 200 ALA 190 H CYS 191 n 201 CYS 191 H GLU 192 n 202 GLU 192 H GLY 193 n 203 GLY 193 H ASP 194 n 204 ASP 194 H SER 195 n 205 SER 195 H GLY 196 n 206 GLY 196 H GLY 197 n 207 GLY 197 H PRO 198 n 208 PRO 198 H PHE 199 n 209 PHE 199 H VAL 200 n 210 VAL 200 H MET 201 n 211 MET 201 H LYS 202 n 212 LYS 202 H SER 203 n 213 SER 203 H PRO 204 n 214 PRO 204 H TYR 204 n 215 A TYR 204 H ASN 204 n 216 B ASN 204 H ASN 205 n 217 ASN 205 H ARG 206 n 218 ARG 206 H TRP 207 n 219 TRP 207 H TYR 208 n 220 TYR 208 H GLN 209 n 221 GLN 209 H MET 210 n 222 MET 210 H GLY 211 n 223 GLY 211 H ILE 212 n 224 ILE 212 H VAL 213 n 225 VAL 213 H SER 214 n 226 SER 214 H TRP 215 n 227 TRP 215 H GLY 216 n 228 GLY 216 H GLU 217 n 229 GLU 217 H GLY 219 n 230 GLY 219 H CYS 220 n 231 CYS 220 H ASP 221 n 232 A ASP 221 H ARG 221 n 233 ARG 221 H ASP 222 n 234 ASP 222 H GLY 223 n 235 GLY 223 H LYS 224 n 236 LYS 224 H TYR 225 n 237 TYR 225 H GLY 226 n 238 GLY 226 H PHE 227 n 239 PHE 227 H TYR 228 n 240 TYR 228 H THR 229 n 241 THR 229 H HIS 230 n 242 HIS 230 H VAL 231 n 243 VAL 231 H PHE 232 n 244 PHE 232 H ARG 233 n 245 ARG 233 H LEU 234 n 246 LEU 234 H LYS 235 n 247 LYS 235 H LYS 236 n 248 LYS 236 H TRP 237 n 249 TRP 237 H ILE 238 n 250 ILE 238 H GLN 239 n 251 GLN 239 H LYS 240 n 252 LYS 240 H VAL 241 n 253 VAL 241 H ILE 242 n 254 ILE 242 H ASP 243 n 255 ASP 243 H ARG 244 n 256 ARG 244 H LEU 245 n 257 LEU 245 H GLY 246 n 258 GLY 246 H SER 247 n 259 SER 247 H author_and_software_defined_assembly PISA 2 dimeric 2570 -12 14440 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 1 L THR -12 A THR 1 1 Y 1 L SER -11 A SER 2 1 Y 1 L GLU -10 A GLU 3 1 Y 1 L ASP -9 A ASP 4 1 Y 1 L HIS -8 A HIS 5 1 Y 1 L PHE -7 A PHE 6 1 Y 1 L GLN -6 A GLN 7 1 Y 1 L PRO -5 A PRO 8 1 Y 1 L PHE -4 A PHE 9 1 Y 1 L PHE -3 A PHE 10 1 Y 1 L ASN -2 A ASN 11 1 Y 1 L GLU -1 A GLU 12 1 Y 1 L LYS 0 A LYS 13 1 Y H 1 L THR 1 A THR 14 0 Y G 1 L PHE 1 A PHE 15 0 Y F 1 L GLY 1 A GLY 16 0 Y E 1 L ALA 1 A ALA 17 0 Y D 1 L GLY 1 A GLY 18 0 Y C 1 L GLU 1 A GLU 19 0 Y B 1 L ALA 1 A ALA 20 0 Y A 1 L ASP 1 A ASP 21 0 Y K 1 L ILE 14 A ILE 46 0 Y L 1 L GLU 14 A GLU 47 0 Y M 1 L GLY 14 A GLY 48 0 Y 1 L ARG 15 A ARG 49 0 Y 1 H TRP 148 B TRP 148 0 Y 1 H THR 149 B THR 149 0 Y A 1 H THR 149 B THR 150 0 Y B 1 H SER 149 B SER 151 0 Y C 1 H VAL 149 B VAL 152 0 Y D 1 H ALA 149 B ALA 153 0 Y E 1 H GLU 149 B GLU 154 0 Y 1 H LYS 236 B LYS 248 0 Y 1 H TRP 237 B TRP 249 0 Y 1 H ILE 238 B ILE 250 0 Y 1 H GLN 239 B GLN 251 0 Y 1 H LYS 240 B LYS 252 0 Y 1 H VAL 241 B VAL 253 0 Y 1 H ILE 242 B ILE 254 0 Y 1 H ASP 243 B ASP 255 0 Y 1 H ARG 244 B ARG 256 0 Y 1 H LEU 245 B LEU 257 0 Y 1 H GLY 246 B GLY 258 0 Y 1 H SER 247 B SER 259 0 Y 1 H H VAL GLU 79 80 -143.26 1 H H PRO PHE 198 199 143.62 1 H H LEU GLY 245 246 -148.62 1 H ARG 187 0.099 SIDE CHAIN 1 H TYR 225 0.167 SIDE CHAIN 1 3.88 0.50 120.30 124.18 L L L NE CZ NH1 ARG ARG ARG 4 4 4 N 1 -3.63 0.50 120.30 116.67 L L L NE CZ NH2 ARG ARG ARG 4 4 4 N B B B 1 -9.89 1.40 112.40 102.51 L L L CA CB CG2 THR THR THR 14 14 14 N J J J 1 -3.70 0.60 121.00 117.30 L L L CB CG CD2 TYR TYR TYR 14 14 14 N 1 6.58 0.80 106.30 112.88 H H H CD1 CG CD2 TRP TRP TRP 51 51 51 N 1 -5.85 0.80 107.30 101.45 H H H CE2 CD2 CG TRP TRP TRP 51 51 51 N D D D 1 6.34 0.80 106.30 112.64 H H H CD1 CG CD2 TRP TRP TRP 60 60 60 N D D D 1 -5.53 0.80 107.30 101.77 H H H CE2 CD2 CG TRP TRP TRP 60 60 60 N 1 -12.92 1.60 110.90 97.98 H H H CG1 CB CG2 VAL VAL VAL 61 61 61 N 1 -4.03 0.60 121.00 116.97 H H H CB CG CD1 TYR TYR TYR 89 89 89 N 1 6.04 0.80 106.30 112.34 H H H CD1 CG CD2 TRP TRP TRP 96 96 96 N 1 -8.50 1.30 127.00 118.50 H H H CB CG CD1 TRP TRP TRP 96 96 96 N 1 -6.47 0.80 107.30 100.83 H H H CE2 CD2 CG TRP TRP TRP 96 96 96 N 1 -12.22 1.70 111.00 98.78 H H H CB CG CD2 LEU LEU LEU 105 105 105 N 1 6.60 0.80 106.30 112.90 H H H CD1 CG CD2 TRP TRP TRP 141 141 141 N 1 -6.01 0.80 107.30 101.29 H H H CE2 CD2 CG TRP TRP TRP 141 141 141 N 1 -3.51 0.50 120.30 116.79 H H H NE CZ NH2 ARG ARG ARG 144 144 144 N 1 -4.71 0.50 120.30 115.59 H H H NE CZ NH2 ARG ARG ARG 145 145 145 N 1 5.38 0.80 106.30 111.68 H H H CD1 CG CD2 TRP TRP TRP 148 148 148 N 1 -8.27 1.30 127.00 118.73 H H H CB CG CD1 TRP TRP TRP 148 148 148 N 1 -4.94 0.80 107.30 102.36 H H H CE2 CD2 CG TRP TRP TRP 148 148 148 N 1 6.64 0.90 133.90 140.54 H H H CG CD2 CE3 TRP TRP TRP 148 148 148 N 1 3.96 0.50 120.30 124.26 H H H NE CZ NH1 ARG ARG ARG 175 175 175 N 1 7.69 1.10 114.20 121.89 H H H CA CB SG CYS CYS CYS 182 182 182 N 1 -3.30 0.50 120.30 117.00 H H H NE CZ NH2 ARG ARG ARG 187 187 187 N 1 -3.08 0.50 120.30 117.22 H H H NE CZ NH2 ARG ARG ARG 206 206 206 N 1 7.12 0.80 106.30 113.42 H H H CD1 CG CD2 TRP TRP TRP 207 207 207 N 1 -5.57 0.80 107.30 101.73 H H H CE2 CD2 CG TRP TRP TRP 207 207 207 N 1 15.91 2.20 117.20 133.11 H H H CA C N SER SER TRP 214 214 215 Y 1 5.49 0.80 106.30 111.79 H H H CD1 CG CD2 TRP TRP TRP 215 215 215 N 1 -5.42 0.80 107.30 101.88 H H H CE2 CD2 CG TRP TRP TRP 215 215 215 N 1 -5.22 0.60 121.00 115.78 H H H CB CG CD2 TYR TYR TYR 225 225 225 N 1 3.67 0.60 121.00 124.67 H H H CB CG CD1 TYR TYR TYR 225 225 225 N 1 6.96 0.80 106.30 113.26 H H H CD1 CG CD2 TRP TRP TRP 237 237 237 N 1 -6.23 1.00 110.10 103.87 H H H CG CD1 NE1 TRP TRP TRP 237 237 237 N 1 -5.63 0.80 107.30 101.67 H H H CE2 CD2 CG TRP TRP TRP 237 237 237 N 1 H H NE2 CD2 HIS HIS 119 119 -0.072 0.011 1.373 1.301 N 1 H H NE2 CD2 HIS HIS 131 131 -0.076 0.011 1.373 1.297 N 1 H H NE2 CD2 HIS HIS 230 230 -0.077 0.011 1.373 1.296 N E 1 L ALA 1 175.56 -170.21 B 1 L ALA 1 -133.40 -122.79 1 L PHE 7 -137.54 -92.29 A 1 L GLN 14 -12.59 -65.34 1 H TRP 29 -38.87 -6.46 1 H LEU 41 -102.31 -60.35 1 H ARG 50 -152.12 10.51 E 1 H ASP 60 39.80 25.40 1 H HIS 71 -156.23 -54.95 1 H LYS 97 -91.08 31.14 A 1 H GLU 97 -169.15 -72.53 1 H ASN 98 -154.46 26.26 1 H ASP 116 -35.68 -23.78 1 H ASN 143 -24.18 124.61 1 H THR 149 -67.29 93.34 E 1 H GLU 149 73.07 -37.87 1 H VAL 150 -75.23 30.82 B 1 H GLU 186 -75.38 20.36 1 H ASN 205 72.96 33.35 THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS. NOTE THAT THE OCCUPANCY OF RESIDUES 148 - 149E IS GIVEN AS 0.0 INDICATING THAT THEY WERE NOT SEEN IN THE ELECTRON DENSITY MAPS. 0.178 0.178 2.3 8.0 1 2.3 8.0 228 2649 37 0 2384 0.012 3.089 model building X-PLOR refinement X-PLOR phasing X-PLOR EPSILON-THROMBIN (E.C.3.4.21.5) NON-COVALENT COMPLEX WITH NAPAP REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS 1 N N 2 N N 3 N N 4 N N 4 N N L GLU 14 A GLU 38 HELX_P 3.6/13 L SER 14 A SER 44 1 1 7 C I H ALA 55 B ALA 41 HELX_P H LEU 59 B LEU 45 5 2 5 H TYR 60 B TYR 47 HELX_P H ASP 60 B ASP 51 5 3 5 A E H ASP 125 B ASP 122 HELX_P 3.6/13 H LEU 129 B LEU 129 1 4 8 C H GLU 164 B GLU 169 HELX_P 3.6/13 H LYS 169 B LYS 174 1 5 6 H CYS 168 B CYS 173 HELX_P H THR 172 B THR 177 5 6 5 H VAL 231 B VAL 243 HELX_P H LYS 235 B LYS 247 5 7 5 H LEU 234 B LEU 246 HELX_P 3.6/13 H ASP 243 B ASP 255 1 8 10 disulf 2.028 L CYS 1 A SG CYS 22 1_555 H CYS 122 B SG CYS 119 1_555 disulf 1.988 H CYS 42 B SG CYS 28 1_555 H CYS 58 B SG CYS 44 1_555 disulf 1.891 H CYS 168 B SG CYS 173 1_555 H CYS 182 B SG CYS 187 1_555 disulf 1.914 H CYS 191 B SG CYS 201 1_555 H CYS 220 B SG CYS 231 1_555 HYDROLASE/HYDROLASE inhibitor SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX H SER 36 B SER 22 A 1 H PRO 37 B PRO 23 -8.21 THRB_BOVIN UNP 1 1 P00735 MARVRGPRLPGCLALAALFSLVHSQHVFLAHQQASSLLQRARRANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSA TDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRN PDGSITGPWCYTTSPTLRREECSVPVCGQDRVTVEVIPRSGGSTTSQSPLLETCVPDRGREYRGRLAVTTSGSRCLAWSS EQAKALSKDQDFNPAVPLAENFCRNPDGDEEGAWCYVADQPGDFEYCDLNYCEEPVDGDLGDRLGEDPDPDAAIEGRTSE DHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGRIVEGQDAEVGLSPWQVMLFRKSPQELLCGASLIS DRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDY IHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGE GKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS THRB_BOVIN UNP 2 1 P00735 MARVRGPRLPGCLALAALFSLVHSQHVFLAHQQASSLLQRARRANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSA TDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRN PDGSITGPWCYTTSPTLRREECSVPVCGQDRVTVEVIPRSGGSTTSQSPLLETCVPDRGREYRGRLAVTTSGSRCLAWSS EQAKALSKDQDFNPAVPLAENFCRNPDGDEEGAWCYVADQPGDFEYCDLNYCEEPVDGDLGDRLGEDPDPDAAIEGRTSE DHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGRIVEGQDAEVGLSPWQVMLFRKSPQELLCGASLIS DRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDY IHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGE GKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS 318 366 1ETS -12 15 P00735 L 1 1 49 367 625 1ETS 16 247 P00735 H 2 1 259 7 7 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel H LYS 81 B LYS 77 H ASN 95 B ASN 91 H ASP 100 B ASP 97 H LYS 109 B LYS 106 H VAL 52 B VAL 38 H THR 54 B THR 40 H GLU 39 B GLU 25 H LEU 46 B LEU 32 H TRP 29 B TRP 14 H ARG 35 B ARG 20 H VAL 66 B VAL 61 H ILE 68 B ILE 63 H LYS 81 B LYS 77 H ASN 95 B ASN 91 H VAL 150 B VAL 155 H LEU 162 B LEU 167 H PHE 134 B PHE 134 H ARG 144 B ARG 144 H PHE 199 B PHE 209 H SER 203 B SER 213 H ARG 206 B ARG 218 H TRP 215 B TRP 227 H GLY 226 B GLY 238 H THR 229 B THR 241 H PHE 181 B PHE 186 H ALA 183 B ALA 188 H VAL 150 B VAL 155 H LEU 162 B LEU 167 BINDING SITE FOR RESIDUE MID H 1 Software 14 H HIS 57 B HIS 43 14 1_555 H TRP 60 B TRP 50 D 14 1_555 H ASN 98 B ASN 95 14 1_555 H LEU 99 B LEU 96 14 1_555 H ASP 189 B ASP 199 14 1_555 H ALA 190 B ALA 200 14 1_555 H GLU 192 B GLU 202 14 1_555 H SER 195 B SER 205 14 1_555 H SER 214 B SER 226 14 1_555 H TRP 215 B TRP 227 14 1_555 H GLY 216 B GLY 228 14 1_555 H GLU 217 B GLU 229 14 1_555 H GLY 219 B GLY 230 14 1_555 H HOH 576 E HOH 14 1_555 94 P 42 21 2