data_1KI8 # _model_server_result.job_id -qd_HfEJ0nGbWdPVHyKH7Q _model_server_result.datetime_utc '2024-11-23 05:16:55' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1ki8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 1KI8 # _exptl.entry_id 1KI8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 333.135 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-BROMOVINYLDEOXYURIDINE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 1KI8 _cell.length_a 113.4 _cell.length_b 116.9 _cell.length_c 108.2 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KI8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 116.9 108.2 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C11 H13 Br N2 O5' _chem_comp.formula_weight 333.135 _chem_comp.id BVD _chem_comp.mon_nstd_flag . _chem_comp.name 5-BROMOVINYLDEOXYURIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' BVD sing 70 n n O5' HO5' BVD sing 71 n n C5' C4' BVD sing 72 n n C5' "H5'1" BVD sing 73 n n C5' "H5'2" BVD sing 74 n n C4' O4' BVD sing 75 n n C4' C3' BVD sing 76 n n C4' H4' BVD sing 77 n n O4' C1' BVD sing 78 n n C1' N1 BVD sing 79 n n C1' C2' BVD sing 80 n n C1' H1' BVD sing 81 n n N1 C6 BVD sing 82 n n N1 C2 BVD sing 83 n n C6 C5 BVD doub 84 n n C6 H6 BVD sing 85 n n C2 O2 BVD doub 86 n n C2 N3 BVD sing 87 n n N3 C4 BVD sing 88 n n N3 HN3 BVD sing 89 n n C4 O4 BVD doub 90 n n C4 C5 BVD sing 91 n n C5 C5A BVD sing 92 n n C5A C5B BVD doub 93 e n C5A H5A BVD sing 94 n n C5B BR BVD sing 95 n n C5B H5B BVD sing 96 n n C2' C3' BVD sing 97 n n C2' "H2'1" BVD sing 98 n n C2' "H2'2" BVD sing 99 n n C3' O3' BVD sing 100 n n C3' H3' BVD sing 101 n n O3' HO3' BVD sing 102 n n # _atom_sites.entry_id 1KI8 _atom_sites.fract_transf_matrix[1][1] 0.008818 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008554 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009242 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SO4 A 1 3 3 SO4 SO4 . D 3 BVD A 1 1 1 BVD BVD . E 2 SO4 B 1 4 4 SO4 SO4 . F 3 BVD B 1 2 2 BVD BVD . G 4 HOH A 1 501 501 HOH HOH . G 4 HOH A 2 502 502 HOH HOH . G 4 HOH A 3 503 503 HOH HOH . G 4 HOH A 4 508 508 HOH HOH . G 4 HOH A 5 510 510 HOH HOH . G 4 HOH A 6 511 511 HOH HOH . G 4 HOH A 7 513 513 HOH HOH . G 4 HOH A 8 514 514 HOH HOH . G 4 HOH A 9 515 515 HOH HOH . G 4 HOH A 10 520 520 HOH HOH . G 4 HOH A 11 521 521 HOH HOH . G 4 HOH A 12 523 523 HOH HOH . G 4 HOH A 13 524 524 HOH HOH . G 4 HOH A 14 525 525 HOH HOH . G 4 HOH A 15 527 527 HOH HOH . G 4 HOH A 16 528 528 HOH HOH . G 4 HOH A 17 530 530 HOH HOH . G 4 HOH A 18 531 531 HOH HOH . G 4 HOH A 19 532 532 HOH HOH . G 4 HOH A 20 535 535 HOH HOH . G 4 HOH A 21 537 537 HOH HOH . G 4 HOH A 22 538 538 HOH HOH . G 4 HOH A 23 540 540 HOH HOH . G 4 HOH A 24 541 541 HOH HOH . G 4 HOH A 25 545 545 HOH HOH . G 4 HOH A 26 546 546 HOH HOH . G 4 HOH A 27 547 547 HOH HOH . G 4 HOH A 28 554 554 HOH HOH . G 4 HOH A 29 555 555 HOH HOH . G 4 HOH A 30 556 556 HOH HOH . G 4 HOH A 31 557 557 HOH HOH . G 4 HOH A 32 558 558 HOH HOH . G 4 HOH A 33 562 562 HOH HOH . G 4 HOH A 34 564 564 HOH HOH . G 4 HOH A 35 566 566 HOH HOH . G 4 HOH A 36 567 567 HOH HOH . G 4 HOH A 37 568 568 HOH HOH . G 4 HOH A 38 569 569 HOH HOH . G 4 HOH A 39 570 570 HOH HOH . G 4 HOH A 40 573 573 HOH HOH . G 4 HOH A 41 574 574 HOH HOH . G 4 HOH A 42 577 577 HOH HOH . G 4 HOH A 43 578 578 HOH HOH . G 4 HOH A 44 580 580 HOH HOH . G 4 HOH A 45 581 581 HOH HOH . G 4 HOH A 46 584 584 HOH HOH . G 4 HOH A 47 586 586 HOH HOH . G 4 HOH A 48 587 587 HOH HOH . G 4 HOH A 49 588 588 HOH HOH . G 4 HOH A 50 589 589 HOH HOH . G 4 HOH A 51 590 590 HOH HOH . G 4 HOH A 52 591 591 HOH HOH . G 4 HOH A 53 593 593 HOH HOH . G 4 HOH A 54 597 597 HOH HOH . G 4 HOH A 55 599 599 HOH HOH . G 4 HOH A 56 603 603 HOH HOH . G 4 HOH A 57 605 605 HOH HOH . G 4 HOH A 58 607 607 HOH HOH . G 4 HOH A 59 614 614 HOH HOH . G 4 HOH A 60 616 616 HOH HOH . G 4 HOH A 61 618 618 HOH HOH . G 4 HOH A 62 622 622 HOH HOH . G 4 HOH A 63 626 626 HOH HOH . G 4 HOH A 64 628 628 HOH HOH . G 4 HOH A 65 631 631 HOH HOH . G 4 HOH A 66 634 634 HOH HOH . G 4 HOH A 67 635 635 HOH HOH . G 4 HOH A 68 636 636 HOH HOH . G 4 HOH A 69 637 637 HOH HOH . G 4 HOH A 70 639 639 HOH HOH . G 4 HOH A 71 640 640 HOH HOH . G 4 HOH A 72 641 641 HOH HOH . G 4 HOH A 73 644 644 HOH HOH . G 4 HOH A 74 645 645 HOH HOH . G 4 HOH A 75 648 648 HOH HOH . G 4 HOH A 76 649 649 HOH HOH . G 4 HOH A 77 652 652 HOH HOH . G 4 HOH A 78 653 653 HOH HOH . G 4 HOH A 79 654 654 HOH HOH . G 4 HOH A 80 655 655 HOH HOH . G 4 HOH A 81 656 656 HOH HOH . G 4 HOH A 82 662 662 HOH HOH . G 4 HOH A 83 664 664 HOH HOH . G 4 HOH A 84 665 665 HOH HOH . G 4 HOH A 85 667 667 HOH HOH . G 4 HOH A 86 668 668 HOH HOH . G 4 HOH A 87 670 670 HOH HOH . G 4 HOH A 88 671 671 HOH HOH . G 4 HOH A 89 673 673 HOH HOH . G 4 HOH A 90 676 676 HOH HOH . G 4 HOH A 91 677 677 HOH HOH . G 4 HOH A 92 678 678 HOH HOH . G 4 HOH A 93 679 679 HOH HOH . G 4 HOH A 94 680 680 HOH HOH . G 4 HOH A 95 681 681 HOH HOH . G 4 HOH A 96 684 684 HOH HOH . G 4 HOH A 97 689 689 HOH HOH . G 4 HOH A 98 690 690 HOH HOH . G 4 HOH A 99 691 691 HOH HOH . G 4 HOH A 100 692 692 HOH HOH . G 4 HOH A 101 693 693 HOH HOH . G 4 HOH A 102 694 694 HOH HOH . G 4 HOH A 103 700 700 HOH HOH . G 4 HOH A 104 704 704 HOH HOH . G 4 HOH A 105 705 705 HOH HOH . G 4 HOH A 106 707 707 HOH HOH . G 4 HOH A 107 708 708 HOH HOH . G 4 HOH A 108 710 710 HOH HOH . G 4 HOH A 109 711 711 HOH HOH . G 4 HOH A 110 712 712 HOH HOH . G 4 HOH A 111 715 715 HOH HOH . G 4 HOH A 112 717 717 HOH HOH . G 4 HOH A 113 718 718 HOH HOH . G 4 HOH A 114 719 719 HOH HOH . G 4 HOH A 115 721 721 HOH HOH . G 4 HOH A 116 722 722 HOH HOH . G 4 HOH A 117 724 724 HOH HOH . G 4 HOH A 118 734 734 HOH HOH . G 4 HOH A 119 736 736 HOH HOH . G 4 HOH A 120 737 737 HOH HOH . G 4 HOH A 121 739 739 HOH HOH . G 4 HOH A 122 740 740 HOH HOH . G 4 HOH A 123 743 743 HOH HOH . G 4 HOH A 124 744 744 HOH HOH . G 4 HOH A 125 746 746 HOH HOH . G 4 HOH A 126 749 749 HOH HOH . H 4 HOH B 1 504 504 HOH HOH . H 4 HOH B 2 505 505 HOH HOH . H 4 HOH B 3 506 506 HOH HOH . H 4 HOH B 4 507 507 HOH HOH . H 4 HOH B 5 509 509 HOH HOH . H 4 HOH B 6 512 512 HOH HOH . H 4 HOH B 7 516 516 HOH HOH . H 4 HOH B 8 517 517 HOH HOH . H 4 HOH B 9 518 518 HOH HOH . H 4 HOH B 10 519 519 HOH HOH . H 4 HOH B 11 522 522 HOH HOH . H 4 HOH B 12 526 526 HOH HOH . H 4 HOH B 13 529 529 HOH HOH . H 4 HOH B 14 533 533 HOH HOH . H 4 HOH B 15 534 534 HOH HOH . H 4 HOH B 16 536 536 HOH HOH . H 4 HOH B 17 539 539 HOH HOH . H 4 HOH B 18 542 542 HOH HOH . H 4 HOH B 19 543 543 HOH HOH . H 4 HOH B 20 544 544 HOH HOH . H 4 HOH B 21 548 548 HOH HOH . H 4 HOH B 22 549 549 HOH HOH . H 4 HOH B 23 550 550 HOH HOH . H 4 HOH B 24 551 551 HOH HOH . H 4 HOH B 25 552 552 HOH HOH . H 4 HOH B 26 553 553 HOH HOH . H 4 HOH B 27 559 559 HOH HOH . H 4 HOH B 28 560 560 HOH HOH . H 4 HOH B 29 561 561 HOH HOH . H 4 HOH B 30 563 563 HOH HOH . H 4 HOH B 31 565 565 HOH HOH . H 4 HOH B 32 571 571 HOH HOH . H 4 HOH B 33 572 572 HOH HOH . H 4 HOH B 34 575 575 HOH HOH . H 4 HOH B 35 576 576 HOH HOH . H 4 HOH B 36 579 579 HOH HOH . H 4 HOH B 37 582 582 HOH HOH . H 4 HOH B 38 583 583 HOH HOH . H 4 HOH B 39 585 585 HOH HOH . H 4 HOH B 40 592 592 HOH HOH . H 4 HOH B 41 594 594 HOH HOH . H 4 HOH B 42 595 595 HOH HOH . H 4 HOH B 43 596 596 HOH HOH . H 4 HOH B 44 598 598 HOH HOH . H 4 HOH B 45 600 600 HOH HOH . H 4 HOH B 46 601 601 HOH HOH . H 4 HOH B 47 602 602 HOH HOH . H 4 HOH B 48 604 604 HOH HOH . H 4 HOH B 49 606 606 HOH HOH . H 4 HOH B 50 608 608 HOH HOH . H 4 HOH B 51 609 609 HOH HOH . H 4 HOH B 52 610 610 HOH HOH . H 4 HOH B 53 611 611 HOH HOH . H 4 HOH B 54 612 612 HOH HOH . H 4 HOH B 55 613 613 HOH HOH . H 4 HOH B 56 615 615 HOH HOH . H 4 HOH B 57 617 617 HOH HOH . H 4 HOH B 58 619 619 HOH HOH . H 4 HOH B 59 620 620 HOH HOH . H 4 HOH B 60 621 621 HOH HOH . H 4 HOH B 61 623 623 HOH HOH . H 4 HOH B 62 624 624 HOH HOH . H 4 HOH B 63 625 625 HOH HOH . H 4 HOH B 64 627 627 HOH HOH . H 4 HOH B 65 629 629 HOH HOH . H 4 HOH B 66 630 630 HOH HOH . H 4 HOH B 67 632 632 HOH HOH . H 4 HOH B 68 633 633 HOH HOH . H 4 HOH B 69 638 638 HOH HOH . H 4 HOH B 70 642 642 HOH HOH . H 4 HOH B 71 643 643 HOH HOH . H 4 HOH B 72 646 646 HOH HOH . H 4 HOH B 73 647 647 HOH HOH . H 4 HOH B 74 650 650 HOH HOH . H 4 HOH B 75 651 651 HOH HOH . H 4 HOH B 76 657 657 HOH HOH . H 4 HOH B 77 658 658 HOH HOH . H 4 HOH B 78 659 659 HOH HOH . H 4 HOH B 79 660 660 HOH HOH . H 4 HOH B 80 661 661 HOH HOH . H 4 HOH B 81 663 663 HOH HOH . H 4 HOH B 82 666 666 HOH HOH . H 4 HOH B 83 669 669 HOH HOH . H 4 HOH B 84 672 672 HOH HOH . H 4 HOH B 85 674 674 HOH HOH . H 4 HOH B 86 675 675 HOH HOH . H 4 HOH B 87 682 682 HOH HOH . H 4 HOH B 88 683 683 HOH HOH . H 4 HOH B 89 685 685 HOH HOH . H 4 HOH B 90 686 686 HOH HOH . H 4 HOH B 91 687 687 HOH HOH . H 4 HOH B 92 688 688 HOH HOH . H 4 HOH B 93 695 695 HOH HOH . H 4 HOH B 94 696 696 HOH HOH . H 4 HOH B 95 697 697 HOH HOH . H 4 HOH B 96 698 698 HOH HOH . H 4 HOH B 97 699 699 HOH HOH . H 4 HOH B 98 701 701 HOH HOH . H 4 HOH B 99 702 702 HOH HOH . H 4 HOH B 100 703 703 HOH HOH . H 4 HOH B 101 706 706 HOH HOH . H 4 HOH B 102 709 709 HOH HOH . H 4 HOH B 103 713 713 HOH HOH . H 4 HOH B 104 714 714 HOH HOH . H 4 HOH B 105 716 716 HOH HOH . H 4 HOH B 106 720 720 HOH HOH . H 4 HOH B 107 723 723 HOH HOH . H 4 HOH B 108 725 725 HOH HOH . H 4 HOH B 109 726 726 HOH HOH . H 4 HOH B 110 727 727 HOH HOH . H 4 HOH B 111 728 728 HOH HOH . H 4 HOH B 112 729 729 HOH HOH . H 4 HOH B 113 730 730 HOH HOH . H 4 HOH B 114 731 731 HOH HOH . H 4 HOH B 115 732 732 HOH HOH . H 4 HOH B 116 733 733 HOH HOH . H 4 HOH B 117 735 735 HOH HOH . H 4 HOH B 118 738 738 HOH HOH . H 4 HOH B 119 741 741 HOH HOH . H 4 HOH B 120 742 742 HOH HOH . H 4 HOH B 121 745 745 HOH HOH . H 4 HOH B 122 747 747 HOH HOH . H 4 HOH B 123 748 748 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' BVD . . . D 3 49.962 82.126 52.892 1 14.4 ? O5' BVD 1 A 1 HETATM 2 C C5' BVD . . . D 3 50.804 83.282 52.944 1 11.77 ? C5' BVD 1 A 1 HETATM 3 C C4' BVD . . . D 3 50.355 84.289 54.037 1 12.83 ? C4' BVD 1 A 1 HETATM 4 O O4' BVD . . . D 3 48.989 84.747 53.847 1 13.03 ? O4' BVD 1 A 1 HETATM 5 C C1' BVD . . . D 3 47.988 84.197 54.765 1 10.27 ? C1' BVD 1 A 1 HETATM 6 N N1 BVD . . . D 3 46.666 83.837 54.093 1 8.03 ? N1 BVD 1 A 1 HETATM 7 C C6 BVD . . . D 3 46.621 82.883 53.108 1 9.01 ? C6 BVD 1 A 1 HETATM 8 C C2 BVD . . . D 3 45.536 84.512 54.435 1 8.69 ? C2 BVD 1 A 1 HETATM 9 O O2 BVD . . . D 3 45.44 85.299 55.369 1 10.99 ? O2 BVD 1 A 1 HETATM 10 N N3 BVD . . . D 3 44.476 84.249 53.705 1 9.35 ? N3 BVD 1 A 1 HETATM 11 C C4 BVD . . . D 3 44.354 83.251 52.783 1 10.21 ? C4 BVD 1 A 1 HETATM 12 O O4 BVD . . . D 3 43.232 82.946 52.405 1 11.15 ? O4 BVD 1 A 1 HETATM 13 C C5 BVD . . . D 3 45.554 82.611 52.377 1 9.65 ? C5 BVD 1 A 1 HETATM 14 C C5A BVD . . . D 3 45.636 81.606 51.428 1 11.86 ? C5A BVD 1 A 1 HETATM 15 C C5B BVD . . . D 3 44.73 81.495 50.423 1 15.72 ? C5B BVD 1 A 1 HETATM 16 BR BR BVD . . . D 3 44.917 80.189 49.01 1 26.88 ? BR BVD 1 A 1 HETATM 17 C C2' BVD . . . D 3 48.811 83.124 55.451 1 10.75 ? C2' BVD 1 A 1 HETATM 18 C C3' BVD . . . D 3 50.266 83.694 55.44 1 11.65 ? C3' BVD 1 A 1 HETATM 19 O O3' BVD . . . D 3 50.296 84.82 56.276 1 11.88 ? O3' BVD 1 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #