data_5YK1 # _model_server_result.job_id kbqJY_Bw4xpJpzh-trHwUg _model_server_result.datetime_utc '2024-11-20 05:27:50' _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 5yk1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5YK1 # _exptl.entry_id 5YK1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 5YK1 _cell.length_a 186.734 _cell.length_b 186.734 _cell.length_c 67.499 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YK1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA hexameric 6 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,I 1 1 A,B,C,D,E,F,G,H,I 2 1,2,3,4,5,6 # 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' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 93.367 -161.716388 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 186.734 0 0 4 'crystal symmetry operation' 10_555 -y,-x,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 33.7495 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 186.734 0 33.7495 6 'crystal symmetry operation' 12_545 x,x-y-1,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 93.367 -161.716388 33.7495 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 5YK1 _atom_sites.fract_transf_matrix[1][1] 0.005355 _atom_sites.fract_transf_matrix[1][2] 0.003092 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006184 _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] 0.014815 _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 B 2 ANP A 1 501 445 ANP ANP . C 3 SO4 A 1 502 447 SO4 SO4 . D 3 SO4 A 1 503 448 SO4 SO4 . E 3 SO4 A 1 504 449 SO4 SO4 . F 3 SO4 A 1 505 450 SO4 SO4 . G 3 SO4 A 1 506 451 SO4 SO4 . H 4 GOL A 1 507 452 GOL GOL . I 5 HOH A 1 601 523 HOH HOH . I 5 HOH A 2 602 681 HOH HOH . I 5 HOH A 3 603 581 HOH HOH . I 5 HOH A 4 604 526 HOH HOH . I 5 HOH A 5 605 632 HOH HOH . I 5 HOH A 6 606 492 HOH HOH . I 5 HOH A 7 607 678 HOH HOH . I 5 HOH A 8 608 531 HOH HOH . I 5 HOH A 9 609 633 HOH HOH . I 5 HOH A 10 610 637 HOH HOH . I 5 HOH A 11 611 460 HOH HOH . I 5 HOH A 12 612 662 HOH HOH . I 5 HOH A 13 613 475 HOH HOH . I 5 HOH A 14 614 609 HOH HOH . I 5 HOH A 15 615 661 HOH HOH . I 5 HOH A 16 616 564 HOH HOH . I 5 HOH A 17 617 509 HOH HOH . I 5 HOH A 18 618 507 HOH HOH . I 5 HOH A 19 619 567 HOH HOH . I 5 HOH A 20 620 464 HOH HOH . I 5 HOH A 21 621 680 HOH HOH . I 5 HOH A 22 622 489 HOH HOH . I 5 HOH A 23 623 476 HOH HOH . I 5 HOH A 24 624 488 HOH HOH . I 5 HOH A 25 625 469 HOH HOH . I 5 HOH A 26 626 629 HOH HOH . I 5 HOH A 27 627 677 HOH HOH . I 5 HOH A 28 628 676 HOH HOH . I 5 HOH A 29 629 496 HOH HOH . I 5 HOH A 30 630 472 HOH HOH . I 5 HOH A 31 631 462 HOH HOH . I 5 HOH A 32 632 479 HOH HOH . I 5 HOH A 33 633 537 HOH HOH . I 5 HOH A 34 634 653 HOH HOH . I 5 HOH A 35 635 463 HOH HOH . I 5 HOH A 36 636 474 HOH HOH . I 5 HOH A 37 637 568 HOH HOH . I 5 HOH A 38 638 466 HOH HOH . I 5 HOH A 39 639 615 HOH HOH . I 5 HOH A 40 640 461 HOH HOH . I 5 HOH A 41 641 565 HOH HOH . I 5 HOH A 42 642 498 HOH HOH . I 5 HOH A 43 643 595 HOH HOH . I 5 HOH A 44 644 611 HOH HOH . I 5 HOH A 45 645 591 HOH HOH . I 5 HOH A 46 646 511 HOH HOH . I 5 HOH A 47 647 482 HOH HOH . I 5 HOH A 48 648 542 HOH HOH . I 5 HOH A 49 649 481 HOH HOH . I 5 HOH A 50 650 467 HOH HOH . I 5 HOH A 51 651 520 HOH HOH . I 5 HOH A 52 652 551 HOH HOH . I 5 HOH A 53 653 557 HOH HOH . I 5 HOH A 54 654 524 HOH HOH . I 5 HOH A 55 655 486 HOH HOH . I 5 HOH A 56 656 625 HOH HOH . I 5 HOH A 57 657 664 HOH HOH . I 5 HOH A 58 658 540 HOH HOH . I 5 HOH A 59 659 628 HOH HOH . I 5 HOH A 60 660 502 HOH HOH . I 5 HOH A 61 661 529 HOH HOH . I 5 HOH A 62 662 570 HOH HOH . I 5 HOH A 63 663 651 HOH HOH . I 5 HOH A 64 664 553 HOH HOH . I 5 HOH A 65 665 477 HOH HOH . I 5 HOH A 66 666 554 HOH HOH . I 5 HOH A 67 667 562 HOH HOH . I 5 HOH A 68 668 548 HOH HOH . I 5 HOH A 69 669 487 HOH HOH . I 5 HOH A 70 670 499 HOH HOH . I 5 HOH A 71 671 541 HOH HOH . I 5 HOH A 72 672 508 HOH HOH . I 5 HOH A 73 673 468 HOH HOH . I 5 HOH A 74 674 533 HOH HOH . I 5 HOH A 75 675 543 HOH HOH . I 5 HOH A 76 676 535 HOH HOH . I 5 HOH A 77 677 506 HOH HOH . I 5 HOH A 78 678 485 HOH HOH . I 5 HOH A 79 679 679 HOH HOH . I 5 HOH A 80 680 601 HOH HOH . I 5 HOH A 81 681 470 HOH HOH . I 5 HOH A 82 682 655 HOH HOH . I 5 HOH A 83 683 586 HOH HOH . I 5 HOH A 84 684 635 HOH HOH . I 5 HOH A 85 685 530 HOH HOH . I 5 HOH A 86 686 643 HOH HOH . I 5 HOH A 87 687 552 HOH HOH . I 5 HOH A 88 688 623 HOH HOH . I 5 HOH A 89 689 534 HOH HOH . I 5 HOH A 90 690 503 HOH HOH . I 5 HOH A 91 691 483 HOH HOH . I 5 HOH A 92 692 596 HOH HOH . I 5 HOH A 93 693 480 HOH HOH . I 5 HOH A 94 694 577 HOH HOH . I 5 HOH A 95 695 649 HOH HOH . I 5 HOH A 96 696 668 HOH HOH . I 5 HOH A 97 697 518 HOH HOH . I 5 HOH A 98 698 528 HOH HOH . I 5 HOH A 99 699 606 HOH HOH . I 5 HOH A 100 700 490 HOH HOH . I 5 HOH A 101 701 605 HOH HOH . I 5 HOH A 102 702 547 HOH HOH . I 5 HOH A 103 703 555 HOH HOH . I 5 HOH A 104 704 522 HOH HOH . I 5 HOH A 105 705 561 HOH HOH . I 5 HOH A 106 706 550 HOH HOH . I 5 HOH A 107 707 569 HOH HOH . I 5 HOH A 108 708 504 HOH HOH . I 5 HOH A 109 709 588 HOH HOH . I 5 HOH A 110 710 580 HOH HOH . I 5 HOH A 111 711 494 HOH HOH . I 5 HOH A 112 712 624 HOH HOH . I 5 HOH A 113 713 493 HOH HOH . I 5 HOH A 114 714 560 HOH HOH . I 5 HOH A 115 715 616 HOH HOH . I 5 HOH A 116 716 572 HOH HOH . I 5 HOH A 117 717 585 HOH HOH . I 5 HOH A 118 718 589 HOH HOH . I 5 HOH A 119 719 563 HOH HOH . I 5 HOH A 120 720 544 HOH HOH . I 5 HOH A 121 721 671 HOH HOH . I 5 HOH A 122 722 604 HOH HOH . I 5 HOH A 123 723 545 HOH HOH . I 5 HOH A 124 724 636 HOH HOH . I 5 HOH A 125 725 519 HOH HOH . I 5 HOH A 126 726 669 HOH HOH . I 5 HOH A 127 727 634 HOH HOH . I 5 HOH A 128 728 614 HOH HOH . I 5 HOH A 129 729 471 HOH HOH . I 5 HOH A 130 730 573 HOH HOH . I 5 HOH A 131 731 648 HOH HOH . I 5 HOH A 132 732 574 HOH HOH . I 5 HOH A 133 733 647 HOH HOH . I 5 HOH A 134 734 510 HOH HOH . I 5 HOH A 135 735 491 HOH HOH . I 5 HOH A 136 736 558 HOH HOH . I 5 HOH A 137 737 578 HOH HOH . I 5 HOH A 138 738 538 HOH HOH . I 5 HOH A 139 739 516 HOH HOH . I 5 HOH A 140 740 501 HOH HOH . I 5 HOH A 141 741 500 HOH HOH . I 5 HOH A 142 742 600 HOH HOH . I 5 HOH A 143 743 495 HOH HOH . I 5 HOH A 144 744 619 HOH HOH . I 5 HOH A 145 745 587 HOH HOH . I 5 HOH A 146 746 665 HOH HOH . I 5 HOH A 147 747 590 HOH HOH . I 5 HOH A 148 748 549 HOH HOH . I 5 HOH A 149 749 618 HOH HOH . I 5 HOH A 150 750 478 HOH HOH . I 5 HOH A 151 751 525 HOH HOH . I 5 HOH A 152 752 667 HOH HOH . I 5 HOH A 153 753 657 HOH HOH . I 5 HOH A 154 754 673 HOH HOH . I 5 HOH A 155 755 654 HOH HOH . I 5 HOH A 156 756 597 HOH HOH . I 5 HOH A 157 757 583 HOH HOH . I 5 HOH A 158 758 584 HOH HOH . I 5 HOH A 159 759 631 HOH HOH . I 5 HOH A 160 760 645 HOH HOH . I 5 HOH A 161 761 497 HOH HOH . I 5 HOH A 162 762 620 HOH HOH . I 5 HOH A 163 763 582 HOH HOH . I 5 HOH A 164 764 579 HOH HOH . I 5 HOH A 165 765 663 HOH HOH . I 5 HOH A 166 766 594 HOH HOH . I 5 HOH A 167 767 571 HOH HOH . I 5 HOH A 168 768 556 HOH HOH . I 5 HOH A 169 769 675 HOH HOH . I 5 HOH A 170 770 515 HOH HOH . I 5 HOH A 171 771 644 HOH HOH . I 5 HOH A 172 772 513 HOH HOH . I 5 HOH A 173 773 505 HOH HOH . I 5 HOH A 174 774 627 HOH HOH . I 5 HOH A 175 775 532 HOH HOH . I 5 HOH A 176 776 622 HOH HOH . I 5 HOH A 177 777 607 HOH HOH . I 5 HOH A 178 778 546 HOH HOH . I 5 HOH A 179 779 650 HOH HOH . I 5 HOH A 180 780 539 HOH HOH . I 5 HOH A 181 781 670 HOH HOH . I 5 HOH A 182 782 660 HOH HOH . I 5 HOH A 183 783 672 HOH HOH . I 5 HOH A 184 784 592 HOH HOH . I 5 HOH A 185 785 658 HOH HOH . I 5 HOH A 186 786 638 HOH HOH . I 5 HOH A 187 787 639 HOH HOH . I 5 HOH A 188 788 674 HOH HOH . I 5 HOH A 189 789 599 HOH HOH . I 5 HOH A 190 790 612 HOH HOH . I 5 HOH A 191 791 652 HOH HOH . I 5 HOH A 192 792 682 HOH HOH . I 5 HOH A 193 794 630 HOH HOH . I 5 HOH A 194 795 517 HOH HOH . I 5 HOH A 195 796 626 HOH HOH . I 5 HOH A 196 797 656 HOH HOH . I 5 HOH A 197 799 608 HOH HOH . I 5 HOH A 198 800 646 HOH HOH . I 5 HOH A 199 801 610 HOH HOH . I 5 HOH A 200 802 575 HOH HOH . I 5 HOH A 201 803 617 HOH HOH . I 5 HOH A 202 804 521 HOH HOH . I 5 HOH A 203 805 621 HOH HOH . I 5 HOH A 204 806 514 HOH HOH . I 5 HOH A 205 807 593 HOH HOH . I 5 HOH A 206 808 666 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 P PG ANP . . . B 2 68.768 -17.785 13.134 0.72 94.44 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 67.52 -17.395 12.241 0.72 63.98 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 68.268 -18.467 14.464 0.72 112.41 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 69.637 -18.748 12.389 0.72 93.83 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 68.662 -15.231 14.198 0.72 53.73 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 67.234 -15.623 13.994 0.72 47.31 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 68.957 -15.134 15.726 0.72 39.66 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 69.66 -16.394 13.516 0.72 104.88 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 69.362 -13.698 12.023 0.72 70.26 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 69.178 -14.969 11.284 0.72 69.52 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 70.805 -13.184 12.042 0.72 69.47 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 68.924 -13.835 13.548 0.72 118.44 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 68.384 -12.636 11.383 0.72 56.16 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 67.029 -12.47 11.845 0.72 54.06 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 66.417 -11.318 11.088 0.72 57.41 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 67.223 -10.137 11.281 0.72 55.03 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 66.28 -11.531 9.577 0.72 61.6 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 64.939 -11.337 9.143 0.72 65.34 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 67.253 -10.513 8.962 0.72 58.43 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 66.71 -9.94 7.777 0.72 61.69 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 67.383 -9.455 10.057 0.72 50.78 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 68.685 -8.793 10.077 0.72 45.03 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 69.781 -9.161 10.817 0.72 42.55 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 70.829 -8.397 10.634 0.72 45.89 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 70.4 -7.459 9.706 0.72 39.7 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 71.041 -6.367 9.091 0.72 33.89 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 72.311 -6.02 9.329 0.72 23.86 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 70.328 -5.635 8.206 0.72 32.31 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 69.06 -5.98 7.962 0.72 36.46 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 68.349 -6.986 8.481 0.72 37.66 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 69.082 -7.694 9.351 0.72 40.64 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #