data_4G3P # _model_server_result.job_id tXDSrRN0cJOdI_qAdBhV4A _model_server_result.datetime_utc '2024-11-13 21:28:19' _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 4g3p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4G3P # _exptl.entry_id 4G3P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.959 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYROPHOSPHATE 2-' _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 4G3P _cell.length_a 77.47 _cell.length_b 77.47 _cell.length_c 277.5 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G3P _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD2 ASP 120 A ASP 114 1_555 D CO CO . A CO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A OD1 ASN 245 A ASN 239 1_555 D CO CO . A CO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 A OD1 ASP 423 A ASP 417 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc4 A OD2 ASP 423 A ASP 417 1_555 F CO CO . A CO 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc5 B O4 POP . A POP 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc6 B O1 POP . A POP 501 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc7 C MG MG . A MG 502 1_555 H O HOH . A HOH 759 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc8 D CO CO . A CO 503 1_555 G O1B UD1 . A UD1 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc9 D CO CO . A CO 503 1_555 G O2A UD1 . A UD1 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc10 D CO CO . A CO 503 1_555 H O HOH . A HOH 753 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc11 D CO CO . A CO 503 1_555 H O HOH . A HOH 754 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc12 E MG MG . A MG 504 1_555 H O HOH . A HOH 755 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc13 E MG MG . A MG 504 1_555 H O HOH . A HOH 756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? metalc ? metalc14 E MG MG . A MG 504 1_555 H O HOH . A HOH 798 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _chem_comp.formula 'H2 O7 P2 -2' _chem_comp.formula_weight 175.959 _chem_comp.id POP _chem_comp.mon_nstd_flag . _chem_comp.name 'PYROPHOSPHATE 2-' _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 P1 O1 POP doub 260 n n P1 O2 POP sing 261 n n P1 O3 POP sing 262 n n P1 O POP sing 263 n n O2 HO2 POP sing 264 n n O P2 POP sing 265 n n P2 O4 POP doub 266 n n P2 O5 POP sing 267 n n P2 O6 POP sing 268 n n O5 HO5 POP sing 269 n n # _atom_sites.entry_id 4G3P _atom_sites.fract_transf_matrix[1][1] 0.012908 _atom_sites.fract_transf_matrix[1][2] 0.007453 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014905 _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] 0.003604 _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 POP A 1 501 497 POP POP . C 3 MG A 1 502 498 MG MG . D 4 CO A 1 503 499 CO CO . E 3 MG A 1 504 500 MG MG . F 4 CO A 1 505 501 CO CO . G 5 UD1 A 1 506 496 UD1 UD1 . H 6 HOH A 1 601 502 HOH HOH . H 6 HOH A 2 602 503 HOH HOH . H 6 HOH A 3 603 504 HOH HOH . H 6 HOH A 4 604 505 HOH HOH . H 6 HOH A 5 605 506 HOH HOH . H 6 HOH A 6 606 507 HOH HOH . H 6 HOH A 7 607 508 HOH HOH . H 6 HOH A 8 608 509 HOH HOH . H 6 HOH A 9 609 510 HOH HOH . H 6 HOH A 10 610 511 HOH HOH . H 6 HOH A 11 611 512 HOH HOH . H 6 HOH A 12 612 513 HOH HOH . H 6 HOH A 13 613 514 HOH HOH . H 6 HOH A 14 614 515 HOH HOH . H 6 HOH A 15 615 516 HOH HOH . H 6 HOH A 16 616 517 HOH HOH . H 6 HOH A 17 617 518 HOH HOH . H 6 HOH A 18 618 519 HOH HOH . H 6 HOH A 19 619 520 HOH HOH . H 6 HOH A 20 620 521 HOH HOH . H 6 HOH A 21 621 522 HOH HOH . H 6 HOH A 22 622 523 HOH HOH . H 6 HOH A 23 623 524 HOH HOH . H 6 HOH A 24 624 525 HOH HOH . H 6 HOH A 25 625 526 HOH HOH . H 6 HOH A 26 626 527 HOH HOH . H 6 HOH A 27 627 528 HOH HOH . H 6 HOH A 28 628 529 HOH HOH . H 6 HOH A 29 629 530 HOH HOH . H 6 HOH A 30 630 531 HOH HOH . H 6 HOH A 31 631 532 HOH HOH . H 6 HOH A 32 632 533 HOH HOH . H 6 HOH A 33 633 534 HOH HOH . H 6 HOH A 34 634 535 HOH HOH . H 6 HOH A 35 635 536 HOH HOH . H 6 HOH A 36 636 537 HOH HOH . H 6 HOH A 37 637 538 HOH HOH . H 6 HOH A 38 638 539 HOH HOH . H 6 HOH A 39 639 540 HOH HOH . H 6 HOH A 40 640 541 HOH HOH . H 6 HOH A 41 641 542 HOH HOH . H 6 HOH A 42 642 543 HOH HOH . H 6 HOH A 43 643 544 HOH HOH . H 6 HOH A 44 644 545 HOH HOH . H 6 HOH A 45 645 546 HOH HOH . H 6 HOH A 46 646 547 HOH HOH . H 6 HOH A 47 647 548 HOH HOH . H 6 HOH A 48 648 549 HOH HOH . H 6 HOH A 49 649 550 HOH HOH . H 6 HOH A 50 650 551 HOH HOH . H 6 HOH A 51 651 552 HOH HOH . H 6 HOH A 52 652 553 HOH HOH . H 6 HOH A 53 653 554 HOH HOH . H 6 HOH A 54 654 555 HOH HOH . H 6 HOH A 55 655 556 HOH HOH . H 6 HOH A 56 656 557 HOH HOH . H 6 HOH A 57 657 558 HOH HOH . H 6 HOH A 58 658 559 HOH HOH . H 6 HOH A 59 659 560 HOH HOH . H 6 HOH A 60 660 561 HOH HOH . H 6 HOH A 61 661 562 HOH HOH . H 6 HOH A 62 662 563 HOH HOH . H 6 HOH A 63 663 564 HOH HOH . H 6 HOH A 64 664 565 HOH HOH . H 6 HOH A 65 665 566 HOH HOH . H 6 HOH A 66 666 567 HOH HOH . H 6 HOH A 67 667 568 HOH HOH . H 6 HOH A 68 668 569 HOH HOH . H 6 HOH A 69 669 570 HOH HOH . H 6 HOH A 70 670 571 HOH HOH . H 6 HOH A 71 671 572 HOH HOH . H 6 HOH A 72 672 573 HOH HOH . H 6 HOH A 73 673 574 HOH HOH . H 6 HOH A 74 674 575 HOH HOH . H 6 HOH A 75 675 576 HOH HOH . H 6 HOH A 76 676 577 HOH HOH . H 6 HOH A 77 677 578 HOH HOH . H 6 HOH A 78 678 579 HOH HOH . H 6 HOH A 79 679 580 HOH HOH . H 6 HOH A 80 680 581 HOH HOH . H 6 HOH A 81 681 582 HOH HOH . H 6 HOH A 82 682 583 HOH HOH . H 6 HOH A 83 683 584 HOH HOH . H 6 HOH A 84 684 585 HOH HOH . H 6 HOH A 85 685 586 HOH HOH . H 6 HOH A 86 686 587 HOH HOH . H 6 HOH A 87 687 588 HOH HOH . H 6 HOH A 88 688 589 HOH HOH . H 6 HOH A 89 689 590 HOH HOH . H 6 HOH A 90 690 591 HOH HOH . H 6 HOH A 91 691 592 HOH HOH . H 6 HOH A 92 692 593 HOH HOH . H 6 HOH A 93 693 594 HOH HOH . H 6 HOH A 94 694 595 HOH HOH . H 6 HOH A 95 695 596 HOH HOH . H 6 HOH A 96 696 597 HOH HOH . H 6 HOH A 97 697 598 HOH HOH . H 6 HOH A 98 698 599 HOH HOH . H 6 HOH A 99 699 600 HOH HOH . H 6 HOH A 100 700 601 HOH HOH . H 6 HOH A 101 701 602 HOH HOH . H 6 HOH A 102 702 603 HOH HOH . H 6 HOH A 103 703 604 HOH HOH . H 6 HOH A 104 704 605 HOH HOH . H 6 HOH A 105 705 606 HOH HOH . H 6 HOH A 106 706 607 HOH HOH . H 6 HOH A 107 707 608 HOH HOH . H 6 HOH A 108 708 609 HOH HOH . H 6 HOH A 109 709 610 HOH HOH . H 6 HOH A 110 710 611 HOH HOH . H 6 HOH A 111 711 612 HOH HOH . H 6 HOH A 112 712 613 HOH HOH . H 6 HOH A 113 713 614 HOH HOH . H 6 HOH A 114 714 615 HOH HOH . H 6 HOH A 115 715 616 HOH HOH . H 6 HOH A 116 716 617 HOH HOH . H 6 HOH A 117 717 618 HOH HOH . H 6 HOH A 118 718 619 HOH HOH . H 6 HOH A 119 719 620 HOH HOH . H 6 HOH A 120 720 621 HOH HOH . H 6 HOH A 121 721 622 HOH HOH . H 6 HOH A 122 722 623 HOH HOH . H 6 HOH A 123 723 624 HOH HOH . H 6 HOH A 124 724 625 HOH HOH . H 6 HOH A 125 725 626 HOH HOH . H 6 HOH A 126 726 627 HOH HOH . H 6 HOH A 127 727 628 HOH HOH . H 6 HOH A 128 728 629 HOH HOH . H 6 HOH A 129 729 630 HOH HOH . H 6 HOH A 130 730 631 HOH HOH . H 6 HOH A 131 731 632 HOH HOH . H 6 HOH A 132 732 633 HOH HOH . H 6 HOH A 133 733 634 HOH HOH . H 6 HOH A 134 734 635 HOH HOH . H 6 HOH A 135 735 636 HOH HOH . H 6 HOH A 136 736 637 HOH HOH . H 6 HOH A 137 737 638 HOH HOH . H 6 HOH A 138 738 639 HOH HOH . H 6 HOH A 139 739 640 HOH HOH . H 6 HOH A 140 740 641 HOH HOH . H 6 HOH A 141 741 642 HOH HOH . H 6 HOH A 142 742 643 HOH HOH . H 6 HOH A 143 743 644 HOH HOH . H 6 HOH A 144 744 645 HOH HOH . H 6 HOH A 145 745 646 HOH HOH . H 6 HOH A 146 746 647 HOH HOH . H 6 HOH A 147 747 648 HOH HOH . H 6 HOH A 148 748 649 HOH HOH . H 6 HOH A 149 749 650 HOH HOH . H 6 HOH A 150 750 651 HOH HOH . H 6 HOH A 151 751 652 HOH HOH . H 6 HOH A 152 752 653 HOH HOH . H 6 HOH A 153 753 654 HOH HOH . H 6 HOH A 154 754 655 HOH HOH . H 6 HOH A 155 755 656 HOH HOH . H 6 HOH A 156 756 657 HOH HOH . H 6 HOH A 157 757 658 HOH HOH . H 6 HOH A 158 758 659 HOH HOH . H 6 HOH A 159 759 660 HOH HOH . H 6 HOH A 160 760 661 HOH HOH . H 6 HOH A 161 761 662 HOH HOH . H 6 HOH A 162 762 663 HOH HOH . H 6 HOH A 163 763 664 HOH HOH . H 6 HOH A 164 764 665 HOH HOH . H 6 HOH A 165 765 666 HOH HOH . H 6 HOH A 166 766 667 HOH HOH . H 6 HOH A 167 767 668 HOH HOH . H 6 HOH A 168 768 669 HOH HOH . H 6 HOH A 169 769 670 HOH HOH . H 6 HOH A 170 770 671 HOH HOH . H 6 HOH A 171 771 672 HOH HOH . H 6 HOH A 172 772 673 HOH HOH . H 6 HOH A 173 773 674 HOH HOH . H 6 HOH A 174 774 675 HOH HOH . H 6 HOH A 175 775 676 HOH HOH . H 6 HOH A 176 776 677 HOH HOH . H 6 HOH A 177 777 678 HOH HOH . H 6 HOH A 178 778 679 HOH HOH . H 6 HOH A 179 779 680 HOH HOH . H 6 HOH A 180 780 681 HOH HOH . H 6 HOH A 181 781 682 HOH HOH . H 6 HOH A 182 782 683 HOH HOH . H 6 HOH A 183 783 684 HOH HOH . H 6 HOH A 184 784 685 HOH HOH . H 6 HOH A 185 785 686 HOH HOH . H 6 HOH A 186 786 687 HOH HOH . H 6 HOH A 187 787 688 HOH HOH . H 6 HOH A 188 788 689 HOH HOH . H 6 HOH A 189 789 690 HOH HOH . H 6 HOH A 190 790 691 HOH HOH . H 6 HOH A 191 791 692 HOH HOH . H 6 HOH A 192 792 693 HOH HOH . H 6 HOH A 193 793 694 HOH HOH . H 6 HOH A 194 794 695 HOH HOH . H 6 HOH A 195 795 696 HOH HOH . H 6 HOH A 196 796 697 HOH HOH . H 6 HOH A 197 797 698 HOH HOH . H 6 HOH A 198 798 699 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 P1 POP . . . B 2 -24.368 -15.07 -12.175 1 30.92 ? P1 POP 501 A 1 HETATM 2 O O1 POP . . . B 2 -24.619 -15.047 -13.664 1 29.23 ? O1 POP 501 A 1 HETATM 3 O O2 POP . . . B 2 -22.946 -14.649 -11.893 1 33.49 ? O2 POP 501 A 1 HETATM 4 O O3 POP . . . B 2 -25.324 -14.128 -11.484 1 31.35 ? O3 POP 501 A 1 HETATM 5 O O POP . . . B 2 -24.605 -16.571 -11.643 1 34.44 ? O POP 501 A 1 HETATM 6 P P2 POP . . . B 2 -24.463 -17.824 -12.644 1 39.64 ? P2 POP 501 A 1 HETATM 7 O O4 POP . . . B 2 -24.339 -17.297 -14.053 1 36.39 ? O4 POP 501 A 1 HETATM 8 O O5 POP . . . B 2 -25.687 -18.703 -12.536 1 35.85 ? O5 POP 501 A 1 HETATM 9 O O6 POP . . . B 2 -23.231 -18.622 -12.289 1 35.49 ? O6 POP 501 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 9 #