data_2RGA # _model_server_result.job_id wDfLYJNHxIu4NnS7CBmO9w _model_server_result.datetime_utc '2024-11-02 18:17:10' _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 2rga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":528}' # _entry.id 2RGA # _exptl.entry_id 2RGA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 2RGA _cell.length_a 88.342 _cell.length_b 88.342 _cell.length_c 133.419 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 OG SER 17 A SER 17 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc2 A OE2 GLU 31 A GLU 31 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc3 A OD1 ASP 33 A ASP 33 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc4 A OD2 ASP 33 A ASP 33 1_555 B CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc5 A OG1 THR 35 A THR 35 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc6 E O2B GNP . A GNP 528 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc7 E O2G GNP . A GNP 528 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc8 B CA CA . A CA 601 1_555 F O HOH . A HOH 686 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc9 B CA CA . A CA 601 1_555 F O HOH . A HOH 687 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc10 C MG MG . A MG 602 1_555 F O HOH . A HOH 688 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc11 C MG MG . A MG 602 1_555 F O HOH . A HOH 689 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc12 D MG MG . A MG 603 1_555 F O HOH . A HOH 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc13 D MG MG . A MG 603 1_555 F O HOH . A HOH 670 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 2RGA _atom_sites.fract_transf_matrix[1][1] 0.01132 _atom_sites.fract_transf_matrix[1][2] 0.006535 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013071 _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] 0.007495 _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 CA A 1 601 1 CA CA . C 3 MG A 1 602 2 MG MG . D 3 MG A 1 603 3 MG MG . E 4 GNP A 1 528 528 GNP GNP . F 5 HOH A 1 604 529 HOH HOH . F 5 HOH A 2 605 530 HOH HOH . F 5 HOH A 3 606 531 HOH HOH . F 5 HOH A 4 607 532 HOH HOH . F 5 HOH A 5 608 533 HOH HOH . F 5 HOH A 6 609 534 HOH HOH . F 5 HOH A 7 610 535 HOH HOH . F 5 HOH A 8 611 536 HOH HOH . F 5 HOH A 9 612 537 HOH HOH . F 5 HOH A 10 613 538 HOH HOH . F 5 HOH A 11 614 539 HOH HOH . F 5 HOH A 12 615 540 HOH HOH . F 5 HOH A 13 616 541 HOH HOH . F 5 HOH A 14 617 542 HOH HOH . F 5 HOH A 15 618 543 HOH HOH . F 5 HOH A 16 619 544 HOH HOH . F 5 HOH A 17 620 545 HOH HOH . F 5 HOH A 18 621 546 HOH HOH . F 5 HOH A 19 622 547 HOH HOH . F 5 HOH A 20 623 548 HOH HOH . F 5 HOH A 21 624 549 HOH HOH . F 5 HOH A 22 625 550 HOH HOH . F 5 HOH A 23 626 552 HOH HOH . F 5 HOH A 24 627 553 HOH HOH . F 5 HOH A 25 628 554 HOH HOH . F 5 HOH A 26 629 555 HOH HOH . F 5 HOH A 27 630 556 HOH HOH . F 5 HOH A 28 631 557 HOH HOH . F 5 HOH A 29 632 558 HOH HOH . F 5 HOH A 30 633 559 HOH HOH . F 5 HOH A 31 634 560 HOH HOH . F 5 HOH A 32 635 561 HOH HOH . F 5 HOH A 33 636 562 HOH HOH . F 5 HOH A 34 637 563 HOH HOH . F 5 HOH A 35 638 564 HOH HOH . F 5 HOH A 36 639 565 HOH HOH . F 5 HOH A 37 640 566 HOH HOH . F 5 HOH A 38 641 567 HOH HOH . F 5 HOH A 39 642 568 HOH HOH . F 5 HOH A 40 643 569 HOH HOH . F 5 HOH A 41 644 570 HOH HOH . F 5 HOH A 42 645 572 HOH HOH . F 5 HOH A 43 646 573 HOH HOH . F 5 HOH A 44 647 574 HOH HOH . F 5 HOH A 45 648 575 HOH HOH . F 5 HOH A 46 649 576 HOH HOH . F 5 HOH A 47 650 577 HOH HOH . F 5 HOH A 48 651 578 HOH HOH . F 5 HOH A 49 652 579 HOH HOH . F 5 HOH A 50 653 581 HOH HOH . F 5 HOH A 51 654 582 HOH HOH . F 5 HOH A 52 655 583 HOH HOH . F 5 HOH A 53 656 584 HOH HOH . F 5 HOH A 54 657 585 HOH HOH . F 5 HOH A 55 658 586 HOH HOH . F 5 HOH A 56 659 587 HOH HOH . F 5 HOH A 57 660 588 HOH HOH . F 5 HOH A 58 661 589 HOH HOH . F 5 HOH A 59 662 592 HOH HOH . F 5 HOH A 60 663 593 HOH HOH . F 5 HOH A 61 664 594 HOH HOH . F 5 HOH A 62 665 595 HOH HOH . F 5 HOH A 63 666 599 HOH HOH . F 5 HOH A 64 667 600 HOH HOH . F 5 HOH A 65 668 601 HOH HOH . F 5 HOH A 66 669 602 HOH HOH . F 5 HOH A 67 670 603 HOH HOH . F 5 HOH A 68 671 604 HOH HOH . F 5 HOH A 69 672 605 HOH HOH . F 5 HOH A 70 673 606 HOH HOH . F 5 HOH A 71 674 607 HOH HOH . F 5 HOH A 72 675 608 HOH HOH . F 5 HOH A 73 676 609 HOH HOH . F 5 HOH A 74 677 610 HOH HOH . F 5 HOH A 75 678 611 HOH HOH . F 5 HOH A 76 679 612 HOH HOH . F 5 HOH A 77 680 613 HOH HOH . F 5 HOH A 78 681 614 HOH HOH . F 5 HOH A 79 682 615 HOH HOH . F 5 HOH A 80 683 616 HOH HOH . F 5 HOH A 81 684 617 HOH HOH . F 5 HOH A 82 685 618 HOH HOH . F 5 HOH A 83 686 619 HOH HOH . F 5 HOH A 84 687 620 HOH HOH . F 5 HOH A 85 688 621 HOH HOH . F 5 HOH A 86 689 622 HOH HOH . F 5 HOH A 87 690 623 HOH HOH . F 5 HOH A 88 691 624 HOH HOH . F 5 HOH A 89 692 625 HOH HOH . F 5 HOH A 90 693 626 HOH HOH . F 5 HOH A 91 694 627 HOH HOH . F 5 HOH A 92 695 628 HOH HOH . F 5 HOH A 93 696 629 HOH HOH . F 5 HOH A 94 697 630 HOH HOH . F 5 HOH A 95 698 631 HOH HOH . F 5 HOH A 96 699 632 HOH HOH . F 5 HOH A 97 700 633 HOH HOH . F 5 HOH A 98 701 634 HOH HOH . F 5 HOH A 99 702 635 HOH HOH . F 5 HOH A 100 703 636 HOH HOH . F 5 HOH A 101 704 637 HOH HOH . F 5 HOH A 102 705 638 HOH HOH . F 5 HOH A 103 706 639 HOH HOH . F 5 HOH A 104 707 640 HOH HOH . F 5 HOH A 105 708 641 HOH HOH . F 5 HOH A 106 709 642 HOH HOH . F 5 HOH A 107 710 643 HOH HOH . F 5 HOH A 108 711 644 HOH HOH . F 5 HOH A 109 712 645 HOH HOH . F 5 HOH A 110 713 646 HOH HOH . F 5 HOH A 111 714 647 HOH HOH . F 5 HOH A 112 715 648 HOH HOH . F 5 HOH A 113 716 649 HOH HOH . F 5 HOH A 114 717 650 HOH HOH . F 5 HOH A 115 718 651 HOH HOH . F 5 HOH A 116 719 652 HOH HOH . F 5 HOH A 117 720 653 HOH HOH . F 5 HOH A 118 721 654 HOH HOH . F 5 HOH A 119 722 655 HOH HOH . F 5 HOH A 120 723 656 HOH HOH . F 5 HOH A 121 724 657 HOH HOH . F 5 HOH A 122 725 658 HOH HOH . F 5 HOH A 123 726 659 HOH HOH . F 5 HOH A 124 727 660 HOH HOH . F 5 HOH A 125 728 661 HOH HOH . F 5 HOH A 126 729 662 HOH HOH . F 5 HOH A 127 730 663 HOH HOH . F 5 HOH A 128 731 664 HOH HOH . F 5 HOH A 129 732 665 HOH HOH . F 5 HOH A 130 733 666 HOH HOH . F 5 HOH A 131 734 667 HOH HOH . F 5 HOH A 132 735 668 HOH HOH . F 5 HOH A 133 736 669 HOH HOH . F 5 HOH A 134 737 670 HOH HOH . F 5 HOH A 135 738 671 HOH HOH . F 5 HOH A 136 739 672 HOH HOH . F 5 HOH A 137 740 673 HOH HOH . F 5 HOH A 138 741 674 HOH HOH . F 5 HOH A 139 742 675 HOH HOH . F 5 HOH A 140 743 676 HOH HOH . F 5 HOH A 141 744 677 HOH HOH . F 5 HOH A 142 745 678 HOH HOH . F 5 HOH A 143 746 679 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 GNP . . . E 4 -9.761 64.37 -66.561 1 16.75 ? PG GNP 528 A 1 HETATM 2 O O1G GNP . . . E 4 -8.917 63.927 -65.442 1 17.02 ? O1G GNP 528 A 1 HETATM 3 O O2G GNP . . . E 4 -10.794 65.258 -66.095 1 16.85 ? O2G GNP 528 A 1 HETATM 4 O O3G GNP . . . E 4 -10.601 63.162 -67.016 1 16.02 ? O3G GNP 528 A 1 HETATM 5 N N3B GNP . . . E 4 -8.861 64.884 -67.817 1 14.23 ? N3B GNP 528 A 1 HETATM 6 P PB GNP . . . E 4 -9.468 65.472 -69.228 1 15.32 ? PB GNP 528 A 1 HETATM 7 O O1B GNP . . . E 4 -9.831 64.439 -70.219 1 13.09 ? O1B GNP 528 A 1 HETATM 8 O O2B GNP . . . E 4 -10.5 66.497 -69.103 1 12.76 ? O2B GNP 528 A 1 HETATM 9 O O3A GNP . . . E 4 -8.227 66.262 -69.845 1 12.33 ? O3A GNP 528 A 1 HETATM 10 P PA GNP . . . E 4 -7.94 67.872 -69.849 1 14.78 ? PA GNP 528 A 1 HETATM 11 O O1A GNP . . . E 4 -8.9 68.563 -70.765 1 13.48 ? O1A GNP 528 A 1 HETATM 12 O O2A GNP . . . E 4 -7.788 68.375 -68.464 1 13.74 ? O2A GNP 528 A 1 HETATM 13 O O5' GNP . . . E 4 -6.534 67.874 -70.614 1 14.14 ? O5' GNP 528 A 1 HETATM 14 C C5' GNP . . . E 4 -5.369 67.267 -69.982 1 14.85 ? C5' GNP 528 A 1 HETATM 15 C C4' GNP . . . E 4 -4.072 67.831 -70.586 1 14.91 ? C4' GNP 528 A 1 HETATM 16 O O4' GNP . . . E 4 -4.107 67.637 -72.02 1 14.75 ? O4' GNP 528 A 1 HETATM 17 C C3' GNP . . . E 4 -3.897 69.35 -70.364 1 14.76 ? C3' GNP 528 A 1 HETATM 18 O O3' GNP . . . E 4 -2.523 69.7 -70.072 1 15.94 ? O3' GNP 528 A 1 HETATM 19 C C2' GNP . . . E 4 -4.429 69.937 -71.667 1 14.04 ? C2' GNP 528 A 1 HETATM 20 O O2' GNP . . . E 4 -3.86 71.19 -72.043 1 13.19 ? O2' GNP 528 A 1 HETATM 21 C C1' GNP . . . E 4 -3.975 68.891 -72.69 1 13.05 ? C1' GNP 528 A 1 HETATM 22 N N9 GNP . . . E 4 -4.833 68.876 -73.894 1 14.9 ? N9 GNP 528 A 1 HETATM 23 C C8 GNP . . . E 4 -6.209 68.699 -74 1 13.71 ? C8 GNP 528 A 1 HETATM 24 N N7 GNP . . . E 4 -6.671 68.734 -75.207 1 13.55 ? N7 GNP 528 A 1 HETATM 25 C C5 GNP . . . E 4 -5.524 68.948 -75.997 1 13.46 ? C5 GNP 528 A 1 HETATM 26 C C6 GNP . . . E 4 -5.36 69.088 -77.44 1 13.88 ? C6 GNP 528 A 1 HETATM 27 O O6 GNP . . . E 4 -6.222 69.041 -78.325 1 13.35 ? O6 GNP 528 A 1 HETATM 28 N N1 GNP . . . E 4 -4.023 69.292 -77.808 1 15.15 ? N1 GNP 528 A 1 HETATM 29 C C2 GNP . . . E 4 -2.939 69.369 -76.93 1 17.35 ? C2 GNP 528 A 1 HETATM 30 N N2 GNP . . . E 4 -1.719 69.574 -77.452 1 16.58 ? N2 GNP 528 A 1 HETATM 31 N N3 GNP . . . E 4 -3.087 69.242 -75.588 1 15.34 ? N3 GNP 528 A 1 HETATM 32 C C4 GNP . . . E 4 -4.392 69.036 -75.187 1 13.86 ? C4 GNP 528 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #