data_2RGC # _model_server_result.job_id c4JhX596mvDaP8QEBw4luQ _model_server_result.datetime_utc '2024-12-04 02:35:43' _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 2rgc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":528}' # _entry.id 2RGC # _exptl.entry_id 2RGC _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 2RGC _cell.length_a 88.43 _cell.length_b 88.43 _cell.length_c 132.69 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RGC _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 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc2 A OE2 GLU 31 A GLU 31 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 A OD1 ASP 33 A ASP 33 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc4 A OD2 ASP 33 A ASP 33 1_555 C CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc5 A OG1 THR 35 A THR 35 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc6 E O2B GNP . A GNP 528 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc7 E O2G GNP . A GNP 528 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc8 B MG MG . A MG 601 1_555 F O HOH . A HOH 635 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc9 B MG MG . A MG 601 1_555 F O HOH . A HOH 636 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc10 C CA CA . A CA 602 1_555 F O HOH . A HOH 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc11 C CA CA . A CA 602 1_555 F O HOH . A HOH 642 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc12 D MG MG . A MG 603 1_555 F O HOH . A HOH 692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc13 D MG MG . A MG 603 1_555 F O HOH . A HOH 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? # _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 2RGC _atom_sites.fract_transf_matrix[1][1] 0.011308 _atom_sites.fract_transf_matrix[1][2] 0.006529 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013058 _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] 0.007536 _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 MG A 1 601 1 MG MG . C 3 CA A 1 602 2 CA CA . D 2 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 2 605 531 HOH HOH . F 5 HOH A 3 606 532 HOH HOH . F 5 HOH A 4 607 534 HOH HOH . F 5 HOH A 5 608 535 HOH HOH . F 5 HOH A 6 609 536 HOH HOH . F 5 HOH A 7 610 537 HOH HOH . F 5 HOH A 8 611 538 HOH HOH . F 5 HOH A 9 612 539 HOH HOH . F 5 HOH A 10 613 540 HOH HOH . F 5 HOH A 11 614 541 HOH HOH . F 5 HOH A 12 615 542 HOH HOH . F 5 HOH A 13 616 543 HOH HOH . F 5 HOH A 14 617 544 HOH HOH . F 5 HOH A 15 618 545 HOH HOH . F 5 HOH A 16 619 546 HOH HOH . F 5 HOH A 17 620 547 HOH HOH . F 5 HOH A 18 621 551 HOH HOH . F 5 HOH A 19 622 553 HOH HOH . F 5 HOH A 20 623 554 HOH HOH . F 5 HOH A 21 624 555 HOH HOH . F 5 HOH A 22 625 556 HOH HOH . F 5 HOH A 23 626 559 HOH HOH . F 5 HOH A 24 627 562 HOH HOH . F 5 HOH A 25 628 563 HOH HOH . F 5 HOH A 26 629 565 HOH HOH . F 5 HOH A 27 630 567 HOH HOH . F 5 HOH A 28 631 568 HOH HOH . F 5 HOH A 29 632 571 HOH HOH . F 5 HOH A 30 633 572 HOH HOH . F 5 HOH A 31 634 578 HOH HOH . F 5 HOH A 32 635 579 HOH HOH . F 5 HOH A 33 636 580 HOH HOH . F 5 HOH A 34 637 581 HOH HOH . F 5 HOH A 35 638 582 HOH HOH . F 5 HOH A 36 639 583 HOH HOH . F 5 HOH A 37 640 584 HOH HOH . F 5 HOH A 38 641 585 HOH HOH . F 5 HOH A 39 642 586 HOH HOH . F 5 HOH A 40 643 587 HOH HOH . F 5 HOH A 41 644 588 HOH HOH . F 5 HOH A 42 645 589 HOH HOH . F 5 HOH A 43 646 590 HOH HOH . F 5 HOH A 44 647 591 HOH HOH . F 5 HOH A 45 648 592 HOH HOH . F 5 HOH A 46 649 593 HOH HOH . F 5 HOH A 47 650 594 HOH HOH . F 5 HOH A 48 651 595 HOH HOH . F 5 HOH A 49 652 596 HOH HOH . F 5 HOH A 50 653 597 HOH HOH . F 5 HOH A 51 654 598 HOH HOH . F 5 HOH A 52 655 599 HOH HOH . F 5 HOH A 53 656 600 HOH HOH . F 5 HOH A 54 657 601 HOH HOH . F 5 HOH A 55 658 602 HOH HOH . F 5 HOH A 56 659 603 HOH HOH . F 5 HOH A 57 660 604 HOH HOH . F 5 HOH A 58 661 605 HOH HOH . F 5 HOH A 59 662 606 HOH HOH . F 5 HOH A 60 663 607 HOH HOH . F 5 HOH A 61 664 608 HOH HOH . F 5 HOH A 62 665 609 HOH HOH . F 5 HOH A 63 666 610 HOH HOH . F 5 HOH A 64 667 611 HOH HOH . F 5 HOH A 65 668 612 HOH HOH . F 5 HOH A 66 669 613 HOH HOH . F 5 HOH A 67 670 614 HOH HOH . F 5 HOH A 68 671 615 HOH HOH . F 5 HOH A 69 672 616 HOH HOH . F 5 HOH A 70 673 617 HOH HOH . F 5 HOH A 71 674 618 HOH HOH . F 5 HOH A 72 675 619 HOH HOH . F 5 HOH A 73 676 620 HOH HOH . F 5 HOH A 74 677 621 HOH HOH . F 5 HOH A 75 678 622 HOH HOH . F 5 HOH A 76 679 623 HOH HOH . F 5 HOH A 77 680 624 HOH HOH . F 5 HOH A 78 681 625 HOH HOH . F 5 HOH A 79 682 626 HOH HOH . F 5 HOH A 80 683 627 HOH HOH . F 5 HOH A 81 684 628 HOH HOH . F 5 HOH A 82 685 629 HOH HOH . F 5 HOH A 83 686 630 HOH HOH . F 5 HOH A 84 687 631 HOH HOH . F 5 HOH A 85 688 632 HOH HOH . F 5 HOH A 86 689 633 HOH HOH . F 5 HOH A 87 690 634 HOH HOH . F 5 HOH A 88 691 635 HOH HOH . F 5 HOH A 89 692 636 HOH HOH . F 5 HOH A 90 693 637 HOH HOH . F 5 HOH A 91 694 638 HOH HOH . F 5 HOH A 92 695 639 HOH HOH . F 5 HOH A 93 696 640 HOH HOH . F 5 HOH A 94 697 641 HOH HOH . F 5 HOH A 95 698 642 HOH HOH . F 5 HOH A 96 699 643 HOH HOH . F 5 HOH A 97 700 644 HOH HOH . F 5 HOH A 98 701 645 HOH HOH . F 5 HOH A 99 702 646 HOH HOH . F 5 HOH A 100 703 647 HOH HOH . F 5 HOH A 101 704 648 HOH HOH . F 5 HOH A 102 705 649 HOH HOH . F 5 HOH A 103 706 650 HOH HOH . F 5 HOH A 104 707 651 HOH HOH . F 5 HOH A 105 708 652 HOH HOH . F 5 HOH A 106 709 653 HOH HOH . F 5 HOH A 107 710 654 HOH HOH . F 5 HOH A 108 711 655 HOH HOH . F 5 HOH A 109 712 656 HOH HOH . F 5 HOH A 110 713 657 HOH HOH . F 5 HOH A 111 714 658 HOH HOH . F 5 HOH A 112 715 659 HOH HOH . F 5 HOH A 113 716 660 HOH HOH . F 5 HOH A 114 717 661 HOH HOH . F 5 HOH A 115 718 662 HOH HOH . F 5 HOH A 116 719 663 HOH HOH . F 5 HOH A 117 720 664 HOH HOH . F 5 HOH A 118 721 665 HOH HOH . F 5 HOH A 119 722 666 HOH HOH . F 5 HOH A 120 723 671 HOH HOH . F 5 HOH A 121 724 672 HOH HOH . F 5 HOH A 122 725 673 HOH HOH . F 5 HOH A 123 726 674 HOH HOH . F 5 HOH A 124 727 675 HOH HOH . F 5 HOH A 125 728 676 HOH HOH . F 5 HOH A 126 729 677 HOH HOH . F 5 HOH A 127 730 678 HOH HOH . F 5 HOH A 128 731 679 HOH HOH . F 5 HOH A 129 732 680 HOH HOH . F 5 HOH A 130 733 681 HOH HOH . F 5 HOH A 131 734 682 HOH HOH . F 5 HOH A 132 735 683 HOH HOH . F 5 HOH A 133 736 684 HOH HOH . F 5 HOH A 134 737 685 HOH HOH . F 5 HOH A 135 738 686 HOH HOH . F 5 HOH A 136 739 687 HOH HOH . F 5 HOH A 137 740 688 HOH HOH . F 5 HOH A 138 741 689 HOH HOH . F 5 HOH A 139 742 690 HOH HOH . F 5 HOH A 140 743 691 HOH HOH . F 5 HOH A 141 744 692 HOH HOH . F 5 HOH A 142 745 693 HOH HOH . F 5 HOH A 143 746 694 HOH HOH . F 5 HOH A 144 747 695 HOH HOH . F 5 HOH A 145 748 696 HOH HOH . F 5 HOH A 146 749 697 HOH HOH . F 5 HOH A 147 750 698 HOH HOH . F 5 HOH A 148 751 699 HOH HOH . F 5 HOH A 149 752 700 HOH HOH . F 5 HOH A 150 753 701 HOH HOH . F 5 HOH A 151 754 702 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 -9.867 64.469 -66.097 1 18.33 ? PG GNP 528 A 1 HETATM 2 O O1G GNP . . . E 4 -9.049 64.041 -64.947 1 20.08 ? O1G GNP 528 A 1 HETATM 3 O O2G GNP . . . E 4 -10.913 65.365 -65.679 1 17.73 ? O2G GNP 528 A 1 HETATM 4 O O3G GNP . . . E 4 -10.677 63.253 -66.551 1 19.92 ? O3G GNP 528 A 1 HETATM 5 N N3B GNP . . . E 4 -8.947 64.984 -67.339 1 15.62 ? N3B GNP 528 A 1 HETATM 6 P PB GNP . . . E 4 -9.563 65.574 -68.755 1 17.16 ? PB GNP 528 A 1 HETATM 7 O O1B GNP . . . E 4 -9.955 64.534 -69.73 1 17.24 ? O1B GNP 528 A 1 HETATM 8 O O2B GNP . . . E 4 -10.584 66.609 -68.603 1 16.59 ? O2B GNP 528 A 1 HETATM 9 O O3A GNP . . . E 4 -8.317 66.346 -69.399 1 16.37 ? O3A GNP 528 A 1 HETATM 10 P PA GNP . . . E 4 -8.003 67.953 -69.397 1 17.23 ? PA GNP 528 A 1 HETATM 11 O O1A GNP . . . E 4 -8.967 68.676 -70.276 1 17.33 ? O1A GNP 528 A 1 HETATM 12 O O2A GNP . . . E 4 -7.795 68.44 -68.008 1 16.72 ? O2A GNP 528 A 1 HETATM 13 O O5' GNP . . . E 4 -6.621 67.958 -70.189 1 16.33 ? O5' GNP 528 A 1 HETATM 14 C C5' GNP . . . E 4 -5.462 67.313 -69.586 1 19.36 ? C5' GNP 528 A 1 HETATM 15 C C4' GNP . . . E 4 -4.161 67.897 -70.158 1 18.58 ? C4' GNP 528 A 1 HETATM 16 O O4' GNP . . . E 4 -4.164 67.708 -71.589 1 17.32 ? O4' GNP 528 A 1 HETATM 17 C C3' GNP . . . E 4 -4.005 69.411 -69.932 1 18.57 ? C3' GNP 528 A 1 HETATM 18 O O3' GNP . . . E 4 -2.632 69.758 -69.644 1 18.44 ? O3' GNP 528 A 1 HETATM 19 C C2' GNP . . . E 4 -4.514 70.003 -71.237 1 16.27 ? C2' GNP 528 A 1 HETATM 20 O O2' GNP . . . E 4 -3.932 71.255 -71.6 1 16.02 ? O2' GNP 528 A 1 HETATM 21 C C1' GNP . . . E 4 -4.038 68.961 -72.255 1 16.96 ? C1' GNP 528 A 1 HETATM 22 N N9 GNP . . . E 4 -4.886 68.928 -73.461 1 16.29 ? N9 GNP 528 A 1 HETATM 23 C C8 GNP . . . E 4 -6.255 68.715 -73.573 1 17.64 ? C8 GNP 528 A 1 HETATM 24 N N7 GNP . . . E 4 -6.713 68.744 -74.778 1 17.06 ? N7 GNP 528 A 1 HETATM 25 C C5 GNP . . . E 4 -5.568 68.998 -75.562 1 16.12 ? C5 GNP 528 A 1 HETATM 26 C C6 GNP . . . E 4 -5.406 69.145 -77 1 17.62 ? C6 GNP 528 A 1 HETATM 27 O O6 GNP . . . E 4 -6.267 69.08 -77.878 1 18.6 ? O6 GNP 528 A 1 HETATM 28 N N1 GNP . . . E 4 -4.077 69.393 -77.367 1 17.84 ? N1 GNP 528 A 1 HETATM 29 C C2 GNP . . . E 4 -2.997 69.494 -76.485 1 19.66 ? C2 GNP 528 A 1 HETATM 30 N N2 GNP . . . E 4 -1.777 69.737 -77.002 1 19.78 ? N2 GNP 528 A 1 HETATM 31 N N3 GNP . . . E 4 -3.147 69.354 -75.143 1 17.67 ? N3 GNP 528 A 1 HETATM 32 C C4 GNP . . . E 4 -4.444 69.112 -74.749 1 16.48 ? C4 GNP 528 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #