data_8XRG # _model_server_result.job_id tIBp-eQ93kVxMjo56dS01g _model_server_result.datetime_utc '2024-10-12 16:33:47' _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 8xrg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8XRG # _exptl.entry_id 8XRG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 8XRG _cell.length_a 85.256 _cell.length_b 85.256 _cell.length_c 209.538 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XRG _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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 _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 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 OD1 ASN 64 A ASN 64 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc2 B O3B ADP . A ADP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc3 B O1A ADP . A ADP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc4 C O3 PO4 . A PO4 502 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc5 D MG MG . A MG 503 1_555 E O HOH . A HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc6 D MG MG . A MG 503 1_555 E O HOH . A HOH 663 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 8XRG _atom_sites.fract_transf_matrix[1][1] 0.011729 _atom_sites.fract_transf_matrix[1][2] 0.006772 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013544 _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] 0.004772 _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 ADP A 1 501 1 ADP ADP . C 3 PO4 A 1 502 1 PO4 PO4 . D 4 MG A 1 503 1 MG MG . E 5 HOH A 1 601 210 HOH HOH . E 5 HOH A 2 602 144 HOH HOH . E 5 HOH A 3 603 48 HOH HOH . E 5 HOH A 4 604 99 HOH HOH . E 5 HOH A 5 605 9 HOH HOH . E 5 HOH A 6 606 19 HOH HOH . E 5 HOH A 7 607 215 HOH HOH . E 5 HOH A 8 608 110 HOH HOH . E 5 HOH A 9 609 60 HOH HOH . E 5 HOH A 10 610 120 HOH HOH . E 5 HOH A 11 611 114 HOH HOH . E 5 HOH A 12 612 203 HOH HOH . E 5 HOH A 13 613 12 HOH HOH . E 5 HOH A 14 614 166 HOH HOH . E 5 HOH A 15 615 155 HOH HOH . E 5 HOH A 16 616 107 HOH HOH . E 5 HOH A 17 617 129 HOH HOH . E 5 HOH A 18 618 80 HOH HOH . E 5 HOH A 19 619 21 HOH HOH . E 5 HOH A 20 620 6 HOH HOH . E 5 HOH A 21 621 104 HOH HOH . E 5 HOH A 22 622 206 HOH HOH . E 5 HOH A 23 623 59 HOH HOH . E 5 HOH A 24 624 147 HOH HOH . E 5 HOH A 25 625 135 HOH HOH . E 5 HOH A 26 626 20 HOH HOH . E 5 HOH A 27 627 159 HOH HOH . E 5 HOH A 28 628 222 HOH HOH . E 5 HOH A 29 629 56 HOH HOH . E 5 HOH A 30 630 125 HOH HOH . E 5 HOH A 31 631 169 HOH HOH . E 5 HOH A 32 632 127 HOH HOH . E 5 HOH A 33 633 154 HOH HOH . E 5 HOH A 34 634 181 HOH HOH . E 5 HOH A 35 635 214 HOH HOH . E 5 HOH A 36 636 82 HOH HOH . E 5 HOH A 37 637 44 HOH HOH . E 5 HOH A 38 638 50 HOH HOH . E 5 HOH A 39 639 71 HOH HOH . E 5 HOH A 40 640 118 HOH HOH . E 5 HOH A 41 641 179 HOH HOH . E 5 HOH A 42 642 17 HOH HOH . E 5 HOH A 43 643 70 HOH HOH . E 5 HOH A 44 644 42 HOH HOH . E 5 HOH A 45 645 100 HOH HOH . E 5 HOH A 46 646 63 HOH HOH . E 5 HOH A 47 647 196 HOH HOH . E 5 HOH A 48 648 92 HOH HOH . E 5 HOH A 49 649 54 HOH HOH . E 5 HOH A 50 650 64 HOH HOH . E 5 HOH A 51 651 148 HOH HOH . E 5 HOH A 52 652 134 HOH HOH . E 5 HOH A 53 653 103 HOH HOH . E 5 HOH A 54 654 97 HOH HOH . E 5 HOH A 55 655 14 HOH HOH . E 5 HOH A 56 656 213 HOH HOH . E 5 HOH A 57 657 192 HOH HOH . E 5 HOH A 58 658 26 HOH HOH . E 5 HOH A 59 659 207 HOH HOH . E 5 HOH A 60 660 76 HOH HOH . E 5 HOH A 61 661 67 HOH HOH . E 5 HOH A 62 662 87 HOH HOH . E 5 HOH A 63 663 22 HOH HOH . E 5 HOH A 64 664 81 HOH HOH . E 5 HOH A 65 665 47 HOH HOH . E 5 HOH A 66 666 170 HOH HOH . E 5 HOH A 67 667 167 HOH HOH . E 5 HOH A 68 668 122 HOH HOH . E 5 HOH A 69 669 115 HOH HOH . E 5 HOH A 70 670 121 HOH HOH . E 5 HOH A 71 671 86 HOH HOH . E 5 HOH A 72 672 180 HOH HOH . E 5 HOH A 73 673 223 HOH HOH . E 5 HOH A 74 674 91 HOH HOH . E 5 HOH A 75 675 199 HOH HOH . E 5 HOH A 76 676 7 HOH HOH . E 5 HOH A 77 677 51 HOH HOH . E 5 HOH A 78 678 8 HOH HOH . E 5 HOH A 79 679 45 HOH HOH . E 5 HOH A 80 680 58 HOH HOH . E 5 HOH A 81 681 29 HOH HOH . E 5 HOH A 82 682 77 HOH HOH . E 5 HOH A 83 683 41 HOH HOH . E 5 HOH A 84 684 176 HOH HOH . E 5 HOH A 85 685 194 HOH HOH . E 5 HOH A 86 686 184 HOH HOH . E 5 HOH A 87 687 109 HOH HOH . E 5 HOH A 88 688 117 HOH HOH . E 5 HOH A 89 689 79 HOH HOH . E 5 HOH A 90 690 53 HOH HOH . E 5 HOH A 91 691 11 HOH HOH . E 5 HOH A 92 692 23 HOH HOH . E 5 HOH A 93 693 98 HOH HOH . E 5 HOH A 94 694 34 HOH HOH . E 5 HOH A 95 695 96 HOH HOH . E 5 HOH A 96 696 27 HOH HOH . E 5 HOH A 97 697 177 HOH HOH . E 5 HOH A 98 698 145 HOH HOH . E 5 HOH A 99 699 46 HOH HOH . E 5 HOH A 100 700 28 HOH HOH . E 5 HOH A 101 701 153 HOH HOH . E 5 HOH A 102 702 161 HOH HOH . E 5 HOH A 103 703 191 HOH HOH . E 5 HOH A 104 704 174 HOH HOH . E 5 HOH A 105 705 78 HOH HOH . E 5 HOH A 106 706 5 HOH HOH . E 5 HOH A 107 707 94 HOH HOH . E 5 HOH A 108 708 185 HOH HOH . E 5 HOH A 109 709 38 HOH HOH . E 5 HOH A 110 710 69 HOH HOH . E 5 HOH A 111 711 101 HOH HOH . E 5 HOH A 112 712 211 HOH HOH . E 5 HOH A 113 713 72 HOH HOH . E 5 HOH A 114 714 31 HOH HOH . E 5 HOH A 115 715 35 HOH HOH . E 5 HOH A 116 716 151 HOH HOH . E 5 HOH A 117 717 88 HOH HOH . E 5 HOH A 118 718 52 HOH HOH . E 5 HOH A 119 719 172 HOH HOH . E 5 HOH A 120 720 43 HOH HOH . E 5 HOH A 121 721 13 HOH HOH . E 5 HOH A 122 722 10 HOH HOH . E 5 HOH A 123 723 142 HOH HOH . E 5 HOH A 124 724 57 HOH HOH . E 5 HOH A 125 725 74 HOH HOH . E 5 HOH A 126 726 40 HOH HOH . E 5 HOH A 127 727 68 HOH HOH . E 5 HOH A 128 728 163 HOH HOH . E 5 HOH A 129 729 83 HOH HOH . E 5 HOH A 130 730 1 HOH HOH . E 5 HOH A 131 731 137 HOH HOH . E 5 HOH A 132 732 141 HOH HOH . E 5 HOH A 133 733 171 HOH HOH . E 5 HOH A 134 734 165 HOH HOH . E 5 HOH A 135 735 55 HOH HOH . E 5 HOH A 136 736 219 HOH HOH . E 5 HOH A 137 737 183 HOH HOH . E 5 HOH A 138 738 198 HOH HOH . E 5 HOH A 139 739 175 HOH HOH . E 5 HOH A 140 740 204 HOH HOH . E 5 HOH A 141 741 84 HOH HOH . E 5 HOH A 142 742 24 HOH HOH . E 5 HOH A 143 743 39 HOH HOH . E 5 HOH A 144 744 61 HOH HOH . E 5 HOH A 145 745 15 HOH HOH . E 5 HOH A 146 746 113 HOH HOH . E 5 HOH A 147 747 93 HOH HOH . E 5 HOH A 148 748 190 HOH HOH . E 5 HOH A 149 749 200 HOH HOH . E 5 HOH A 150 750 157 HOH HOH . E 5 HOH A 151 751 18 HOH HOH . E 5 HOH A 152 752 162 HOH HOH . E 5 HOH A 153 753 205 HOH HOH . E 5 HOH A 154 754 75 HOH HOH . E 5 HOH A 155 755 217 HOH HOH . E 5 HOH A 156 756 168 HOH HOH . E 5 HOH A 157 757 133 HOH HOH . E 5 HOH A 158 758 89 HOH HOH . E 5 HOH A 159 759 32 HOH HOH . E 5 HOH A 160 760 128 HOH HOH . E 5 HOH A 161 761 16 HOH HOH . E 5 HOH A 162 762 33 HOH HOH . E 5 HOH A 163 763 218 HOH HOH . E 5 HOH A 164 764 158 HOH HOH . E 5 HOH A 165 765 95 HOH HOH . E 5 HOH A 166 766 4 HOH HOH . E 5 HOH A 167 767 195 HOH HOH . E 5 HOH A 168 768 212 HOH HOH . E 5 HOH A 169 769 49 HOH HOH . E 5 HOH A 170 770 119 HOH HOH . E 5 HOH A 171 771 2 HOH HOH . E 5 HOH A 172 772 193 HOH HOH . E 5 HOH A 173 773 202 HOH HOH . E 5 HOH A 174 774 73 HOH HOH . E 5 HOH A 175 775 108 HOH HOH . E 5 HOH A 176 776 30 HOH HOH . E 5 HOH A 177 777 209 HOH HOH . E 5 HOH A 178 778 173 HOH HOH . E 5 HOH A 179 779 25 HOH HOH . E 5 HOH A 180 780 149 HOH HOH . E 5 HOH A 181 781 201 HOH HOH . E 5 HOH A 182 782 66 HOH HOH . E 5 HOH A 183 783 220 HOH HOH . E 5 HOH A 184 784 150 HOH HOH . E 5 HOH A 185 785 116 HOH HOH . E 5 HOH A 186 786 138 HOH HOH . E 5 HOH A 187 787 221 HOH HOH . E 5 HOH A 188 788 216 HOH HOH . E 5 HOH A 189 789 187 HOH HOH . E 5 HOH A 190 790 186 HOH HOH . E 5 HOH A 191 791 188 HOH HOH . E 5 HOH A 192 792 132 HOH HOH . E 5 HOH A 193 793 140 HOH HOH . E 5 HOH A 194 794 189 HOH HOH . E 5 HOH A 195 795 208 HOH HOH . E 5 HOH A 196 796 152 HOH HOH . E 5 HOH A 197 797 197 HOH HOH . E 5 HOH A 198 798 126 HOH HOH . E 5 HOH A 199 799 90 HOH HOH . E 5 HOH A 200 800 156 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 PB ADP . . . B 2 20.926 8.331 -10.155 1 16.41 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 20.186 8.1 -11.433 1 19.2 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 21.364 7.033 -9.576 1 16.71 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 22.005 9.365 -10.222 1 17.36 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 19.736 10.172 -8.202 1 16.84 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 21.118 10.664 -7.905 1 14.72 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 18.787 9.864 -7.071 1 17.6 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 19.811 8.845 -9.113 1 17.19 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 19.029 11.221 -9.178 1 17.29 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 17.701 10.859 -9.614 1 17.64 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 17.442 11.314 -11.038 1 20.62 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 17.225 12.725 -11.09 1 21.1 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 18.608 11.042 -11.973 1 18.27 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 18.512 9.728 -12.521 1 20.37 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 18.467 12.12 -13.038 1 20.03 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 17.547 11.674 -14.038 1 22.83 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 17.789 13.257 -12.293 1 22.26 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 18.761 14.293 -11.87 1 20.27 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 19.342 14.417 -10.658 1 20.98 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 20.158 15.505 -10.604 1 19.34 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 20.053 16.11 -11.804 1 17.26 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 20.658 17.306 -12.4 1 20.65 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 21.53 18.076 -11.691 1 22.46 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 20.301 17.583 -13.662 1 22.35 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 19.442 16.827 -14.374 1 24.61 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 18.846 15.714 -13.903 1 25.65 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 19.139 15.32 -12.635 1 19.78 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #