data_9QYF # _model_server_result.job_id yPhPu1tWv5mLkd8p6J1zUw _model_server_result.datetime_utc '2025-07-23 05:33:20' _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 9qyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 9QYF # _exptl.entry_id 9QYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 90 _cell.entry_id 9QYF _cell.length_a 52.143 _cell.length_b 52.143 _cell.length_c 132.158 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9QYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 9QYF _atom_sites.fract_transf_matrix[1][1] 0.019178 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019178 _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] 0.007567 _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 APR A 1 501 1 APR APR . C 3 AR6 A 1 502 2 AR6 AR6 . D 4 HOH A 1 601 218 HOH HOH . D 4 HOH A 2 602 190 HOH HOH . D 4 HOH A 3 603 195 HOH HOH . D 4 HOH A 4 604 231 HOH HOH . D 4 HOH A 5 605 101 HOH HOH . D 4 HOH A 6 606 194 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 96 HOH HOH . D 4 HOH A 9 609 133 HOH HOH . D 4 HOH A 10 610 191 HOH HOH . D 4 HOH A 11 611 62 HOH HOH . D 4 HOH A 12 612 232 HOH HOH . D 4 HOH A 13 613 65 HOH HOH . D 4 HOH A 14 614 170 HOH HOH . D 4 HOH A 15 615 10 HOH HOH . D 4 HOH A 16 616 52 HOH HOH . D 4 HOH A 17 617 144 HOH HOH . D 4 HOH A 18 618 161 HOH HOH . D 4 HOH A 19 619 75 HOH HOH . D 4 HOH A 20 620 11 HOH HOH . D 4 HOH A 21 621 70 HOH HOH . D 4 HOH A 22 622 115 HOH HOH . D 4 HOH A 23 623 149 HOH HOH . D 4 HOH A 24 624 236 HOH HOH . D 4 HOH A 25 625 110 HOH HOH . D 4 HOH A 26 626 47 HOH HOH . D 4 HOH A 27 627 2 HOH HOH . D 4 HOH A 28 628 74 HOH HOH . D 4 HOH A 29 629 100 HOH HOH . D 4 HOH A 30 630 1 HOH HOH . D 4 HOH A 31 631 69 HOH HOH . D 4 HOH A 32 632 23 HOH HOH . D 4 HOH A 33 633 159 HOH HOH . D 4 HOH A 34 634 51 HOH HOH . D 4 HOH A 35 635 95 HOH HOH . D 4 HOH A 36 636 129 HOH HOH . D 4 HOH A 37 637 116 HOH HOH . D 4 HOH A 38 638 9 HOH HOH . D 4 HOH A 39 639 85 HOH HOH . D 4 HOH A 40 640 31 HOH HOH . D 4 HOH A 41 641 239 HOH HOH . D 4 HOH A 42 642 6 HOH HOH . D 4 HOH A 43 643 42 HOH HOH . D 4 HOH A 44 644 150 HOH HOH . D 4 HOH A 45 645 210 HOH HOH . D 4 HOH A 46 646 157 HOH HOH . D 4 HOH A 47 647 117 HOH HOH . D 4 HOH A 48 648 130 HOH HOH . D 4 HOH A 49 649 82 HOH HOH . D 4 HOH A 50 650 234 HOH HOH . D 4 HOH A 51 651 71 HOH HOH . D 4 HOH A 52 652 26 HOH HOH . D 4 HOH A 53 653 203 HOH HOH . D 4 HOH A 54 654 97 HOH HOH . D 4 HOH A 55 655 113 HOH HOH . D 4 HOH A 56 656 108 HOH HOH . D 4 HOH A 57 657 66 HOH HOH . D 4 HOH A 58 658 22 HOH HOH . D 4 HOH A 59 659 141 HOH HOH . D 4 HOH A 60 660 81 HOH HOH . D 4 HOH A 61 661 255 HOH HOH . D 4 HOH A 62 662 158 HOH HOH . D 4 HOH A 63 663 59 HOH HOH . D 4 HOH A 64 664 79 HOH HOH . D 4 HOH A 65 665 84 HOH HOH . D 4 HOH A 66 666 5 HOH HOH . D 4 HOH A 67 667 43 HOH HOH . D 4 HOH A 68 668 240 HOH HOH . D 4 HOH A 69 669 49 HOH HOH . D 4 HOH A 70 670 91 HOH HOH . D 4 HOH A 71 671 114 HOH HOH . D 4 HOH A 72 672 13 HOH HOH . D 4 HOH A 73 673 105 HOH HOH . D 4 HOH A 74 674 25 HOH HOH . D 4 HOH A 75 675 48 HOH HOH . D 4 HOH A 76 676 189 HOH HOH . D 4 HOH A 77 677 206 HOH HOH . D 4 HOH A 78 678 17 HOH HOH . D 4 HOH A 79 679 16 HOH HOH . D 4 HOH A 80 680 107 HOH HOH . D 4 HOH A 81 681 140 HOH HOH . D 4 HOH A 82 682 61 HOH HOH . D 4 HOH A 83 683 146 HOH HOH . D 4 HOH A 84 684 211 HOH HOH . D 4 HOH A 85 685 248 HOH HOH . D 4 HOH A 86 686 50 HOH HOH . D 4 HOH A 87 687 12 HOH HOH . D 4 HOH A 88 688 153 HOH HOH . D 4 HOH A 89 689 53 HOH HOH . D 4 HOH A 90 690 32 HOH HOH . D 4 HOH A 91 691 39 HOH HOH . D 4 HOH A 92 692 54 HOH HOH . D 4 HOH A 93 693 73 HOH HOH . D 4 HOH A 94 694 8 HOH HOH . D 4 HOH A 95 695 89 HOH HOH . D 4 HOH A 96 696 235 HOH HOH . D 4 HOH A 97 697 175 HOH HOH . D 4 HOH A 98 698 44 HOH HOH . D 4 HOH A 99 699 29 HOH HOH . D 4 HOH A 100 700 109 HOH HOH . D 4 HOH A 101 701 57 HOH HOH . D 4 HOH A 102 702 30 HOH HOH . D 4 HOH A 103 703 134 HOH HOH . D 4 HOH A 104 704 63 HOH HOH . D 4 HOH A 105 705 169 HOH HOH . D 4 HOH A 106 706 18 HOH HOH . D 4 HOH A 107 707 20 HOH HOH . D 4 HOH A 108 708 111 HOH HOH . D 4 HOH A 109 709 182 HOH HOH . D 4 HOH A 110 710 3 HOH HOH . D 4 HOH A 111 711 77 HOH HOH . D 4 HOH A 112 712 35 HOH HOH . D 4 HOH A 113 713 86 HOH HOH . D 4 HOH A 114 714 45 HOH HOH . D 4 HOH A 115 715 24 HOH HOH . D 4 HOH A 116 716 83 HOH HOH . D 4 HOH A 117 717 21 HOH HOH . D 4 HOH A 118 718 68 HOH HOH . D 4 HOH A 119 719 58 HOH HOH . D 4 HOH A 120 720 177 HOH HOH . D 4 HOH A 121 721 37 HOH HOH . D 4 HOH A 122 722 99 HOH HOH . D 4 HOH A 123 723 64 HOH HOH . D 4 HOH A 124 724 41 HOH HOH . D 4 HOH A 125 725 38 HOH HOH . D 4 HOH A 126 726 88 HOH HOH . D 4 HOH A 127 727 14 HOH HOH . D 4 HOH A 128 728 27 HOH HOH . D 4 HOH A 129 729 213 HOH HOH . D 4 HOH A 130 730 229 HOH HOH . D 4 HOH A 131 731 80 HOH HOH . D 4 HOH A 132 732 67 HOH HOH . D 4 HOH A 133 733 55 HOH HOH . D 4 HOH A 134 734 145 HOH HOH . D 4 HOH A 135 735 33 HOH HOH . D 4 HOH A 136 736 139 HOH HOH . D 4 HOH A 137 737 119 HOH HOH . D 4 HOH A 138 738 19 HOH HOH . D 4 HOH A 139 739 164 HOH HOH . D 4 HOH A 140 740 106 HOH HOH . D 4 HOH A 141 741 87 HOH HOH . D 4 HOH A 142 742 112 HOH HOH . D 4 HOH A 143 743 36 HOH HOH . D 4 HOH A 144 744 132 HOH HOH . D 4 HOH A 145 745 148 HOH HOH . D 4 HOH A 146 746 160 HOH HOH . D 4 HOH A 147 747 121 HOH HOH . D 4 HOH A 148 748 243 HOH HOH . D 4 HOH A 149 749 237 HOH HOH . D 4 HOH A 150 750 28 HOH HOH . D 4 HOH A 151 751 127 HOH HOH . D 4 HOH A 152 752 183 HOH HOH . D 4 HOH A 153 753 125 HOH HOH . D 4 HOH A 154 754 227 HOH HOH . D 4 HOH A 155 755 128 HOH HOH . D 4 HOH A 156 756 233 HOH HOH . D 4 HOH A 157 757 225 HOH HOH . D 4 HOH A 158 758 174 HOH HOH . D 4 HOH A 159 759 184 HOH HOH . D 4 HOH A 160 760 226 HOH HOH . D 4 HOH A 161 761 56 HOH HOH . D 4 HOH A 162 762 135 HOH HOH . D 4 HOH A 163 763 76 HOH HOH . D 4 HOH A 164 764 244 HOH HOH . D 4 HOH A 165 765 98 HOH HOH . D 4 HOH A 166 766 102 HOH HOH . D 4 HOH A 167 767 92 HOH HOH . D 4 HOH A 168 768 176 HOH HOH . D 4 HOH A 169 769 200 HOH HOH . D 4 HOH A 170 770 224 HOH HOH . D 4 HOH A 171 771 78 HOH HOH . D 4 HOH A 172 772 154 HOH HOH . D 4 HOH A 173 773 209 HOH HOH . D 4 HOH A 174 774 192 HOH HOH . D 4 HOH A 175 775 204 HOH HOH . D 4 HOH A 176 776 247 HOH HOH . D 4 HOH A 177 777 40 HOH HOH . D 4 HOH A 178 778 60 HOH HOH . D 4 HOH A 179 779 72 HOH HOH . D 4 HOH A 180 780 196 HOH HOH . D 4 HOH A 181 781 238 HOH HOH . D 4 HOH A 182 782 242 HOH HOH . D 4 HOH A 183 783 245 HOH HOH . D 4 HOH A 184 784 156 HOH HOH . D 4 HOH A 185 785 137 HOH HOH . D 4 HOH A 186 786 180 HOH HOH . D 4 HOH A 187 787 155 HOH HOH . D 4 HOH A 188 788 120 HOH HOH . D 4 HOH A 189 789 228 HOH HOH . D 4 HOH A 190 790 93 HOH HOH . D 4 HOH A 191 791 131 HOH HOH . D 4 HOH A 192 792 168 HOH HOH . D 4 HOH A 193 793 152 HOH HOH . D 4 HOH A 194 794 217 HOH HOH . D 4 HOH A 195 795 142 HOH HOH . D 4 HOH A 196 796 122 HOH HOH . D 4 HOH A 197 797 124 HOH HOH . D 4 HOH A 198 798 126 HOH HOH . D 4 HOH A 199 799 34 HOH HOH . D 4 HOH A 200 800 193 HOH HOH . D 4 HOH A 201 801 241 HOH HOH . D 4 HOH A 202 802 103 HOH HOH . D 4 HOH A 203 803 246 HOH HOH . D 4 HOH A 204 804 179 HOH HOH . D 4 HOH A 205 805 185 HOH HOH . D 4 HOH A 206 806 250 HOH HOH . D 4 HOH A 207 807 251 HOH HOH . D 4 HOH A 208 808 249 HOH HOH . D 4 HOH A 209 809 252 HOH HOH . D 4 HOH A 210 810 253 HOH HOH . D 4 HOH A 211 811 254 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 N N1 APR . A . B 2 -8.11 17.794 -1.453 0.5 13.32 ? N1 APR 501 A 1 HETATM 2 C C2 APR . A . B 2 -8.359 16.53 -1.797 0.5 13.77 ? C2 APR 501 A 1 HETATM 3 N N3 APR . A . B 2 -7.714 15.43 -1.452 0.5 12.78 ? N3 APR 501 A 1 HETATM 4 C C4 APR . A . B 2 -6.617 15.713 -0.723 0.5 13.08 ? C4 APR 501 A 1 HETATM 5 C C5 APR . A . B 2 -6.216 16.951 -0.304 0.5 13.35 ? C5 APR 501 A 1 HETATM 6 C C6 APR . A . B 2 -7.001 18.041 -0.706 0.5 13.07 ? C6 APR 501 A 1 HETATM 7 N N6 APR . A . B 2 -6.706 19.285 -0.361 0.5 12.53 ? N6 APR 501 A 1 HETATM 8 N N7 APR . A . B 2 -5.062 16.868 0.462 0.5 13.57 ? N7 APR 501 A 1 HETATM 9 C C8 APR . A . B 2 -4.787 15.577 0.504 0.5 12.42 ? C8 APR 501 A 1 HETATM 10 N N9 APR . A . B 2 -5.705 14.836 -0.213 0.5 12.85 ? N9 APR 501 A 1 HETATM 11 C C1' APR . A . B 2 -5.767 13.389 -0.305 0.5 12.6 ? C1' APR 501 A 1 HETATM 12 C C2' APR . A . B 2 -4.531 12.594 0.074 0.5 13.72 ? C2' APR 501 A 1 HETATM 13 O O2' APR . A . B 2 -3.535 12.614 -0.928 0.5 14.77 ? O2' APR 501 A 1 HETATM 14 C C3' APR . A . B 2 -5.192 11.242 0.334 0.5 12.62 ? C3' APR 501 A 1 HETATM 15 O O3' APR . A . B 2 -5.421 10.583 -0.905 0.5 14.47 ? O3' APR 501 A 1 HETATM 16 O O4' APR . A . B 2 -6.749 12.988 0.634 0.5 13.46 ? O4' APR 501 A 1 HETATM 17 C C4' APR . A . B 2 -6.507 11.611 1.027 0.5 12.2 ? C4' APR 501 A 1 HETATM 18 C C5' APR . A . B 2 -6.519 11.481 2.539 0.5 12.68 ? C5' APR 501 A 1 HETATM 19 O O5' APR . A . B 2 -5.207 11.822 3.082 0.5 13.67 ? O5' APR 501 A 1 HETATM 20 P PA APR . A . B 2 -5.019 12.404 4.583 0.5 14.62 ? PA APR 501 A 1 HETATM 21 O O1A APR . A . B 2 -5.274 13.875 4.566 0.5 14.32 ? O1A APR 501 A 1 HETATM 22 O O2A APR . A . B 2 -3.663 11.972 5.046 0.5 14.85 ? O2A APR 501 A 1 HETATM 23 O O3A APR . A . B 2 -6.188 11.708 5.45 0.5 14.04 ? O3A APR 501 A 1 HETATM 24 P PB APR . A . B 2 -6.462 10.181 5.837 0.5 14.83 ? PB APR 501 A 1 HETATM 25 O O1B APR . A . B 2 -5.607 9.255 5.021 0.5 14.26 ? O1B APR 501 A 1 HETATM 26 O O2B APR . A . B 2 -7.946 10.042 5.835 0.5 12.65 ? O2B APR 501 A 1 HETATM 27 O O5D APR . A . B 2 -5.88 10.15 7.334 0.5 14.94 ? O5D APR 501 A 1 HETATM 28 C C5D APR . A . B 2 -6.384 11.064 8.331 0.5 17.24 ? C5D APR 501 A 1 HETATM 29 O O4D APR . A . B 2 -4.339 12.171 8.885 0.5 19.23 ? O4D APR 501 A 1 HETATM 30 O O1D APR . A . B 2 -5.665 13.833 9.603 0.5 19.59 ? O1D APR 501 A 1 HETATM 31 C C1D APR . A . B 2 -4.443 13.258 9.754 0.5 19.84 ? C1D APR 501 A 1 HETATM 32 O O2D APR . A . B 2 -3.42 11.839 11.524 0.5 21.1 ? O2D APR 501 A 1 HETATM 33 C C2D APR . A . B 2 -4.537 12.608 11.127 0.5 18.77 ? C2D APR 501 A 1 HETATM 34 O O3D APR . A . B 2 -6.102 10.861 11.694 0.5 21.67 ? O3D APR 501 A 1 HETATM 35 C C3D APR . A . B 2 -5.788 11.831 10.722 0.5 19.11 ? C3D APR 501 A 1 HETATM 36 C C4D APR . A . B 2 -5.325 11.232 9.386 0.5 18.47 ? C4D APR 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #