data_3VMM # _model_server_result.job_id fMZgUb34RPIcCFwN0v6s5A _model_server_result.datetime_utc '2025-03-09 02:33:58' _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 3vmm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 3VMM # _exptl.entry_id 3VMM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 3VMM _cell.length_a 130.787 _cell.length_b 130.787 _cell.length_c 147.742 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VMM _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 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,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 3 _struct_asym.id D _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 OE2 GLU 111 A GLU 109 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc2 A O LEU 184 A LEU 182 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? metalc ? metalc3 A OE1 GLU 313 A GLU 311 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc4 A OE2 GLU 326 A GLU 324 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc5 A OE1 GLU 326 A GLU 324 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc6 B MG MG . A MG 501 1_555 D O1B ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc7 B MG MG . A MG 501 1_555 D O1A ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 B MG MG . A MG 501 1_555 E O5P P0D . A P0D 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc9 B MG MG . A MG 501 1_555 F O HOH . A HOH 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc10 C MG MG . A MG 502 1_555 D O3B ADP . A ADP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc11 C MG MG . A MG 502 1_555 E O3P P0D . A P0D 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc12 C MG MG . A MG 502 1_555 F O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? # _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 3VMM _atom_sites.fract_transf_matrix[1][1] 0.007646 _atom_sites.fract_transf_matrix[1][2] 0.004414 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008829 _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] 0.006769 _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 1 501 501 MG MG . C 2 MG A 1 502 502 MG MG . D 3 ADP A 1 503 503 ADP ADP . E 4 P0D A 1 504 504 P0D P0D . F 5 HOH A 1 601 1 HOH HOH . F 5 HOH A 2 602 2 HOH HOH . F 5 HOH A 3 603 3 HOH HOH . F 5 HOH A 4 604 4 HOH HOH . F 5 HOH A 5 605 5 HOH HOH . F 5 HOH A 6 606 6 HOH HOH . F 5 HOH A 7 607 7 HOH HOH . F 5 HOH A 8 608 8 HOH HOH . F 5 HOH A 9 609 9 HOH HOH . F 5 HOH A 10 610 10 HOH HOH . F 5 HOH A 11 611 11 HOH HOH . F 5 HOH A 12 612 12 HOH HOH . F 5 HOH A 13 613 13 HOH HOH . F 5 HOH A 14 614 16 HOH HOH . F 5 HOH A 15 615 17 HOH HOH . F 5 HOH A 16 616 18 HOH HOH . F 5 HOH A 17 617 20 HOH HOH . F 5 HOH A 18 618 21 HOH HOH . F 5 HOH A 19 619 23 HOH HOH . F 5 HOH A 20 620 27 HOH HOH . F 5 HOH A 21 621 28 HOH HOH . F 5 HOH A 22 622 30 HOH HOH . F 5 HOH A 23 623 31 HOH HOH . F 5 HOH A 24 624 34 HOH HOH . F 5 HOH A 25 625 35 HOH HOH . F 5 HOH A 26 626 36 HOH HOH . F 5 HOH A 27 627 37 HOH HOH . F 5 HOH A 28 628 38 HOH HOH . F 5 HOH A 29 629 39 HOH HOH . F 5 HOH A 30 630 41 HOH HOH . F 5 HOH A 31 631 43 HOH HOH . F 5 HOH A 32 632 44 HOH HOH . F 5 HOH A 33 633 48 HOH HOH . F 5 HOH A 34 634 49 HOH HOH . F 5 HOH A 35 635 50 HOH HOH . F 5 HOH A 36 636 52 HOH HOH . F 5 HOH A 37 637 53 HOH HOH . F 5 HOH A 38 638 55 HOH HOH . F 5 HOH A 39 639 56 HOH HOH . F 5 HOH A 40 640 57 HOH HOH . F 5 HOH A 41 641 59 HOH HOH . F 5 HOH A 42 642 60 HOH HOH . F 5 HOH A 43 643 62 HOH HOH . F 5 HOH A 44 644 63 HOH HOH . F 5 HOH A 45 645 64 HOH HOH . F 5 HOH A 46 646 65 HOH HOH . F 5 HOH A 47 647 67 HOH HOH . F 5 HOH A 48 648 68 HOH HOH . F 5 HOH A 49 649 69 HOH HOH . F 5 HOH A 50 650 70 HOH HOH . F 5 HOH A 51 651 71 HOH HOH . F 5 HOH A 52 652 73 HOH HOH . F 5 HOH A 53 653 75 HOH HOH . F 5 HOH A 54 654 76 HOH HOH . F 5 HOH A 55 655 77 HOH HOH . F 5 HOH A 56 656 78 HOH HOH . F 5 HOH A 57 657 79 HOH HOH . F 5 HOH A 58 658 82 HOH HOH . F 5 HOH A 59 659 87 HOH HOH . F 5 HOH A 60 660 88 HOH HOH . F 5 HOH A 61 661 89 HOH HOH . F 5 HOH A 62 662 90 HOH HOH . F 5 HOH A 63 663 91 HOH HOH . F 5 HOH A 64 664 95 HOH HOH . F 5 HOH A 65 665 99 HOH HOH . F 5 HOH A 66 666 103 HOH HOH . F 5 HOH A 67 667 104 HOH HOH . F 5 HOH A 68 668 105 HOH HOH . F 5 HOH A 69 669 107 HOH HOH . F 5 HOH A 70 670 108 HOH HOH . F 5 HOH A 71 671 109 HOH HOH . F 5 HOH A 72 672 110 HOH HOH . F 5 HOH A 73 673 114 HOH HOH . F 5 HOH A 74 674 115 HOH HOH . F 5 HOH A 75 675 116 HOH HOH . F 5 HOH A 76 676 117 HOH HOH . F 5 HOH A 77 677 119 HOH HOH . F 5 HOH A 78 678 121 HOH HOH . F 5 HOH A 79 679 122 HOH HOH . F 5 HOH A 80 680 124 HOH HOH . F 5 HOH A 81 681 127 HOH HOH . F 5 HOH A 82 682 128 HOH HOH . F 5 HOH A 83 683 131 HOH HOH . F 5 HOH A 84 684 132 HOH HOH . F 5 HOH A 85 685 133 HOH HOH . F 5 HOH A 86 686 138 HOH HOH . F 5 HOH A 87 687 139 HOH HOH . F 5 HOH A 88 688 141 HOH HOH . F 5 HOH A 89 689 143 HOH HOH . F 5 HOH A 90 690 145 HOH HOH . F 5 HOH A 91 691 146 HOH HOH . F 5 HOH A 92 692 147 HOH HOH . F 5 HOH A 93 693 148 HOH HOH . F 5 HOH A 94 694 149 HOH HOH . F 5 HOH A 95 695 150 HOH HOH . F 5 HOH A 96 696 153 HOH HOH . F 5 HOH A 97 697 154 HOH HOH . F 5 HOH A 98 698 155 HOH HOH . F 5 HOH A 99 699 156 HOH HOH . F 5 HOH A 100 700 157 HOH HOH . F 5 HOH A 101 701 158 HOH HOH . F 5 HOH A 102 702 159 HOH HOH . F 5 HOH A 103 703 160 HOH HOH . F 5 HOH A 104 704 161 HOH HOH . F 5 HOH A 105 705 163 HOH HOH . F 5 HOH A 106 706 164 HOH HOH . F 5 HOH A 107 707 165 HOH HOH . F 5 HOH A 108 708 166 HOH HOH . F 5 HOH A 109 709 167 HOH HOH . F 5 HOH A 110 710 168 HOH HOH . F 5 HOH A 111 711 169 HOH HOH . F 5 HOH A 112 712 170 HOH HOH . F 5 HOH A 113 713 171 HOH HOH . F 5 HOH A 114 714 172 HOH HOH . F 5 HOH A 115 715 173 HOH HOH . F 5 HOH A 116 716 174 HOH HOH . F 5 HOH A 117 717 175 HOH HOH . F 5 HOH A 118 718 176 HOH HOH . F 5 HOH A 119 719 177 HOH HOH . F 5 HOH A 120 720 178 HOH HOH . F 5 HOH A 121 721 179 HOH HOH . F 5 HOH A 122 722 180 HOH HOH . F 5 HOH A 123 723 181 HOH HOH . F 5 HOH A 124 724 182 HOH HOH . F 5 HOH A 125 725 183 HOH HOH . F 5 HOH A 126 726 184 HOH HOH . F 5 HOH A 127 727 185 HOH HOH . F 5 HOH A 128 728 186 HOH HOH . F 5 HOH A 129 729 187 HOH HOH . F 5 HOH A 130 730 189 HOH HOH . F 5 HOH A 131 731 190 HOH HOH . F 5 HOH A 132 732 192 HOH HOH . F 5 HOH A 133 733 193 HOH HOH . F 5 HOH A 134 734 194 HOH HOH . F 5 HOH A 135 735 195 HOH HOH . F 5 HOH A 136 736 196 HOH HOH . F 5 HOH A 137 737 197 HOH HOH . F 5 HOH A 138 738 198 HOH HOH . F 5 HOH A 139 739 199 HOH HOH . F 5 HOH A 140 740 200 HOH HOH . F 5 HOH A 141 741 201 HOH HOH . F 5 HOH A 142 742 202 HOH HOH . F 5 HOH A 143 743 203 HOH HOH . F 5 HOH A 144 744 204 HOH HOH . F 5 HOH A 145 745 205 HOH HOH . F 5 HOH A 146 746 206 HOH HOH . F 5 HOH A 147 747 207 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 . . . D 3 -1.703 -41.221 -4.825 1 36.75 ? PB ADP 503 A 1 HETATM 2 O O1B ADP . . . D 3 -2.692 -41.731 -5.835 1 36.13 ? O1B ADP 503 A 1 HETATM 3 O O2B ADP . . . D 3 -1.939 -41.786 -3.445 1 35.39 ? O2B ADP 503 A 1 HETATM 4 O O3B ADP . . . D 3 -0.273 -41.288 -5.303 1 36.47 ? O3B ADP 503 A 1 HETATM 5 P PA ADP . . . D 3 -3.122 -38.728 -5.338 1 36.36 ? PA ADP 503 A 1 HETATM 6 O O1A ADP . . . D 3 -3.449 -39.342 -6.673 1 34.51 ? O1A ADP 503 A 1 HETATM 7 O O2A ADP . . . D 3 -2.712 -37.278 -5.249 1 37.02 ? O2A ADP 503 A 1 HETATM 8 O O3A ADP . . . D 3 -1.954 -39.624 -4.654 1 38.07 ? O3A ADP 503 A 1 HETATM 9 O O5' ADP . . . D 3 -4.405 -38.91 -4.382 1 36.67 ? O5' ADP 503 A 1 HETATM 10 C C5' ADP . . . D 3 -5.31 -40 -4.585 1 34.92 ? C5' ADP 503 A 1 HETATM 11 C C4' ADP . . . D 3 -6.7 -39.473 -4.924 1 34.54 ? C4' ADP 503 A 1 HETATM 12 O O4' ADP . . . D 3 -7.081 -38.44 -4.013 1 36.52 ? O4' ADP 503 A 1 HETATM 13 C C3' ADP . . . D 3 -6.812 -38.809 -6.29 1 34.03 ? C3' ADP 503 A 1 HETATM 14 O O3' ADP . . . D 3 -7.05 -39.749 -7.332 1 32.12 ? O3' ADP 503 A 1 HETATM 15 C C2' ADP . . . D 3 -7.986 -37.866 -6.12 1 35.52 ? C2' ADP 503 A 1 HETATM 16 O O2' ADP . . . D 3 -9.232 -38.558 -6.245 1 34.93 ? O2' ADP 503 A 1 HETATM 17 C C1' ADP . . . D 3 -7.853 -37.435 -4.678 1 36.71 ? C1' ADP 503 A 1 HETATM 18 N N9 ADP . . . D 3 -7.109 -36.157 -4.596 1 39.08 ? N9 ADP 503 A 1 HETATM 19 C C8 ADP . . . D 3 -5.789 -36.035 -4.321 1 39.57 ? C8 ADP 503 A 1 HETATM 20 N N7 ADP . . . D 3 -5.419 -34.735 -4.318 1 40.39 ? N7 ADP 503 A 1 HETATM 21 C C5 ADP . . . D 3 -6.513 -33.996 -4.59 1 40.6 ? C5 ADP 503 A 1 HETATM 22 C C6 ADP . . . D 3 -6.835 -32.55 -4.721 1 41.4 ? C6 ADP 503 A 1 HETATM 23 N N6 ADP . . . D 3 -5.886 -31.6 -4.569 1 42.32 ? N6 ADP 503 A 1 HETATM 24 N N1 ADP . . . D 3 -8.115 -32.214 -5.008 1 40.94 ? N1 ADP 503 A 1 HETATM 25 C C2 ADP . . . D 3 -9.079 -33.138 -5.167 1 39.04 ? C2 ADP 503 A 1 HETATM 26 N N3 ADP . . . D 3 -8.859 -34.46 -5.056 1 38.07 ? N3 ADP 503 A 1 HETATM 27 C C4 ADP . . . D 3 -7.627 -34.941 -4.774 1 38.71 ? C4 ADP 503 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #