data_8OM9 # _model_server_result.job_id apkotNrOuZt2JFEb65xI5A _model_server_result.datetime_utc '2025-02-22 22:40:15' _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 8om9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2000}' # _entry.id 8OM9 # _exptl.entry_id 8OM9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 8OM9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 G N 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 676 A SER 676 1_555 F MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc2 E O3B ADP . A ADP 2000 1_555 F MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc3 B OG SER 903 B SER 903 1_555 H MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc4 G O2B ADP . B ADP 2000 1_555 H MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? hydrog WATSON-CRICK hydrog1 C N1 DA 4 C DA 28 1_555 D N3 DT 20 D DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N6 DA 4 C DA 28 1_555 D O4 DT 20 D DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N3 DT 5 C DT 29 1_555 D N1 DA 19 D DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C O4 DT 5 C DT 29 1_555 D N6 DA 19 D DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N1 DA 13 C DA 37 1_555 D N3 DT 17 D DT 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N6 DA 13 C DA 37 1_555 D O4 DT 17 D DT 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N1 DG 14 C DG 38 1_555 D N3 DC 16 D DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N2 DG 14 C DG 38 1_555 D O2 DC 16 D DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C O6 DG 14 C DG 38 1_555 D N4 DC 16 D DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N3 DC 15 C DC 39 1_555 D N1 DG 15 D DG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N4 DC 15 C DC 39 1_555 D O6 DG 15 D DG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O2 DC 15 C DC 39 1_555 D N2 DG 15 D DG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N3 DT 16 C DT 40 1_555 D N1 DA 14 D DA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C O4 DT 16 C DT 40 1_555 D N6 DA 14 D DA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N3 DC 17 C DC 41 1_555 D N1 DG 13 D DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N4 DC 17 C DC 41 1_555 D O6 DG 13 D DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O2 DC 17 C DC 41 1_555 D N2 DG 13 D DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N1 DG 18 C DG 42 1_555 D N3 DC 12 D DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N2 DG 18 C DG 42 1_555 D O2 DC 12 D DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C O6 DG 18 C DG 42 1_555 D N4 DC 12 D DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N1 DG 19 C DG 43 1_555 D N3 DC 11 D DC 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C N2 DG 19 C DG 43 1_555 D O2 DC 11 D DC 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C O6 DG 19 C DG 43 1_555 D N4 DC 11 D DC 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N3 DT 20 C DT 44 1_555 D N1 DA 10 D DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O4 DT 20 C DT 44 1_555 D N6 DA 10 D DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N1 DG 21 C DG 45 1_555 D N3 DC 9 D DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N2 DG 21 C DG 45 1_555 D O2 DC 9 D DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C O6 DG 21 C DG 45 1_555 D N4 DC 9 D DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C N3 DC 22 C DC 46 1_555 D N1 DG 8 D DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N4 DC 22 C DC 46 1_555 D O6 DG 8 D DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C O2 DC 22 C DC 46 1_555 D N2 DG 8 D DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C N1 DA 23 C DA 47 1_555 D N3 DT 7 D DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N6 DA 23 C DA 47 1_555 D O4 DT 7 D DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N1 DA 24 C DA 48 1_555 D N3 DT 6 D DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C N6 DA 24 C DA 48 1_555 D O4 DT 6 D DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N3 DT 25 C DT 49 1_555 D N1 DA 5 D DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C O4 DT 25 C DT 49 1_555 D N6 DA 5 D DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N3 DT 26 C DT 50 1_555 D N1 DA 4 D DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C O4 DT 26 C DT 50 1_555 D N6 DA 4 D DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N3 DC 27 C DC 51 1_555 D N1 DG 3 D DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N4 DC 27 C DC 51 1_555 D O6 DG 3 D DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C O2 DC 27 C DC 51 1_555 D N2 DG 3 D DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N1 DA 28 C DA 52 1_555 D N3 DT 2 D DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C N6 DA 28 C DA 52 1_555 D O4 DT 2 D DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C N1 DG 29 C DG 53 1_555 D N3 DC 1 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 C N2 DG 29 C DG 53 1_555 D O2 DC 1 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 C O6 DG 29 C DG 53 1_555 D N4 DC 1 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 8OM9 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 E 5 ADP A 1 2000 2000 ADP ADP . F 6 MG A 1 2001 2001 MG MG . G 5 ADP B 1 2000 2000 ADP ADP . H 6 MG B 1 2001 2001 MG MG . # 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 . . . E 5 152.332 135.076 128.844 1 44.06 ? PB ADP 2000 A 1 HETATM 2 O O1B ADP . . . E 5 152.202 135.023 127.35 1 48.64 ? O1B ADP 2000 A 1 HETATM 3 O O2B ADP . . . E 5 153.021 133.865 129.412 1 53.33 ? O2B ADP 2000 A 1 HETATM 4 O O3B ADP . . . E 5 151.023 135.381 129.524 1 35.83 ? O3B ADP 2000 A 1 HETATM 5 P PA ADP . . . E 5 152.956 137.878 129.192 1 59.18 ? PA ADP 2000 A 1 HETATM 6 O O1A ADP . . . E 5 152.682 138.348 127.803 1 66.12 ? O1A ADP 2000 A 1 HETATM 7 O O2A ADP . . . E 5 151.902 138.103 130.223 1 72.9 ? O2A ADP 2000 A 1 HETATM 8 O O3A ADP . . . E 5 153.298 136.317 129.154 1 47.6 ? O3A ADP 2000 A 1 HETATM 9 O O5' ADP . . . E 5 154.343 138.484 129.712 1 58.59 ? O5' ADP 2000 A 1 HETATM 10 C C5' ADP . . . E 5 154.335 139.788 130.338 1 60.14 ? C5' ADP 2000 A 1 HETATM 11 C C4' ADP . . . E 5 155.738 140.117 130.778 1 59.73 ? C4' ADP 2000 A 1 HETATM 12 O O4' ADP . . . E 5 156.619 139.957 129.638 1 44.9 ? O4' ADP 2000 A 1 HETATM 13 C C3' ADP . . . E 5 155.975 141.547 131.282 1 72.94 ? C3' ADP 2000 A 1 HETATM 14 O O3' ADP . . . E 5 156.93 141.556 132.334 1 82.61 ? O3' ADP 2000 A 1 HETATM 15 C C2' ADP . . . E 5 156.535 142.238 130.038 1 65.69 ? C2' ADP 2000 A 1 HETATM 16 O O2' ADP . . . E 5 157.293 143.392 130.326 1 72.92 ? O2' ADP 2000 A 1 HETATM 17 C C1' ADP . . . E 5 157.398 141.117 129.477 1 45.54 ? C1' ADP 2000 A 1 HETATM 18 N N9 ADP . . . E 5 157.702 141.267 128.062 1 42.07 ? N9 ADP 2000 A 1 HETATM 19 C C8 ADP . . . E 5 156.87 140.98 127.011 1 39.45 ? C8 ADP 2000 A 1 HETATM 20 N N7 ADP . . . E 5 157.417 141.201 125.842 1 41.63 ? N7 ADP 2000 A 1 HETATM 21 C C5 ADP . . . E 5 158.695 141.647 126.14 1 39.44 ? C5 ADP 2000 A 1 HETATM 22 C C6 ADP . . . E 5 159.772 142.044 125.327 1 34.97 ? C6 ADP 2000 A 1 HETATM 23 N N6 ADP . . . E 5 159.732 142.05 123.998 1 33.6 ? N6 ADP 2000 A 1 HETATM 24 N N1 ADP . . . E 5 160.91 142.436 125.945 1 44.34 ? N1 ADP 2000 A 1 HETATM 25 C C2 ADP . . . E 5 160.947 142.423 127.282 1 52.47 ? C2 ADP 2000 A 1 HETATM 26 N N3 ADP . . . E 5 160 142.071 128.147 1 45.72 ? N3 ADP 2000 A 1 HETATM 27 C C4 ADP . . . E 5 158.885 141.689 127.507 1 42.22 ? C4 ADP 2000 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #