data_8OO9 # _model_server_result.job_id LcUqj3vcWYqBgp8nNECE9w _model_server_result.datetime_utc '2025-04-02 05:24:47' _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 8oo9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2001}' # _entry.id 8OO9 # _exptl.entry_id 8OO9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 90 _cell.entry_id 8OO9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OO9 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 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 D O2B ADP . G ADP 2001 1_555 E MG MG . G MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? hydrog WATSON-CRICK hydrog1 B N1 DG 94 K DG 20 1_555 C N3 DC 133 L DC -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 94 K DG 20 1_555 C O2 DC 133 L DC -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 94 K DG 20 1_555 C N4 DC 133 L DC -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog4 B O2 DC 95 K DC 21 1_555 C N1 DG 132 L DG -21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N3 DC 96 K DC 22 1_555 C N1 DG 131 L DG -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N4 DC 96 K DC 22 1_555 C O6 DG 131 L DG -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O2 DC 96 K DC 22 1_555 C N2 DG 131 L DG -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 97 K DA 23 1_555 C N3 DT 130 L DT -23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 97 K DA 23 1_555 C O4 DT 130 L DT -23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 98 K DA 24 1_555 C N3 DT 129 L DT -24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 98 K DA 24 1_555 C O4 DT 129 L DT -24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog12 B N2 DG 99 K DG 25 1_555 C N3 DC 128 L DC -25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 100 K DG 26 1_555 C N3 DC 127 L DC -26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 100 K DG 26 1_555 C O2 DC 127 L DC -26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 100 K DG 26 1_555 C N4 DC 127 L DC -26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 101 K DG 27 1_555 C N3 DC 126 L DC -27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 101 K DG 27 1_555 C O2 DC 126 L DC -27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 101 K DG 27 1_555 C N4 DC 126 L DC -27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 102 K DG 28 1_555 C N3 DC 125 L DC -28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 102 K DG 28 1_555 C O2 DC 125 L DC -28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 102 K DG 28 1_555 C N4 DC 125 L DC -28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DA 103 K DA 29 1_555 C N3 DT 124 L DT -29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N6 DA 103 K DA 29 1_555 C O4 DT 124 L DT -29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DT 104 K DT 30 1_555 C N1 DA 123 L DA -30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 DT 104 K DT 30 1_555 C N6 DA 123 L DA -30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog26 B N3 DT 105 K DT 31 1_555 C N1 DA 122 L DA -31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N1 DA 106 K DA 32 1_555 C N3 DT 121 L DT -32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N6 DA 106 K DA 32 1_555 C O4 DT 121 L DT -32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N3 DC 107 K DC 33 1_555 C N1 DG 120 L DG -33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N4 DC 107 K DC 33 1_555 C O6 DG 120 L DG -33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B O2 DC 107 K DC 33 1_555 C N2 DG 120 L DG -33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N3 DT 108 K DT 34 1_555 C N1 DA 119 L DA -34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B O4 DT 108 K DT 34 1_555 C N6 DA 119 L DA -34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N3 DC 109 K DC 35 1_555 C N1 DG 118 L DG -35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N4 DC 109 K DC 35 1_555 C O6 DG 118 L DG -35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B O2 DC 109 K DC 35 1_555 C N2 DG 118 L DG -35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog37 B O2 DC 110 K DC 36 1_555 C N2 DG 117 L DG -36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N3 DC 111 K DC 37 1_555 C N1 DG 116 L DG -37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B N4 DC 111 K DC 37 1_555 C O6 DG 116 L DG -37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 B O2 DC 111 K DC 37 1_555 C N2 DG 116 L DG -37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 B N3 DT 112 K DT 38 1_555 C N1 DA 115 L DA -38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 B O4 DT 112 K DT 38 1_555 C N6 DA 115 L DA -38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 B N1 DA 113 K DA 39 1_555 C N3 DT 114 L DT -39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 B N6 DA 113 K DA 39 1_555 C O4 DT 114 L DT -39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog45 B N2 DG 114 K DG 40 1_555 C O2 DC 113 L DC -40 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 8OO9 _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 D 4 ADP G 1 2001 2001 ADP ADP . E 5 MG G 1 2002 2002 MG MG . F 6 ALF G 1 2003 2003 ALF ALF . # 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 4 172.115 196.367 129.778 1 39.89 ? PB ADP 2001 G 1 HETATM 2 O O1B ADP . . . D 4 171.264 195.616 128.809 1 51.92 ? O1B ADP 2001 G 1 HETATM 3 O O2B ADP . . . D 4 172.455 195.551 130.986 1 58.58 ? O2B ADP 2001 G 1 HETATM 4 O O3B ADP . . . D 4 171.701 197.794 129.998 1 52.64 ? O3B ADP 2001 G 1 HETATM 5 P PA ADP . . . D 4 174.879 196.279 129.952 1 55.49 ? PA ADP 2001 G 1 HETATM 6 O O1A ADP . . . D 4 175.122 194.805 130.094 1 58.59 ? O1A ADP 2001 G 1 HETATM 7 O O2A ADP . . . D 4 174.8 197.126 131.176 1 54.58 ? O2A ADP 2001 G 1 HETATM 8 O O3A ADP . . . D 4 173.551 196.534 129.098 1 57.56 ? O3A ADP 2001 G 1 HETATM 9 O O5' ADP . . . D 4 176.023 196.931 129.059 1 51.52 ? O5' ADP 2001 G 1 HETATM 10 C C5' ADP . . . D 4 176.52 196.246 127.929 1 54.74 ? C5' ADP 2001 G 1 HETATM 11 C C4' ADP . . . D 4 177.997 196.57 127.871 1 60.13 ? C4' ADP 2001 G 1 HETATM 12 O O4' ADP . . . D 4 178.178 197.945 128.194 1 61.12 ? O4' ADP 2001 G 1 HETATM 13 C C3' ADP . . . D 4 178.774 195.802 128.919 1 61.24 ? C3' ADP 2001 G 1 HETATM 14 O O3' ADP . . . D 4 179.757 195.009 128.264 1 60.11 ? O3' ADP 2001 G 1 HETATM 15 C C2' ADP . . . D 4 179.457 196.845 129.771 1 56.03 ? C2' ADP 2001 G 1 HETATM 16 O O2' ADP . . . D 4 180.826 196.479 129.93 1 63.47 ? O2' ADP 2001 G 1 HETATM 17 C C1' ADP . . . D 4 179.404 198.068 128.9 1 55.65 ? C1' ADP 2001 G 1 HETATM 18 N N9 ADP . . . D 4 179.427 199.321 129.685 1 55.13 ? N9 ADP 2001 G 1 HETATM 19 C C8 ADP . . . D 4 178.362 199.985 130.149 1 57.73 ? C8 ADP 2001 G 1 HETATM 20 N N7 ADP . . . D 4 178.741 201.109 130.809 1 59.52 ? N7 ADP 2001 G 1 HETATM 21 C C5 ADP . . . D 4 180.08 201.173 130.761 1 56.48 ? C5 ADP 2001 G 1 HETATM 22 C C6 ADP . . . D 4 181.126 202.092 131.256 1 56.96 ? C6 ADP 2001 G 1 HETATM 23 N N6 ADP . . . D 4 180.836 203.211 131.958 1 61.37 ? N6 ADP 2001 G 1 HETATM 24 N N1 ADP . . . D 4 182.405 201.785 130.987 1 59.53 ? N1 ADP 2001 G 1 HETATM 25 C C2 ADP . . . D 4 182.732 200.685 130.296 1 60.74 ? C2 ADP 2001 G 1 HETATM 26 N N3 ADP . . . D 4 181.838 199.812 129.82 1 60.78 ? N3 ADP 2001 G 1 HETATM 27 C C4 ADP . . . D 4 180.52 199.996 130.015 1 56.39 ? C4 ADP 2001 G 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #