data_9DH3 # _model_server_result.job_id V3wvob4mEFRsQW-Ub8kYxg _model_server_result.datetime_utc '2025-02-26 08:59:08' _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 9dh3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1101}' # _entry.id 9DH3 # _exptl.entry_id 9DH3 _exptl.method 'ELECTRON MICROSCOPY' # _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 4 _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 9DH3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DH3 _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_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H N N ? 2 K N N ? 2 N N N # _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 43 n n PB O2B ADP sing 44 n n PB O3B ADP sing 45 n n PB O3A ADP sing 46 n n O2B HOB2 ADP sing 47 n n O3B HOB3 ADP sing 48 n n PA O1A ADP doub 49 n n PA O2A ADP sing 50 n n PA O3A ADP sing 51 n n PA O5' ADP sing 52 n n O2A HOA2 ADP sing 53 n n O5' C5' ADP sing 54 n n C5' C4' ADP sing 55 n n C5' "H5'1" ADP sing 56 n n C5' "H5'2" ADP sing 57 n n C4' O4' ADP sing 58 n n C4' C3' ADP sing 59 n n C4' H4' ADP sing 60 n n O4' C1' ADP sing 61 n n C3' O3' ADP sing 62 n n C3' C2' ADP sing 63 n n C3' H3' ADP sing 64 n n O3' HO3' ADP sing 65 n n C2' O2' ADP sing 66 n n C2' C1' ADP sing 67 n n C2' H2' ADP sing 68 n n O2' HO2' ADP sing 69 n n C1' N9 ADP sing 70 n n C1' H1' ADP sing 71 n n N9 C8 ADP sing 72 n y N9 C4 ADP sing 73 n y C8 N7 ADP doub 74 n y C8 H8 ADP sing 75 n n N7 C5 ADP sing 76 n y C5 C6 ADP sing 77 n y C5 C4 ADP doub 78 n y C6 N6 ADP sing 79 n n C6 N1 ADP doub 80 n y N6 HN61 ADP sing 81 n n N6 HN62 ADP sing 82 n n N1 C2 ADP sing 83 n y C2 N3 ADP doub 84 n y C2 H2 ADP sing 85 n n N3 C4 ADP sing 86 n y # _atom_sites.entry_id 9DH3 _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 2 ADP A 1 1101 1039 ADP ADP . F 3 A1A4L A 1 1102 1139 A1A4L LIG . G 4 CPS A 1 1103 1239 CPS CPS . H 2 ADP B 1 1101 1039 ADP ADP . I 3 A1A4L B 1 1102 1139 A1A4L LIG . J 4 CPS B 1 1103 1239 CPS CPS . K 2 ADP C 1 1101 1039 ADP ADP . L 3 A1A4L C 1 1102 1139 A1A4L LIG . M 4 CPS C 1 1103 1239 CPS CPS . N 2 ADP D 1 1101 1039 ADP ADP . O 3 A1A4L D 1 1102 1139 A1A4L LIG . P 4 CPS D 1 1103 1239 CPS CPS . # 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 . . . N 2 190.429 139.703 123.577 1 49.65 ? PB ADP 1101 D 1 HETATM 2 O O1B ADP . . . N 2 191.198 140.761 122.844 1 52.35 ? O1B ADP 1101 D 1 HETATM 3 O O2B ADP . . . N 2 191.162 138.399 123.64 1 53.01 -1 O2B ADP 1101 D 1 HETATM 4 O O3B ADP . . . N 2 189.941 140.153 124.921 1 40.01 ? O3B ADP 1101 D 1 HETATM 5 P PA ADP . . . N 2 187.793 138.646 123.056 1 34.45 ? PA ADP 1101 D 1 HETATM 6 O O1A ADP . . . N 2 188.111 137.378 123.776 1 29.92 -1 O1A ADP 1101 D 1 HETATM 7 O O2A ADP . . . N 2 186.821 139.577 123.7 1 29.94 ? O2A ADP 1101 D 1 HETATM 8 O O3A ADP . . . N 2 189.119 139.431 122.705 1 37.22 ? O3A ADP 1101 D 1 HETATM 9 O O5' ADP . . . N 2 187.238 138.267 121.593 1 27.12 ? O5' ADP 1101 D 1 HETATM 10 C C5' ADP . . . N 2 185.809 138.028 121.457 1 24.69 ? C5' ADP 1101 D 1 HETATM 11 C C4' ADP . . . N 2 185.497 137.315 120.159 1 26.8 ? C4' ADP 1101 D 1 HETATM 12 O O4' ADP . . . N 2 184.066 137.211 120.063 1 24.23 ? O4' ADP 1101 D 1 HETATM 13 C C3' ADP . . . N 2 185.969 137.936 118.825 1 29.16 ? C3' ADP 1101 D 1 HETATM 14 O O3' ADP . . . N 2 186.421 136.903 117.962 1 34.94 ? O3' ADP 1101 D 1 HETATM 15 C C2' ADP . . . N 2 184.668 138.545 118.276 1 26.75 ? C2' ADP 1101 D 1 HETATM 16 O O2' ADP . . . N 2 184.604 138.763 116.893 1 37.84 ? O2' ADP 1101 D 1 HETATM 17 C C1' ADP . . . N 2 183.651 137.502 118.747 1 20.22 ? C1' ADP 1101 D 1 HETATM 18 N N9 ADP . . . N 2 182.236 137.977 118.764 1 23.37 ? N9 ADP 1101 D 1 HETATM 19 C C8 ADP . . . N 2 181.412 138.022 117.676 1 30.97 ? C8 ADP 1101 D 1 HETATM 20 N N7 ADP . . . N 2 180.223 138.461 117.918 1 32.75 ? N7 ADP 1101 D 1 HETATM 21 C C5 ADP . . . N 2 180.227 138.725 119.27 1 19.42 ? C5 ADP 1101 D 1 HETATM 22 C C6 ADP . . . N 2 179.225 139.218 120.203 1 26.15 ? C6 ADP 1101 D 1 HETATM 23 N N6 ADP . . . N 2 177.973 139.526 119.894 1 50.92 ? N6 ADP 1101 D 1 HETATM 24 N N1 ADP . . . N 2 179.559 139.356 121.484 1 30.55 ? N1 ADP 1101 D 1 HETATM 25 C C2 ADP . . . N 2 180.82 139.038 121.862 1 30.05 ? C2 ADP 1101 D 1 HETATM 26 N N3 ADP . . . N 2 181.827 138.58 121.115 1 24.84 ? N3 ADP 1101 D 1 HETATM 27 C C4 ADP . . . N 2 181.479 138.435 119.813 1 17.24 ? C4 ADP 1101 D 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #