data_9DNB # _model_server_result.job_id FmQdjXGpHzvjIz-8YhnsOw _model_server_result.datetime_utc '2025-07-04 10:38:46' _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 9dnb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":4102}' # _entry.id 9DNB # _exptl.entry_id 9DNB _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 3 _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 9DNB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DNB _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,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 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 ? 4 E N N ? 4 F N N ? 4 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 OG1 THR 586 A THR 1803 1_555 H MG MG . A MG 4105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc2 A OD1 ASP 631 A ASP 1848 1_555 H MG MG . A MG 4105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc3 A OD2 ASP 631 A ASP 1848 1_555 H MG MG . A MG 4105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? metalc ? metalc4 A OE2 GLU 632 A GLU 1849 1_555 H MG MG . A MG 4105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc5 G O3B ADP . A ADP 4104 1_555 H MG MG . A MG 4105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _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 9DNB _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 3 ATP A 1 4101 4102 ATP ATP . E 4 ADP A 1 4102 4104 ADP ADP . F 4 ADP A 1 4103 4105 ADP ADP . G 4 ADP A 1 4104 4106 ADP ADP . H 5 MG A 1 4105 1 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 4 175.372 132.321 150.243 1 40.82 ? PB ADP 4102 A 1 HETATM 2 O O1B ADP . . . E 4 176.168 131.172 150.813 1 35.75 ? O1B ADP 4102 A 1 HETATM 3 O O2B ADP . . . E 4 173.889 132.059 150.154 1 44.23 ? O2B ADP 4102 A 1 HETATM 4 O O3B ADP . . . E 4 175.739 133.675 150.8 1 40.51 ? O3B ADP 4102 A 1 HETATM 5 P PA ADP . . . E 4 175.261 131.359 147.619 1 33.74 ? PA ADP 4102 A 1 HETATM 6 O O1A ADP . . . E 4 175.08 130.02 148.287 1 40.48 ? O1A ADP 4102 A 1 HETATM 7 O O2A ADP . . . E 4 174.081 131.998 146.928 1 38.95 ? O2A ADP 4102 A 1 HETATM 8 O O3A ADP . . . E 4 175.843 132.391 148.707 1 28.5 ? O3A ADP 4102 A 1 HETATM 9 O O5' ADP . . . E 4 176.476 131.238 146.572 1 38.21 ? O5' ADP 4102 A 1 HETATM 10 C C5' ADP . . . E 4 176.56 130.135 145.673 1 38.13 ? C5' ADP 4102 A 1 HETATM 11 C C4' ADP . . . E 4 177.614 130.436 144.616 1 30.75 ? C4' ADP 4102 A 1 HETATM 12 O O4' ADP . . . E 4 178.676 129.483 144.649 1 33.59 ? O4' ADP 4102 A 1 HETATM 13 C C3' ADP . . . E 4 177.028 130.372 143.218 1 31.44 ? C3' ADP 4102 A 1 HETATM 14 O O3' ADP . . . E 4 176.758 131.691 142.755 1 34.51 ? O3' ADP 4102 A 1 HETATM 15 C C2' ADP . . . E 4 178.09 129.721 142.357 1 35.4 ? C2' ADP 4102 A 1 HETATM 16 O O2' ADP . . . E 4 178.637 130.678 141.447 1 46.7 ? O2' ADP 4102 A 1 HETATM 17 C C1' ADP . . . E 4 179.162 129.252 143.325 1 31.55 ? C1' ADP 4102 A 1 HETATM 18 N N9 ADP . . . E 4 179.408 127.807 143.107 1 31.92 ? N9 ADP 4102 A 1 HETATM 19 C C8 ADP . . . E 4 178.752 127.021 142.233 1 29.57 ? C8 ADP 4102 A 1 HETATM 20 N N7 ADP . . . E 4 179.22 125.749 142.271 1 25.81 ? N7 ADP 4102 A 1 HETATM 21 C C5 ADP . . . E 4 180.206 125.713 143.184 1 31.87 ? C5 ADP 4102 A 1 HETATM 22 C C6 ADP . . . E 4 181.122 124.684 143.723 1 44.38 ? C6 ADP 4102 A 1 HETATM 23 N N6 ADP . . . E 4 181.075 123.409 143.274 1 48.87 ? N6 ADP 4102 A 1 HETATM 24 N N1 ADP . . . E 4 182.006 125.061 144.673 1 47.54 ? N1 ADP 4102 A 1 HETATM 25 C C2 ADP . . . E 4 182.062 126.328 145.125 1 42.79 ? C2 ADP 4102 A 1 HETATM 26 N N3 ADP . . . E 4 181.26 127.313 144.683 1 34.09 ? N3 ADP 4102 A 1 HETATM 27 C C4 ADP . . . E 4 180.333 127.074 143.726 1 30.4 ? C4 ADP 4102 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #