data_9DNB # _model_server_result.job_id idC8GYEOb_S3ZFrIpBcShA _model_server_result.datetime_utc '2025-07-05 20:56:07' _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":"F","auth_seq_id":4103}' # _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 . . . F 4 161.612 158.905 136.722 1 37.43 ? PB ADP 4103 A 1 HETATM 2 O O1B ADP . . . F 4 161.474 157.414 136.54 1 29.84 ? O1B ADP 4103 A 1 HETATM 3 O O2B ADP . . . F 4 160.437 159.57 137.395 1 35.84 ? O2B ADP 4103 A 1 HETATM 4 O O3B ADP . . . F 4 162.955 159.348 137.245 1 38.83 ? O3B ADP 4103 A 1 HETATM 5 P PA ADP . . . F 4 160.415 159.112 134.182 1 31.64 ? PA ADP 4103 A 1 HETATM 6 O O1A ADP . . . F 4 160.709 157.757 133.591 1 34.78 ? O1A ADP 4103 A 1 HETATM 7 O O2A ADP . . . F 4 159.081 159.37 134.833 1 37.62 ? O2A ADP 4103 A 1 HETATM 8 O O3A ADP . . . F 4 161.587 159.483 135.222 1 30.6 ? O3A ADP 4103 A 1 HETATM 9 O O5' ADP . . . F 4 160.648 160.253 133.074 1 26.11 ? O5' ADP 4103 A 1 HETATM 10 C C5' ADP . . . F 4 159.549 160.871 132.414 1 25.04 ? C5' ADP 4103 A 1 HETATM 11 C C4' ADP . . . F 4 159.916 162.323 132.135 1 26.29 ? C4' ADP 4103 A 1 HETATM 12 O O4' ADP . . . F 4 161.319 162.433 131.892 1 24.7 ? O4' ADP 4103 A 1 HETATM 13 C C3' ADP . . . F 4 159.186 162.863 130.919 1 32.38 ? C3' ADP 4103 A 1 HETATM 14 O O3' ADP . . . F 4 158.303 163.917 131.312 1 44.05 ? O3' ADP 4103 A 1 HETATM 15 C C2' ADP . . . F 4 160.262 163.404 130.001 1 33.91 ? C2' ADP 4103 A 1 HETATM 16 O O2' ADP . . . F 4 160.057 164.803 129.784 1 40.45 ? O2' ADP 4103 A 1 HETATM 17 C C1' ADP . . . F 4 161.59 163.182 130.707 1 28.57 ? C1' ADP 4103 A 1 HETATM 18 N N9 ADP . . . F 4 162.487 162.367 129.853 1 33.85 ? N9 ADP 4103 A 1 HETATM 19 C C8 ADP . . . F 4 163.032 161.193 130.219 1 34.1 ? C8 ADP 4103 A 1 HETATM 20 N N7 ADP . . . F 4 163.81 160.682 129.234 1 29.18 ? N7 ADP 4103 A 1 HETATM 21 C C5 ADP . . . F 4 163.769 161.545 128.205 1 28.16 ? C5 ADP 4103 A 1 HETATM 22 C C6 ADP . . . F 4 164.367 161.612 126.854 1 30.55 ? C6 ADP 4103 A 1 HETATM 23 N N6 ADP . . . F 4 165.18 160.626 126.405 1 31.05 ? N6 ADP 4103 A 1 HETATM 24 N N1 ADP . . . F 4 164.075 162.686 126.089 1 36.14 ? N1 ADP 4103 A 1 HETATM 25 C C2 ADP . . . F 4 163.269 163.668 126.528 1 32.14 ? C2 ADP 4103 A 1 HETATM 26 N N3 ADP . . . F 4 162.693 163.673 127.743 1 31.3 ? N3 ADP 4103 A 1 HETATM 27 C C4 ADP . . . F 4 162.9 162.658 128.616 1 32.17 ? C4 ADP 4103 A 1 # _model_server_stats.io_time_ms 118 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #