data_8DNH # _model_server_result.job_id j6eZVFkErBKTFWI-lFwmwA _model_server_result.datetime_utc '2024-11-18 21:24:27' _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 8dnh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 8DNH # _exptl.entry_id 8DNH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 8DNH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DNH _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,I,J,K,L _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 ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 covale ? covale1 A C ACE 1 A ACE 0 1_555 A N ASP 2 A ASP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C GLU 72 A GLU 71 1_555 A N HIC 73 A HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C HIC 73 A HIC 72 1_555 A N GLY 74 A GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 B C ACE 1 B ACE 0 1_555 B N ASP 2 B ASP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 B C GLU 72 B GLU 71 1_555 B N HIC 73 B HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C HIC 73 B HIC 72 1_555 B N GLY 74 B GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale7 C C ACE 1 C ACE 0 1_555 C N ASP 2 C ASP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 C C GLU 72 C GLU 71 1_555 C N HIC 73 C HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 C C HIC 73 C HIC 72 1_555 C N GLY 74 C GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale10 D C ACE 1 D ACE 0 1_555 D N ASP 2 D ASP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 D C GLU 72 D GLU 71 1_555 D N HIC 73 D HIC 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 D C HIC 73 D HIC 72 1_555 D N GLY 74 D GLY 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 E MG MG . A MG 400 1_555 F O2B ADP . A ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc2 G MG MG . B MG 400 1_555 H O2B ADP . B ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc3 I MG MG . C MG 400 1_555 J O2B ADP . C ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc4 K MG MG . D MG 400 1_555 L O2B ADP . D ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _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 ? # _atom_sites.entry_id 8DNH _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 MG A 1 400 400 MG MG . F 3 ADP A 1 401 401 ADP ADP . G 2 MG B 1 400 400 MG MG . H 3 ADP B 1 401 401 ADP ADP . I 2 MG C 1 400 400 MG MG . J 3 ADP C 1 401 401 ADP ADP . K 2 MG D 1 400 400 MG MG . L 3 ADP D 1 401 401 ADP ADP . # 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 . . . J 3 118.704 96.291 124.505 1 127.41 ? PB ADP 401 C 1 HETATM 2 O O1B ADP . . . J 3 117.79 96.85 123.44 1 108.86 ? O1B ADP 401 C 1 HETATM 3 O O2B ADP . . . J 3 118.353 96.711 125.911 1 128.26 ? O2B ADP 401 C 1 HETATM 4 O O3B ADP . . . J 3 119.015 94.822 124.356 1 128.59 ? O3B ADP 401 C 1 HETATM 5 P PA ADP . . . J 3 121.007 96.559 122.962 1 122.47 ? PA ADP 401 C 1 HETATM 6 O O1A ADP . . . J 3 120.066 96.125 121.866 1 129.25 ? O1A ADP 401 C 1 HETATM 7 O O2A ADP . . . J 3 122.09 95.631 123.456 1 114.38 ? O2A ADP 401 C 1 HETATM 8 O O3A ADP . . . J 3 120.112 97.015 124.218 1 119.65 ? O3A ADP 401 C 1 HETATM 9 O O5' ADP . . . J 3 121.69 97.938 122.498 1 119.56 ? O5' ADP 401 C 1 HETATM 10 C C5' ADP . . . J 3 122.079 98.115 121.138 1 121.12 ? C5' ADP 401 C 1 HETATM 11 C C4' ADP . . . J 3 122.655 99.511 120.951 1 119.8 ? C4' ADP 401 C 1 HETATM 12 O O4' ADP . . . J 3 124.038 99.527 121.306 1 127.77 ? O4' ADP 401 C 1 HETATM 13 C C3' ADP . . . J 3 122.563 99.966 119.505 1 117.41 ? C3' ADP 401 C 1 HETATM 14 O O3' ADP . . . J 3 121.543 100.959 119.369 1 117.58 ? O3' ADP 401 C 1 HETATM 15 C C2' ADP . . . J 3 123.915 100.559 119.17 1 120.36 ? C2' ADP 401 C 1 HETATM 16 O O2' ADP . . . J 3 123.78 101.955 118.892 1 124.15 ? O2' ADP 401 C 1 HETATM 17 C C1' ADP . . . J 3 124.776 100.355 120.406 1 120.96 ? C1' ADP 401 C 1 HETATM 18 N N9 ADP . . . J 3 126.041 99.68 120.026 1 115.1 ? N9 ADP 401 C 1 HETATM 19 C C8 ADP . . . J 3 126.185 98.363 119.795 1 118.41 ? C8 ADP 401 C 1 HETATM 20 N N7 ADP . . . J 3 127.465 98.06 119.466 1 119.2 ? N7 ADP 401 C 1 HETATM 21 C C5 ADP . . . J 3 128.167 99.207 119.481 1 120.48 ? C5 ADP 401 C 1 HETATM 22 C C6 ADP . . . J 3 129.572 99.601 119.228 1 125.26 ? C6 ADP 401 C 1 HETATM 23 N N6 ADP . . . J 3 130.504 98.68 118.883 1 122.02 ? N6 ADP 401 C 1 HETATM 24 N N1 ADP . . . J 3 129.891 100.907 119.352 1 125.43 ? N1 ADP 401 C 1 HETATM 25 C C2 ADP . . . J 3 128.973 101.829 119.695 1 118.67 ? C2 ADP 401 C 1 HETATM 26 N N3 ADP . . . J 3 127.681 101.544 119.939 1 109.27 ? N3 ADP 401 C 1 HETATM 27 C C4 ADP . . . J 3 127.224 100.273 119.85 1 111.73 ? C4 ADP 401 C 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #