data_6PDY # _model_server_result.job_id rIkNRcjxaNYeZ8XCN7PtDQ _model_server_result.datetime_utc '2025-07-07 15:18:24' _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 6pdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":502}' # _entry.id 6PDY # _exptl.entry_id 6PDY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 66.007 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BERYLLIUM TRIFLUORIDE ION' _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 6PDY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PDY _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,M,N,O,P,Q,R,S,T _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 ? 4 I N N ? 4 L N N ? 4 O N N ? 4 S 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 B OD1 ASP 185 A ASP 213 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc2 B OD2 ASP 185 A ASP 213 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 C OG1 THR 133 B THR 161 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc4 K O1B ADP . B ADP 501 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? metalc ? metalc5 K O2B ADP . B ADP 501 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 K O2A ADP . B ADP 501 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc7 D OG1 THR 133 C THR 161 1_555 P MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc8 D OD1 ASP 185 C ASP 213 1_555 P MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc9 E OG1 THR 133 D THR 161 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc10 E OD1 ASP 185 D ASP 213 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc11 E OD2 ASP 185 D ASP 213 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _chem_comp.formula 'Be F3 -1' _chem_comp.formula_weight 66.007 _chem_comp.id BEF _chem_comp.mon_nstd_flag . _chem_comp.name 'BERYLLIUM TRIFLUORIDE ION' _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 BE F1 BEF sing 114 n n BE F2 BEF sing 115 n n BE F3 BEF sing 116 n n # _atom_sites.entry_id 6PDY _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 H 3 ADP A 1 501 501 ADP ADP . I 4 BEF A 1 502 502 BEF BEF . J 5 MG A 1 503 601 MG MG . K 3 ADP B 1 501 501 ADP ADP . L 4 BEF B 1 502 502 BEF BEF . M 5 MG B 1 503 601 MG MG . N 3 ADP C 1 501 501 ADP ADP . O 4 BEF C 1 502 502 BEF BEF . P 5 MG C 1 503 601 MG MG . Q 3 ADP D 1 501 501 ADP ADP . R 5 MG D 1 502 601 MG MG . S 4 BEF E 1 501 502 BEF BEF . T 3 ADP E 1 502 501 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 BE BE BEF . . . L 4 141.272 133.259 106.703 1 54.75 ? BE BEF 502 B 1 HETATM 2 F F1 BEF . . . L 4 139.744 133.322 106.814 1 54.75 ? F1 BEF 502 B 1 HETATM 3 F F2 BEF . . . L 4 141.926 132.499 107.9 1 54.75 ? F2 BEF 502 B 1 HETATM 4 F F3 BEF . . . L 4 141.862 134.686 106.692 1 54.75 ? F3 BEF 502 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #