data_6RDB # _model_server_result.job_id F9GB5ijcPjb4VQkleVoqLw _model_server_result.datetime_utc '2025-09-01 05:20:52' _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 6rdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":1002}' # _entry.id 6RDB # _exptl.entry_id 6RDB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 24.305 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _entity.pdbx_number_of_molecules 5 _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 6RDB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RDB _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 PISA _pdbx_struct_assembly.oligomeric_details eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? 9 V N N ? 9 X N N ? 9 Z N N ? 9 BA N N ? 9 DA 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 U O1G ATP . T ATP 1001 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc2 U O2B ATP . T ATP 1001 1_555 V MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 V MG MG . T MG 1002 1_555 EA O HOH . T HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc4 V MG MG . T MG 1002 1_555 EA O HOH . T HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc5 V MG MG . T MG 1002 1_555 HA O HOH . X HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc6 P OG1 THR 232 U THR 232 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc7 W O1G ATP . U ATP 1001 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc8 W O2B ATP . U ATP 1001 1_555 X MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc9 X MG MG . U MG 1002 1_555 FA O HOH . U HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc10 X MG MG . U MG 1002 1_555 FA O HOH . U HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc11 X MG MG . U MG 1002 1_555 FA O HOH . U HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc12 Q OG1 THR 232 V THR 232 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc13 Y O1G ATP . V ATP 1001 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc14 Y O2B ATP . V ATP 1001 1_555 Z MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc15 Z MG MG . V MG 1002 1_555 GA O HOH . V HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc16 Z MG MG . V MG 1002 1_555 GA O HOH . V HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc17 Z MG MG . V MG 1002 1_555 IA O HOH . Y HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc18 R OG1 THR 190 X THR 190 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc19 R OE2 GLU 215 X GLU 215 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc20 AA O2B ADP . X ADP 601 1_555 BA MG MG . X MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc21 BA MG MG . X MG 602 1_555 HA O HOH . X HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc22 BA MG MG . X MG 602 1_555 HA O HOH . X HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc23 S OG1 THR 190 Y THR 190 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc24 S OE2 GLU 215 Y GLU 215 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc25 CA O3B ADP . Y ADP 601 1_555 DA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc26 DA MG MG . Y MG 602 1_555 IA O HOH . Y HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc27 DA MG MG . Y MG 602 1_555 IA O HOH . Y HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc28 DA MG MG . Y MG 602 1_555 IA O HOH . Y HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6RDB _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 U 8 ATP T 1 1001 1001 ATP ATP . V 9 MG T 1 1002 1002 MG MG . W 8 ATP U 1 1001 1001 ATP ATP . X 9 MG U 1 1002 1002 MG MG . Y 8 ATP V 1 1001 1001 ATP ATP . Z 9 MG V 1 1002 1002 MG MG . AA 10 ADP X 1 601 1028 ADP ADP . BA 9 MG X 1 602 1029 MG MG . CA 10 ADP Y 1 601 1028 ADP ADP . DA 9 MG Y 1 602 1029 MG MG . EA 11 HOH T 1 1101 6 HOH HOH . EA 11 HOH T 2 1102 4 HOH HOH . EA 11 HOH T 3 1103 5 HOH HOH . EA 11 HOH T 4 1104 8 HOH HOH . EA 11 HOH T 5 1105 2 HOH HOH . EA 11 HOH T 6 1106 3 HOH HOH . EA 11 HOH T 7 1107 48 HOH HOH . FA 11 HOH U 1 1101 14 HOH HOH . FA 11 HOH U 2 1102 49 HOH HOH . FA 11 HOH U 3 1103 15 HOH HOH . FA 11 HOH U 4 1104 13 HOH HOH . FA 11 HOH U 5 1105 11 HOH HOH . FA 11 HOH U 6 1106 47 HOH HOH . FA 11 HOH U 7 1107 16 HOH HOH . FA 11 HOH U 8 1108 12 HOH HOH . FA 11 HOH U 9 1109 10 HOH HOH . GA 11 HOH V 1 1101 23 HOH HOH . GA 11 HOH V 2 1102 51 HOH HOH . GA 11 HOH V 3 1103 27 HOH HOH . GA 11 HOH V 4 1104 22 HOH HOH . GA 11 HOH V 5 1105 24 HOH HOH . GA 11 HOH V 6 1106 20 HOH HOH . GA 11 HOH V 7 1107 19 HOH HOH . HA 11 HOH X 1 701 29 HOH HOH . HA 11 HOH X 2 702 32 HOH HOH . HA 11 HOH X 3 703 33 HOH HOH . HA 11 HOH X 4 704 34 HOH HOH . HA 11 HOH X 5 705 7 HOH HOH . HA 11 HOH X 6 706 31 HOH HOH . HA 11 HOH X 7 707 30 HOH HOH . HA 11 HOH X 8 708 9 HOH HOH . HA 11 HOH X 9 709 1 HOH HOH . IA 11 HOH Y 1 701 25 HOH HOH . IA 11 HOH Y 2 702 41 HOH HOH . IA 11 HOH Y 3 703 42 HOH HOH . IA 11 HOH Y 4 704 43 HOH HOH . IA 11 HOH Y 5 705 52 HOH HOH . IA 11 HOH Y 6 706 21 HOH HOH . JA 11 HOH Z 1 601 46 HOH HOH . JA 11 HOH Z 2 602 18 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id X _atom_site.label_entity_id 9 _atom_site.Cartn_x 123.149 _atom_site.Cartn_y 224.35 _atom_site.Cartn_z 252.852 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.05 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 1002 _atom_site.auth_asym_id U _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 376 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #