data_4DL5 # _model_server_result.job_id 3_ZM2qE4l50CZU6ueor9qA _model_server_result.datetime_utc '2024-10-18 17:21:19' _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 4dl5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":101}' # _entry.id 4DL5 # _exptl.entry_id 4DL5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 300.045 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Cisplatin _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 4DL5 _cell.length_a 99.414 _cell.length_b 99.414 _cell.length_c 82.085 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DL5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.322 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.175 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.154 ? metalc ? metalc7 D MG MG . A MG 501 1_555 F O2B 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.139 ? metalc ? metalc8 D MG MG . A MG 501 1_555 F O2G 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.206 ? metalc ? metalc9 D MG MG . A MG 501 1_555 F O1A 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.28 ? metalc ? metalc10 E MG MG . A MG 502 1_555 F O1A 0KX . A 0KX 503 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.259 ? metalc ? metalc11 E MG MG . A MG 502 1_555 C O3' DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.542 ? metalc ? metalc12 B N7 DG 4 T DG 4 1_555 G PT1 CPT . T CPT 101 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.061 ? metalc ? metalc13 B N7 DG 4 T DG 4 1_555 G PT1 CPT . T CPT 101 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.101 ? metalc ? metalc14 B N7 DG 5 T DG 5 1_555 G PT1 CPT . T CPT 101 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.102 ? metalc ? metalc15 B N7 DG 5 T DG 5 1_555 G PT1 CPT . T CPT 101 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.112 ? hydrog WATSON-CRICK hydrog1 B N1 DG 5 T DG 5 1_555 C N3 DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 5 T DG 5 1_555 C O2 DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 5 T DG 5 1_555 C N4 DC 9 P DC 9 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 6 1_555 C N1 DA 8 P DA 8 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 6 T DT 6 1_555 C N6 DA 8 P DA 8 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 7 T DC 7 1_555 C N1 DG 7 P DG 7 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 7 T DC 7 1_555 C O6 DG 7 P DG 7 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 7 T DC 7 1_555 C N2 DG 7 P DG 7 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 8 T DA 8 1_555 C N3 DT 6 P DT 6 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 8 T DA 8 1_555 C O4 DT 6 P DT 6 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 9 T DC 9 1_555 C N1 DG 5 P DG 5 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 9 T DC 9 1_555 C O6 DG 5 P DG 5 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 9 T DC 9 1_555 C N2 DG 5 P DG 5 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 10 T DA 10 1_555 C N3 DT 4 P DT 4 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 10 T DA 10 1_555 C O4 DT 4 P DT 4 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 3 P DG 3 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 3 P DG 3 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 3 P DG 3 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 2 P DA 2 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 2 P DA 2 1_555 ? A ? ? A ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Cl2 H6 N2 Pt' _chem_comp.formula_weight 300.045 _chem_comp.id CPT _chem_comp.mon_nstd_flag . _chem_comp.name Cisplatin _chem_comp.type non-polymer _chem_comp.pdbx_synonyms diammine(dichloro)platinum # 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 PT1 N1 CPT sing 116 n n PT1 N2 CPT sing 117 n n N1 H11 CPT sing 118 n n N1 H12 CPT sing 119 n n N1 H13 CPT sing 120 n n N2 H21 CPT sing 121 n n N2 H22 CPT sing 122 n n N2 H23 CPT sing 123 n n CL2 PT1 CPT sing 124 n n CL1 PT1 CPT sing 125 n n # _atom_sites.entry_id 4DL5 _atom_sites.fract_transf_matrix[1][1] 0.010059 _atom_sites.fract_transf_matrix[1][2] 0.005808 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011615 _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] 0.012182 _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 4 MG A 1 501 433 MG MG2 . E 4 MG A 1 502 434 MG MG2 . F 5 0KX A 1 503 10 0KX DC4 . G 6 CPT T 1 101 13 CPT CPT . # 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 PT PT1 CPT . A . G 6 38.478 1.985 5.262 0.5 271.56 ? PT1 CPT 101 T 1 HETATM 2 PT PT1 CPT . B . G 6 39.039 1.589 7.682 0.5 77.61 ? PT1 CPT 101 T 1 HETATM 3 N N1 CPT . A . G 6 38.005 0.7 6.737 0.5 92.18 ? N1 CPT 101 T 1 HETATM 4 N N1 CPT . B . G 6 38.789 -0.268 8.519 0.5 82.31 ? N1 CPT 101 T 1 HETATM 5 N N2 CPT . A . G 6 37.798 0.647 3.885 0.5 91.01 ? N2 CPT 101 T 1 HETATM 6 N N2 CPT . B . G 6 39.447 0.742 5.911 0.5 90.8 ? N2 CPT 101 T 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #