data_3DD3 # _model_server_result.job_id OWTAyTskpaZZCu6tTikZTw _model_server_result.datetime_utc '2024-12-26 13:37:54' _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 3dd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":211}' # _entry.id 3DD3 # _exptl.entry_id 3DD3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 179.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (eta6-benzene)ruthenium _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 97.81 _cell.angle_gamma 90 _cell.entry_id 3DD3 _cell.length_a 76.69 _cell.length_b 89.54 _cell.length_c 68.99 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DD3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id D _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 SG CYS 102 A CYS 101 1_555 D RU11 RUC . A RUC 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.127 ? metalc ? metalc2 D RU11 RUC . A RUC 211 1_555 B SG CYS 102 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _chem_comp.formula 'C6 H6 Ru' _chem_comp.formula_weight 179.182 _chem_comp.id RUC _chem_comp.mon_nstd_flag . _chem_comp.name (eta6-benzene)ruthenium _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 C29 C30 RUC doub 338 n n C29 C28 RUC sing 339 n n C30 C31 RUC sing 340 n n C31 C26 RUC doub 341 n n C26 C27 RUC sing 342 n n C27 C28 RUC doub 343 n n C29 H29 RUC sing 344 n n C30 H30 RUC sing 345 n n C31 H31 RUC sing 346 n n C26 H26 RUC sing 347 n n C27 H27 RUC sing 348 n n C28 H28 RUC sing 349 n n RU11 C29 RUC sing 350 n n RU11 C30 RUC sing 351 n n RU11 C31 RUC sing 352 n n RU11 C26 RUC sing 353 n n RU11 C27 RUC sing 354 n n RU11 C28 RUC sing 355 n n # _atom_sites.entry_id 3DD3 _atom_sites.fract_transf_matrix[1][1] 0.01304 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001788 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011168 _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] 0.014631 _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 C 2 MES A 1 210 1 MES MES . D 3 RUC A 1 211 1 RUC RUC . E 4 GSH A 1 212 1 GSH GTT . F 2 MES B 1 210 1 MES MES . G 4 GSH B 1 211 1 GSH GTT . H 5 HOH A 1 213 1 HOH HOH . H 5 HOH A 2 214 2 HOH HOH . H 5 HOH A 3 215 3 HOH HOH . H 5 HOH A 4 216 4 HOH HOH . H 5 HOH A 5 217 6 HOH HOH . H 5 HOH A 6 218 8 HOH HOH . H 5 HOH A 7 219 10 HOH HOH . H 5 HOH A 8 220 11 HOH HOH . H 5 HOH A 9 221 12 HOH HOH . H 5 HOH A 10 222 13 HOH HOH . H 5 HOH A 11 223 15 HOH HOH . H 5 HOH A 12 224 19 HOH HOH . H 5 HOH A 13 225 21 HOH HOH . H 5 HOH A 14 226 23 HOH HOH . H 5 HOH A 15 227 25 HOH HOH . H 5 HOH A 16 228 28 HOH HOH . H 5 HOH A 17 229 30 HOH HOH . H 5 HOH A 18 230 31 HOH HOH . H 5 HOH A 19 231 32 HOH HOH . H 5 HOH A 20 232 33 HOH HOH . H 5 HOH A 21 233 34 HOH HOH . H 5 HOH A 22 234 36 HOH HOH . H 5 HOH A 23 235 37 HOH HOH . H 5 HOH A 24 236 40 HOH HOH . H 5 HOH A 25 237 41 HOH HOH . H 5 HOH A 26 238 43 HOH HOH . H 5 HOH A 27 239 44 HOH HOH . H 5 HOH A 28 240 46 HOH HOH . H 5 HOH A 29 241 47 HOH HOH . H 5 HOH A 30 242 48 HOH HOH . H 5 HOH A 31 243 49 HOH HOH . H 5 HOH A 32 244 50 HOH HOH . H 5 HOH A 33 245 51 HOH HOH . H 5 HOH A 34 246 52 HOH HOH . H 5 HOH A 35 247 53 HOH HOH . H 5 HOH A 36 248 55 HOH HOH . H 5 HOH A 37 249 60 HOH HOH . H 5 HOH A 38 250 62 HOH HOH . H 5 HOH A 39 251 63 HOH HOH . H 5 HOH A 40 252 64 HOH HOH . H 5 HOH A 41 253 67 HOH HOH . H 5 HOH A 42 254 68 HOH HOH . I 5 HOH B 1 212 5 HOH HOH . I 5 HOH B 2 213 7 HOH HOH . I 5 HOH B 3 214 9 HOH HOH . I 5 HOH B 4 215 14 HOH HOH . I 5 HOH B 5 216 16 HOH HOH . I 5 HOH B 6 217 17 HOH HOH . I 5 HOH B 7 218 18 HOH HOH . I 5 HOH B 8 219 20 HOH HOH . I 5 HOH B 9 220 22 HOH HOH . I 5 HOH B 10 221 24 HOH HOH . I 5 HOH B 11 222 26 HOH HOH . I 5 HOH B 12 223 27 HOH HOH . I 5 HOH B 13 224 29 HOH HOH . I 5 HOH B 14 225 35 HOH HOH . I 5 HOH B 15 226 38 HOH HOH . I 5 HOH B 16 227 39 HOH HOH . I 5 HOH B 17 228 42 HOH HOH . I 5 HOH B 18 229 45 HOH HOH . I 5 HOH B 19 230 54 HOH HOH . I 5 HOH B 20 231 56 HOH HOH . I 5 HOH B 21 232 57 HOH HOH . I 5 HOH B 22 233 58 HOH HOH . I 5 HOH B 23 234 59 HOH HOH . I 5 HOH B 24 235 61 HOH HOH . I 5 HOH B 25 236 65 HOH HOH . I 5 HOH B 26 237 66 HOH HOH . I 5 HOH B 27 238 69 HOH HOH . I 5 HOH B 28 239 70 HOH HOH . I 5 HOH B 29 240 71 HOH HOH . I 5 HOH B 30 241 72 HOH HOH . I 5 HOH B 31 242 73 HOH HOH . I 5 HOH B 32 243 74 HOH HOH . # 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 RU RU11 RUC . . . D 3 11.546 11.519 16.153 0.3 46.5 ? RU11 RUC 211 A 1 HETATM 2 C C29 RUC . . . D 3 11.61 11.115 18.351 0.3 46.41 ? C29 RUC 211 A 1 HETATM 3 C C30 RUC . . . D 3 12.196 10.05 17.714 0.3 46.08 ? C30 RUC 211 A 1 HETATM 4 C C31 RUC . . . D 3 13.248 10.244 16.851 0.3 45.75 ? C31 RUC 211 A 1 HETATM 5 C C26 RUC . . . D 3 13.735 11.5 16.612 0.3 45.52 ? C26 RUC 211 A 1 HETATM 6 C C27 RUC . . . D 3 13.179 12.56 17.281 0.3 46.24 ? C27 RUC 211 A 1 HETATM 7 C C28 RUC . . . D 3 12.12 12.373 18.14 0.3 46.5 ? C28 RUC 211 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 542 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 7 #