data_3RZK # _model_server_result.job_id Nh68_feKAO-iV7BLqWyj_g _model_server_result.datetime_utc '2024-11-15 07:35:46' _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 3rzk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 3RZK # _exptl.entry_id 3RZK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 76.161 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description propane-1-thiol _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 3RZK _cell.length_a 78.591 _cell.length_b 78.591 _cell.length_c 228.881 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RZK _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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,H _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 F _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 covale ? covale1 F CA XL3 . B XL3 1 1_555 B N4 DC 9 B DC 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale2 B O3' DT 6 B DT 264 1_555 B P EDA 7 B EDA 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? covale ? covale3 B O3' EDA 7 B EDA 265 1_555 B P DA 8 B DA 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.589 ? metalc ? metalc1 D MN MN . A MN 1 1_555 A NE2 HIS 119 A HIS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc2 D MN MN . A MN 1 1_555 A OD1 ASP 121 A ASP 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc3 D MN MN . A MN 1 1_555 A NE2 HIS 184 A HIS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 D MN MN . A MN 1 1_555 E O5 AKG . A AKG 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 D MN MN . A MN 1 1_555 E O2 AKG . A AKG 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? hydrog WATSON-CRICK hydrog1 B N3 DT 2 B DT 260 1_555 C N1 DA 13 C DA 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 2 B DT 260 1_555 C N6 DA 13 C DA 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 3 B DG 261 1_555 C N3 DC 12 C DC 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 3 B DG 261 1_555 C O2 DC 12 C DC 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 3 B DG 261 1_555 C N4 DC 12 C DC 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 4 B DT 262 1_555 C N1 DA 11 C DA 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 4 B DT 262 1_555 C N6 DA 11 C DA 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 5 B DC 263 1_555 C N1 DG 10 C DG 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 5 B DC 263 1_555 C O6 DG 10 C DG 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 5 B DC 263 1_555 C N2 DG 10 C DG 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog11 B N3 DT 6 B DT 264 1_555 C O2 DT 8 C DT 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog12 B O4 DT 6 B DT 264 1_555 C N3 DT 8 C DT 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DA 8 B DA 266 1_555 C N3 DT 7 C DT 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 DA 8 B DA 266 1_555 C O4 DT 7 C DT 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DC 9 B DC 267 1_555 C N1 DG 6 C DG 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N4 DC 9 B DC 267 1_555 C O6 DG 6 C DG 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O2 DC 9 B DC 267 1_555 C N2 DG 6 C DG 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DT 10 B DT 268 1_555 C N1 DA 5 C DA 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O4 DT 10 B DT 268 1_555 C N6 DA 5 C DA 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DG 11 B DG 269 1_555 C N3 DC 4 C DC 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 DG 11 B DG 269 1_555 C O2 DC 4 C DC 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 DG 11 B DG 269 1_555 C N4 DC 4 C DC 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 12 B DC 270 1_555 C N1 DG 3 C DG 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 12 B DC 270 1_555 C O6 DG 3 C DG 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 12 B DC 270 1_555 C N2 DG 3 C DG 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N1 DG 13 B DG 271 1_555 C N3 DC 2 C DC 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N2 DG 13 B DG 271 1_555 C O2 DC 2 C DC 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O6 DG 13 B DG 271 1_555 C N4 DC 2 C DC 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C3 H8 S' _chem_comp.formula_weight 76.161 _chem_comp.id XL3 _chem_comp.mon_nstd_flag . _chem_comp.name propane-1-thiol _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 CA CB XL3 sing 581 n n CA HA XL3 sing 582 n n CA HAA XL3 sing 583 n n CA HAB XL3 sing 584 n n CC CB XL3 sing 585 n n CB HB XL3 sing 586 n n CB HBA XL3 sing 587 n n SG CC XL3 sing 588 n n CC HC XL3 sing 589 n n CC HCA XL3 sing 590 n n SG HSG XL3 sing 591 n n # _atom_sites.entry_id 3RZK _atom_sites.fract_transf_matrix[1][1] 0.012724 _atom_sites.fract_transf_matrix[1][2] 0.007346 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014693 _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] 0.004369 _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 MN A 1 1 1 MN MN . E 5 AKG A 1 262 1 AKG AKG . F 6 XL3 B 1 1 1 XL3 XL3 . G 7 HOH A 1 2 2 HOH HOH . G 7 HOH A 2 3 3 HOH HOH . G 7 HOH A 3 4 4 HOH HOH . G 7 HOH A 4 5 5 HOH HOH . G 7 HOH A 5 6 6 HOH HOH . G 7 HOH A 6 7 7 HOH HOH . G 7 HOH A 7 8 8 HOH HOH . G 7 HOH A 8 9 9 HOH HOH . G 7 HOH A 9 10 10 HOH HOH . G 7 HOH A 10 11 11 HOH HOH . G 7 HOH A 11 263 1 HOH HOH . H 7 HOH B 1 14 14 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 C CA XL3 . . . F 6 6.161 15.061 4.727 1 45.17 ? CA XL3 1 B 1 HETATM 2 C CB XL3 . . . F 6 6.747 15.184 3.324 1 45.55 ? CB XL3 1 B 1 HETATM 3 C CC XL3 . . . F 6 8.015 16.047 3.357 1 46.74 ? CC XL3 1 B 1 HETATM 4 S SG XL3 . . . F 6 7.793 17.603 4.312 1 48.66 ? SG XL3 1 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #