data_1VGN # _model_server_result.job_id W87mBDSaBJp6JSeFPG_6_Q _model_server_result.datetime_utc '2024-11-24 04:03:41' _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 1vgn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1161}' # _entry.id 1VGN # _exptl.entry_id 1VGN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 177.264 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE _entity.pdbx_number_of_molecules 2 _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 1VGN _cell.length_a 49.987 _cell.length_b 53.314 _cell.length_c 196.344 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VGN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 I 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 covale ? covale1 A NZ LYS 161 A LYS 161 1_555 E CL OPS . A OPS 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 B NZ LYS 161 B LYS 161 1_555 I CL OPS . B OPS 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 77 A HIS 77 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc2 A ND1 HIS 79 A HIS 79 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc3 A OD2 ASP 81 A ASP 81 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc4 A NE2 HIS 139 A HIS 139 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc5 A SG CYS 158 A CYS 158 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc6 A NE2 HIS 197 A HIS 197 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc7 C ZN ZN . A ZN 301 1_555 E SW OPS . A OPS 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc8 D ZN ZN . A ZN 302 1_555 E SW OPS . A OPS 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc9 B NE2 HIS 77 B HIS 77 1_555 G ZN ZN . B ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc10 B ND1 HIS 79 B HIS 79 1_555 G ZN ZN . B ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc11 B OD2 ASP 81 B ASP 81 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc12 B NE2 HIS 139 B HIS 139 1_555 G ZN ZN . B ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc13 B SG CYS 158 B CYS 158 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc14 B NE2 HIS 197 B HIS 197 1_555 H ZN ZN . B ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc15 G ZN ZN . B ZN 303 1_555 I SW OPS . B OPS 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc16 H ZN ZN . B ZN 304 1_555 I SW OPS . B OPS 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? # _chem_comp.formula 'C6 H9 O2 S2 -1' _chem_comp.formula_weight 177.264 _chem_comp.id OPS _chem_comp.mon_nstd_flag . _chem_comp.name 3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-(3-OXO-PROPYLSULFANYLCARBONYL)-ETHANETHIOLATE # 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 CL OM OPS doub 225 n n CL CN OPS sing 226 n n CL HL OPS sing 227 n n CN CO OPS sing 228 n n CN HN1 OPS sing 229 n n CN HN2 OPS sing 230 n n CO SR OPS sing 231 n n CO HO1 OPS sing 232 n n CO HO2 OPS sing 233 n n SR CS OPS sing 234 n n CS OT OPS doub 235 n n CS CU OPS sing 236 n n CU CV OPS sing 237 n n CU HU1 OPS sing 238 n n CU HU2 OPS sing 239 n n CV SW OPS sing 240 n n CV HV1 OPS sing 241 n n CV HV2 OPS sing 242 n n # _atom_sites.entry_id 1VGN _atom_sites.fract_transf_matrix[1][1] 0.020005 _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] 0.018757 _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] 0.005093 _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 ZN A 1 301 301 ZN ZN . D 2 ZN A 1 302 302 ZN ZN . E 3 OPS A 1 1161 1161 OPS OPS . F 4 ACY A 1 401 401 ACY ACY . G 2 ZN B 1 303 303 ZN ZN . H 2 ZN B 1 304 304 ZN ZN . I 3 OPS B 1 1161 1161 OPS OPS . J 5 HOH A 1 1162 1 HOH HOH . J 5 HOH A 2 1163 2 HOH HOH . J 5 HOH A 3 1164 4 HOH HOH . J 5 HOH A 4 1165 5 HOH HOH . J 5 HOH A 5 1166 6 HOH HOH . J 5 HOH A 6 1167 7 HOH HOH . J 5 HOH A 7 1168 8 HOH HOH . J 5 HOH A 8 1169 9 HOH HOH . J 5 HOH A 9 1170 11 HOH HOH . J 5 HOH A 10 1171 12 HOH HOH . J 5 HOH A 11 1172 14 HOH HOH . J 5 HOH A 12 1173 15 HOH HOH . J 5 HOH A 13 1174 16 HOH HOH . J 5 HOH A 14 1175 17 HOH HOH . J 5 HOH A 15 1176 18 HOH HOH . J 5 HOH A 16 1177 19 HOH HOH . J 5 HOH A 17 1178 21 HOH HOH . J 5 HOH A 18 1179 22 HOH HOH . J 5 HOH A 19 1180 24 HOH HOH . J 5 HOH A 20 1181 25 HOH HOH . J 5 HOH A 21 1182 26 HOH HOH . J 5 HOH A 22 1183 27 HOH HOH . J 5 HOH A 23 1184 28 HOH HOH . J 5 HOH A 24 1185 29 HOH HOH . J 5 HOH A 25 1186 30 HOH HOH . J 5 HOH A 26 1187 31 HOH HOH . J 5 HOH A 27 1188 32 HOH HOH . J 5 HOH A 28 1189 33 HOH HOH . J 5 HOH A 29 1190 34 HOH HOH . J 5 HOH A 30 1191 35 HOH HOH . J 5 HOH A 31 1192 36 HOH HOH . J 5 HOH A 32 1193 37 HOH HOH . J 5 HOH A 33 1194 38 HOH HOH . J 5 HOH A 34 1195 40 HOH HOH . J 5 HOH A 35 1196 42 HOH HOH . J 5 HOH A 36 1197 43 HOH HOH . J 5 HOH A 37 1198 44 HOH HOH . J 5 HOH A 38 1199 45 HOH HOH . J 5 HOH A 39 1200 46 HOH HOH . J 5 HOH A 40 1201 49 HOH HOH . J 5 HOH A 41 1202 50 HOH HOH . J 5 HOH A 42 1203 51 HOH HOH . J 5 HOH A 43 1204 52 HOH HOH . J 5 HOH A 44 1205 55 HOH HOH . J 5 HOH A 45 1206 56 HOH HOH . J 5 HOH A 46 1207 57 HOH HOH . J 5 HOH A 47 1208 58 HOH HOH . J 5 HOH A 48 1209 59 HOH HOH . J 5 HOH A 49 1210 60 HOH HOH . J 5 HOH A 50 1211 62 HOH HOH . J 5 HOH A 51 1212 63 HOH HOH . J 5 HOH A 52 1213 64 HOH HOH . J 5 HOH A 53 1214 65 HOH HOH . J 5 HOH A 54 1215 66 HOH HOH . J 5 HOH A 55 1216 67 HOH HOH . J 5 HOH A 56 1217 68 HOH HOH . J 5 HOH A 57 1218 70 HOH HOH . J 5 HOH A 58 1219 72 HOH HOH . J 5 HOH A 59 1220 74 HOH HOH . J 5 HOH A 60 1221 75 HOH HOH . J 5 HOH A 61 1222 76 HOH HOH . J 5 HOH A 62 1223 77 HOH HOH . K 5 HOH B 1 1162 3 HOH HOH . K 5 HOH B 2 1163 10 HOH HOH . K 5 HOH B 3 1164 13 HOH HOH . K 5 HOH B 4 1165 20 HOH HOH . K 5 HOH B 5 1166 23 HOH HOH . K 5 HOH B 6 1167 39 HOH HOH . K 5 HOH B 7 1168 41 HOH HOH . K 5 HOH B 8 1169 47 HOH HOH . K 5 HOH B 9 1170 48 HOH HOH . K 5 HOH B 10 1171 53 HOH HOH . K 5 HOH B 11 1172 54 HOH HOH . K 5 HOH B 12 1173 61 HOH HOH . K 5 HOH B 13 1174 69 HOH HOH . K 5 HOH B 14 1175 71 HOH HOH . K 5 HOH B 15 1176 73 HOH HOH . K 5 HOH B 16 1177 78 HOH HOH . K 5 HOH B 17 1178 79 HOH HOH . K 5 HOH B 18 1179 80 HOH HOH . K 5 HOH B 19 1180 81 HOH HOH . K 5 HOH B 20 1181 82 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 CL OPS . . . E 3 25.03 21.479 127.979 1 35.77 ? CL OPS 1161 A 1 HETATM 2 O OM OPS . . . E 3 24.246 21.638 128.92 1 32.89 ? OM OPS 1161 A 1 HETATM 3 C CN OPS . . . E 3 24.887 20.307 127.012 1 35.55 ? CN OPS 1161 A 1 HETATM 4 C CO OPS . . . E 3 24.01 19.181 127.54 1 36.75 ? CO OPS 1161 A 1 HETATM 5 S SR OPS . . . E 3 24.901 18.07 128.674 1 36.88 ? SR OPS 1161 A 1 HETATM 6 C CS OPS . . . E 3 23.788 18.018 130.023 1 36.3 ? CS OPS 1161 A 1 HETATM 7 O OT OPS . . . E 3 22.66 18.51 129.908 1 35.32 ? OT OPS 1161 A 1 HETATM 8 C CU OPS . . . E 3 24.221 17.341 131.321 1 34.2 ? CU OPS 1161 A 1 HETATM 9 C CV OPS . . . E 3 24.047 18.236 132.561 1 32.33 ? CV OPS 1161 A 1 HETATM 10 S SW OPS . . . E 3 24.902 19.844 132.425 1 24.8 ? SW OPS 1161 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #