data_3LGZ # _model_server_result.job_id nBnQcA8w3HewNp5ZDfQC-A _model_server_result.datetime_utc '2024-11-02 13:41:04' _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 3lgz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":288}' # _entry.id 3LGZ # _exptl.entry_id 3LGZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 586.677 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{(1R,2R,3R)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-2-methyl-3-[(1E,5E)-2,6,10-trimethylundeca-1,5,9-trien-1-yl]cyclopropyl}methyl trihydrogen diphosphate' _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 3LGZ _cell.length_a 80.84 _cell.length_b 80.84 _cell.length_c 91.264 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LGZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 2 _struct_asym.id B _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 ASN 174 B ASN 168 1_555 C MG MG . B MG 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc2 A OD2 ASP 178 B ASP 172 1_555 C MG MG . B MG 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc3 B OAJ PS7 . B PS7 288 1_555 D MG MG . B MG 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc4 C MG MG . B MG 289 1_555 E O HOH . B HOH 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc5 C MG MG . B MG 289 1_555 E O HOH . B HOH 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc6 C MG MG . B MG 289 1_555 E O HOH . B HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc7 C MG MG . B MG 289 1_555 E O HOH . B HOH 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc8 D MG MG . B MG 290 1_555 E O HOH . B HOH 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? # _chem_comp.formula 'C30 H52 O7 P2' _chem_comp.formula_weight 586.677 _chem_comp.id PS7 _chem_comp.mon_nstd_flag . _chem_comp.name '{(1R,2R,3R)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-2-methyl-3-[(1E,5E)-2,6,10-trimethylundeca-1,5,9-trien-1-yl]cyclopropyl}methyl trihydrogen diphosphate' _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 CAA CBD PS7 sing 277 n n CAB CBD PS7 sing 278 n n CAC CBE PS7 sing 279 n n CAD CBE PS7 sing 280 n n CAE CBF PS7 sing 281 n n CAF CBG PS7 sing 282 n n CAG CBH PS7 sing 283 n n CAH CBK PS7 sing 284 n n OAI PBL PS7 sing 285 n n OAJ PBM PS7 doub 286 n n OAK PBL PS7 doub 287 n n OAL PBL PS7 sing 288 n n OAM PBM PS7 sing 289 n n CAN CAS PS7 sing 290 n n CAN CBD PS7 doub 291 n n CAO CAT PS7 sing 292 n n CAO CBE PS7 doub 293 n n CAP CAU PS7 sing 294 n n CAP CBF PS7 doub 295 n n CAQ CAV PS7 sing 296 n n CAQ CBG PS7 doub 297 n n CAR CBH PS7 doub 298 n n CAR CBI PS7 sing 299 n n CAS CAW PS7 sing 300 n n CAT CAX PS7 sing 301 n n CAU CAY PS7 sing 302 n n CAV CBA PS7 sing 303 n n CAW CBF PS7 sing 304 n n CAX CBG PS7 sing 305 n n CAY CBH PS7 sing 306 n n CAZ OBB PS7 sing 307 n n CAZ CBJ PS7 sing 308 n n CBA CBK PS7 sing 309 n n OBB PBM PS7 sing 310 n n OBC PBL PS7 sing 311 n n OBC PBM PS7 sing 312 n n CBI CBJ PS7 sing 313 n n CBI CBK PS7 sing 314 n n CBJ CBK PS7 sing 315 n n CAA HAA PS7 sing 316 n n CAA HAAA PS7 sing 317 n n CAA HAAB PS7 sing 318 n n CAB HAB PS7 sing 319 n n CAB HABA PS7 sing 320 n n CAB HABB PS7 sing 321 n n CAC HAC PS7 sing 322 n n CAC HACA PS7 sing 323 n n CAC HACB PS7 sing 324 e n CAD HAD PS7 sing 325 n n CAD HADA PS7 sing 326 n n CAD HADB PS7 sing 327 e n CAE HAE PS7 sing 328 n n CAE HAEA PS7 sing 329 e n CAE HAEB PS7 sing 330 n n CAF HAF PS7 sing 331 n n CAF HAFA PS7 sing 332 n n CAF HAFB PS7 sing 333 n n CAG HAG PS7 sing 334 n n CAG HAGA PS7 sing 335 n n CAG HAGB PS7 sing 336 n n CAH HAH PS7 sing 337 n n CAH HAHA PS7 sing 338 n n CAH HAHB PS7 sing 339 n n OAI HOAI PS7 sing 340 n n OAL HOAL PS7 sing 341 n n OAM HOAM PS7 sing 342 n n CAN HAN PS7 sing 343 n n CAO HAO PS7 sing 344 n n CAP HAP PS7 sing 345 n n CAQ HAQ PS7 sing 346 n n CAR HAR PS7 sing 347 n n CAS HAS PS7 sing 348 n n CAS HASA PS7 sing 349 n n CAT HAT PS7 sing 350 n n CAT HATA PS7 sing 351 n n CAU HAU PS7 sing 352 n n CAU HAUA PS7 sing 353 n n CAV HAV PS7 sing 354 n n CAV HAVA PS7 sing 355 n n CAW HAW PS7 sing 356 n n CAW HAWA PS7 sing 357 n n CAX HAX PS7 sing 358 n n CAX HAXA PS7 sing 359 n n CAY HAY PS7 sing 360 n n CAY HAYA PS7 sing 361 n n CAZ HAZ PS7 sing 362 n n CAZ HAZA PS7 sing 363 n n CBA HBA PS7 sing 364 n n CBA HBAA PS7 sing 365 n n CBI HBI PS7 sing 366 n n CBJ HBJ PS7 sing 367 n n # _atom_sites.entry_id 3LGZ _atom_sites.fract_transf_matrix[1][1] 0.01237 _atom_sites.fract_transf_matrix[1][2] 0.007142 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014284 _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] 0.010957 _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 B 2 PS7 B 1 288 288 PS7 PS7 . C 3 MG B 1 289 289 MG MG . D 3 MG B 1 290 290 MG MG . E 4 HOH B 1 291 291 HOH HOH . E 4 HOH B 2 292 292 HOH HOH . E 4 HOH B 3 293 293 HOH HOH . E 4 HOH B 4 294 294 HOH HOH . E 4 HOH B 5 295 295 HOH HOH . E 4 HOH B 6 296 296 HOH HOH . E 4 HOH B 7 297 297 HOH HOH . E 4 HOH B 8 298 298 HOH HOH . E 4 HOH B 9 299 299 HOH HOH . E 4 HOH B 10 300 300 HOH HOH . E 4 HOH B 11 301 301 HOH HOH . E 4 HOH B 12 302 302 HOH HOH . E 4 HOH B 13 303 303 HOH HOH . E 4 HOH B 14 304 304 HOH HOH . E 4 HOH B 15 305 305 HOH HOH . E 4 HOH B 16 306 306 HOH HOH . E 4 HOH B 17 307 307 HOH HOH . E 4 HOH B 18 308 308 HOH HOH . E 4 HOH B 19 309 309 HOH HOH . E 4 HOH B 20 310 310 HOH HOH . E 4 HOH B 21 311 311 HOH HOH . E 4 HOH B 22 312 312 HOH HOH . E 4 HOH B 23 313 313 HOH HOH . E 4 HOH B 24 314 314 HOH HOH . E 4 HOH B 25 315 315 HOH HOH . E 4 HOH B 26 316 316 HOH HOH . E 4 HOH B 27 317 317 HOH HOH . E 4 HOH B 28 318 318 HOH HOH . E 4 HOH B 29 319 319 HOH HOH . E 4 HOH B 30 320 320 HOH HOH . E 4 HOH B 31 321 321 HOH HOH . E 4 HOH B 32 322 322 HOH HOH . E 4 HOH B 33 323 323 HOH HOH . E 4 HOH B 34 324 324 HOH HOH . E 4 HOH B 35 325 325 HOH HOH . E 4 HOH B 36 326 326 HOH HOH . E 4 HOH B 37 327 327 HOH HOH . E 4 HOH B 38 328 328 HOH HOH . E 4 HOH B 39 329 329 HOH HOH . E 4 HOH B 40 330 330 HOH HOH . E 4 HOH B 41 331 331 HOH HOH . E 4 HOH B 42 332 332 HOH HOH . E 4 HOH B 43 333 333 HOH HOH . E 4 HOH B 44 334 334 HOH HOH . E 4 HOH B 45 335 335 HOH HOH . E 4 HOH B 46 336 336 HOH HOH . E 4 HOH B 47 337 337 HOH HOH . E 4 HOH B 48 338 338 HOH HOH . E 4 HOH B 49 339 339 HOH HOH . E 4 HOH B 50 340 340 HOH HOH . E 4 HOH B 51 341 341 HOH HOH . E 4 HOH B 52 342 342 HOH HOH . E 4 HOH B 53 343 343 HOH HOH . E 4 HOH B 54 344 344 HOH HOH . E 4 HOH B 55 345 345 HOH HOH . E 4 HOH B 56 346 346 HOH HOH . E 4 HOH B 57 347 347 HOH HOH . E 4 HOH B 58 348 348 HOH HOH . E 4 HOH B 59 349 349 HOH HOH . E 4 HOH B 60 350 350 HOH HOH . E 4 HOH B 61 351 351 HOH HOH . E 4 HOH B 62 352 352 HOH HOH . E 4 HOH B 63 353 353 HOH HOH . E 4 HOH B 64 354 354 HOH HOH . E 4 HOH B 65 355 355 HOH HOH . E 4 HOH B 66 356 356 HOH HOH . E 4 HOH B 67 357 357 HOH HOH . E 4 HOH B 68 358 358 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 CAA PS7 . . . B 2 -27.711 15.695 11.585 1 50.31 ? CAA PS7 288 B 1 HETATM 2 C CAB PS7 . . . B 2 -25.176 15.675 12.014 1 46.41 ? CAB PS7 288 B 1 HETATM 3 C CAC PS7 . . . B 2 -22.518 20.601 9.502 1 40.84 ? CAC PS7 288 B 1 HETATM 4 C CAD PS7 . . . B 2 -23.406 22.394 7.909 1 41.83 ? CAD PS7 288 B 1 HETATM 5 C CAE PS7 . . . B 2 -29.125 12.355 8.072 1 57.57 ? CAE PS7 288 B 1 HETATM 6 C CAF PS7 . . . B 2 -23.577 15.986 8.96 1 49.27 ? CAF PS7 288 B 1 HETATM 7 C CAG PS7 . . . B 2 -27.694 8.18 5.535 1 65.62 ? CAG PS7 288 B 1 HETATM 8 C CAH PS7 . . . B 2 -22.913 10.978 5.718 1 54.54 ? CAH PS7 288 B 1 HETATM 9 O OAI PS7 . . . B 2 -20.208 8.045 9.989 1 56.79 ? OAI PS7 288 B 1 HETATM 10 O OAJ PS7 . . . B 2 -24.523 7.072 9.238 1 66.65 ? OAJ PS7 288 B 1 HETATM 11 O OAK PS7 . . . B 2 -21.955 6.506 8.788 1 57.11 ? OAK PS7 288 B 1 HETATM 12 O OAL PS7 . . . B 2 -20.986 6.012 11.128 1 61.97 ? OAL PS7 288 B 1 HETATM 13 O OAM PS7 . . . B 2 -24.966 8.442 11.393 1 63.45 ? OAM PS7 288 B 1 HETATM 14 C CAN PS7 . . . B 2 -26.35 13.828 10.762 1 50.91 ? CAN PS7 288 B 1 HETATM 15 C CAO PS7 . . . B 2 -23.445 19.988 7.284 1 43.51 ? CAO PS7 288 B 1 HETATM 16 C CAP PS7 . . . B 2 -28.909 10.055 8.614 1 61.5 ? CAP PS7 288 B 1 HETATM 17 C CAQ PS7 . . . B 2 -24.348 15.164 6.697 1 46.04 ? CAQ PS7 288 B 1 HETATM 18 C CAR PS7 . . . B 2 -26.78 10.436 6.267 1 59.45 ? CAR PS7 288 B 1 HETATM 19 C CAS PS7 . . . B 2 -27.605 13.186 10.199 1 52.78 ? CAS PS7 288 B 1 HETATM 20 C CAT PS7 . . . B 2 -23.182 18.524 7.566 1 42.73 ? CAT PS7 288 B 1 HETATM 21 C CAU PS7 . . . B 2 -29.866 9.912 7.436 1 60.16 ? CAU PS7 288 B 1 HETATM 22 C CAV PS7 . . . B 2 -24.113 13.707 7.061 1 47.36 ? CAV PS7 288 B 1 HETATM 23 C CAW PS7 . . . B 2 -27.584 11.655 10.062 1 55.55 ? CAW PS7 288 B 1 HETATM 24 C CAX PS7 . . . B 2 -24.344 17.633 7.117 1 43.89 ? CAX PS7 288 B 1 HETATM 25 C CAY PS7 . . . B 2 -29.217 10.218 6.08 1 60.12 ? CAY PS7 288 B 1 HETATM 26 C CAZ PS7 . . . B 2 -23.633 9.634 8.07 1 58.88 ? CAZ PS7 288 B 1 HETATM 27 C CBA PS7 . . . B 2 -24.83 12.748 6.117 1 52.19 ? CBA PS7 288 B 1 HETATM 28 O OBB PS7 . . . B 2 -23.816 9.515 9.467 1 62.42 ? OBB PS7 288 B 1 HETATM 29 O OBC PS7 . . . B 2 -22.555 7.877 10.761 1 62.53 ? OBC PS7 288 B 1 HETATM 30 C CBD PS7 . . . B 2 -26.396 15.009 11.422 1 48.81 ? CBD PS7 288 B 1 HETATM 31 C CBE PS7 . . . B 2 -23.142 20.949 8.194 1 41.63 ? CBE PS7 288 B 1 HETATM 32 C CBF PS7 . . . B 2 -28.531 11.298 8.934 1 58.54 ? CBF PS7 288 B 1 HETATM 33 C CBG PS7 . . . B 2 -24.098 16.201 7.547 1 47 ? CBG PS7 288 B 1 HETATM 34 C CBH PS7 . . . B 2 -27.831 9.629 5.972 1 61.71 ? CBH PS7 288 B 1 HETATM 35 C CBI PS7 . . . B 2 -25.303 10.079 6.252 1 57.58 ? CBI PS7 288 B 1 HETATM 36 C CBJ PS7 . . . B 2 -24.663 10.625 7.544 1 57.74 ? CBJ PS7 288 B 1 HETATM 37 C CBK PS7 . . . B 2 -24.335 11.277 6.198 1 55.25 ? CBK PS7 288 B 1 HETATM 38 P PBL PS7 . . . B 2 -21.335 7.052 10.066 1 60.56 ? PBL PS7 288 B 1 HETATM 39 P PBM PS7 . . . B 2 -24.059 8.114 10.234 1 62.37 ? PBM PS7 288 B 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #