data_4DOJ # _model_server_result.job_id 69jX33ebEn4EUzTdgBU59A _model_server_result.datetime_utc '2025-03-06 09:20:46' _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 4doj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 4DOJ # _exptl.entry_id 4DOJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 751.023 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE' _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 90 _cell.entry_id 4DOJ _cell.length_a 117.44 _cell.length_b 129.32 _cell.length_c 184.86 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DOJ _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 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,I,J _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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C40 H79 O10 P' _chem_comp.formula_weight 751.023 _chem_comp.id PGT _chem_comp.mon_nstd_flag . _chem_comp.name '(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PHOSPHATIDYLGLYCEROL;1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)' # 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 C48 C47 PGT sing 257 n n C48 H481 PGT sing 258 n n C48 H482 PGT sing 259 n n C48 H483 PGT sing 260 n n C47 C46 PGT sing 261 n n C47 H471 PGT sing 262 n n C47 H472 PGT sing 263 n n C46 C45 PGT sing 264 n n C46 H461 PGT sing 265 n n C46 H462 PGT sing 266 n n C45 C44 PGT sing 267 n n C45 H451 PGT sing 268 n n C45 H452 PGT sing 269 n n C44 C43 PGT sing 270 n n C44 H441 PGT sing 271 n n C44 H442 PGT sing 272 n n C43 C42 PGT sing 273 n n C43 H431 PGT sing 274 n n C43 H432 PGT sing 275 n n C42 C41 PGT sing 276 n n C42 H421 PGT sing 277 n n C42 H422 PGT sing 278 n n C41 C40 PGT sing 279 n n C41 H411 PGT sing 280 n n C41 H412 PGT sing 281 n n C40 C39 PGT sing 282 n n C40 H401 PGT sing 283 n n C40 H402 PGT sing 284 n n C39 C38 PGT sing 285 n n C39 H391 PGT sing 286 n n C39 H392 PGT sing 287 n n C38 C37 PGT sing 288 n n C38 H381 PGT sing 289 n n C38 H382 PGT sing 290 n n C37 C36 PGT sing 291 n n C37 H371 PGT sing 292 n n C37 H372 PGT sing 293 n n C36 C35 PGT sing 294 n n C36 H361 PGT sing 295 n n C36 H362 PGT sing 296 n n C35 C34 PGT sing 297 n n C35 H351 PGT sing 298 n n C35 H352 PGT sing 299 n n C34 C33 PGT sing 300 n n C34 H341 PGT sing 301 n n C34 H342 PGT sing 302 n n C33 C32 PGT sing 303 n n C33 H331 PGT sing 304 n n C33 H332 PGT sing 305 n n C32 C31 PGT sing 306 n n C32 H321 PGT sing 307 n n C32 H322 PGT sing 308 n n C31 O31 PGT doub 309 n n C31 O2 PGT sing 310 n n O2 C2 PGT sing 311 n n C2 C1 PGT sing 312 n n C2 C3 PGT sing 313 n n C2 H2 PGT sing 314 n n C1 O3P PGT sing 315 n n C1 H11 PGT sing 316 n n C1 H12 PGT sing 317 n n O3P P PGT sing 318 n n P O1P PGT doub 319 n n P O2P PGT sing 320 n n P O4P PGT sing 321 n n O2P HO2P PGT sing 322 n n O4P C4 PGT sing 323 n n C4 C5 PGT sing 324 n n C4 H41 PGT sing 325 n n C4 H42 PGT sing 326 n n C5 O5 PGT sing 327 n n C5 C6 PGT sing 328 n n C5 H5 PGT sing 329 n n O5 HO5 PGT sing 330 n n C6 O6 PGT sing 331 n n C6 H61 PGT sing 332 n n C6 H62 PGT sing 333 n n O6 HO6 PGT sing 334 n n C3 O3 PGT sing 335 n n C3 H31 PGT sing 336 n n C3 H32 PGT sing 337 n n O3 C11 PGT sing 338 n n C11 O11 PGT doub 339 n n C11 C12 PGT sing 340 n n C12 C13 PGT sing 341 n n C12 H121 PGT sing 342 n n C12 H122 PGT sing 343 n n C13 C14 PGT sing 344 n n C13 H131 PGT sing 345 n n C13 H132 PGT sing 346 n n C14 C15 PGT sing 347 n n C14 H141 PGT sing 348 n n C14 H142 PGT sing 349 n n C15 C16 PGT sing 350 n n C15 H151 PGT sing 351 n n C15 H152 PGT sing 352 n n C16 C17 PGT sing 353 n n C16 H161 PGT sing 354 n n C16 H162 PGT sing 355 n n C17 C18 PGT sing 356 n n C17 H171 PGT sing 357 n n C17 H172 PGT sing 358 n n C18 C19 PGT sing 359 n n C18 H181 PGT sing 360 n n C18 H182 PGT sing 361 n n C19 C20 PGT sing 362 n n C19 H191 PGT sing 363 n n C19 H192 PGT sing 364 n n C20 C21 PGT sing 365 n n C20 H201 PGT sing 366 n n C20 H202 PGT sing 367 n n C21 C22 PGT sing 368 n n C21 H211 PGT sing 369 n n C21 H212 PGT sing 370 n n C22 C23 PGT sing 371 n n C22 H221 PGT sing 372 n n C22 H222 PGT sing 373 n n C23 C24 PGT sing 374 n n C23 H231 PGT sing 375 n n C23 H232 PGT sing 376 n n C24 C25 PGT sing 377 n n C24 H241 PGT sing 378 n n C24 H242 PGT sing 379 n n C25 C26 PGT sing 380 n n C25 H251 PGT sing 381 n n C25 H252 PGT sing 382 n n C26 H261 PGT sing 383 n n C26 H262 PGT sing 384 n n C26 H263 PGT sing 385 n n # _atom_sites.entry_id 4DOJ _atom_sites.fract_transf_matrix[1][1] 0.008515 _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] 0.007733 _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] 0.005409 _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 2 CL A 1 601 1 CL CL . E 3 PGT A 1 602 1 PGT PGT . F 4 CHT C 1 601 2486 CHT CHT . G 2 CL C 1 602 1 CL CL . H 5 HOH A 1 701 12 HOH HOH . H 5 HOH A 2 702 13 HOH HOH . H 5 HOH A 3 703 14 HOH HOH . H 5 HOH A 4 704 16 HOH HOH . H 5 HOH A 5 705 17 HOH HOH . H 5 HOH A 6 706 18 HOH HOH . H 5 HOH A 7 707 37 HOH HOH . I 5 HOH B 1 601 6 HOH HOH . I 5 HOH B 2 602 10 HOH HOH . I 5 HOH B 3 603 21 HOH HOH . I 5 HOH B 4 604 22 HOH HOH . I 5 HOH B 5 605 23 HOH HOH . I 5 HOH B 6 606 24 HOH HOH . I 5 HOH B 7 607 25 HOH HOH . I 5 HOH B 8 608 27 HOH HOH . I 5 HOH B 9 609 28 HOH HOH . I 5 HOH B 10 610 29 HOH HOH . I 5 HOH B 11 611 30 HOH HOH . I 5 HOH B 12 612 31 HOH HOH . J 5 HOH C 1 701 1 HOH HOH . J 5 HOH C 2 702 2 HOH HOH . J 5 HOH C 3 703 3 HOH HOH . J 5 HOH C 4 704 4 HOH HOH . J 5 HOH C 5 705 7 HOH HOH . J 5 HOH C 6 706 8 HOH HOH . J 5 HOH C 7 707 9 HOH HOH . J 5 HOH C 8 708 11 HOH HOH . J 5 HOH C 9 709 32 HOH HOH . J 5 HOH C 10 710 33 HOH HOH . J 5 HOH C 11 711 34 HOH HOH . J 5 HOH C 12 712 35 HOH HOH . J 5 HOH C 13 713 36 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 C48 PGT . . . E 3 -12.334 -18.519 35.908 1 24.8 ? C48 PGT 602 A 1 HETATM 2 C C47 PGT . . . E 3 -12.473 -17.527 34.801 0.21 30.58 ? C47 PGT 602 A 1 HETATM 3 C C46 PGT . . . E 3 -13.799 -16.89 34.606 1 34.82 ? C46 PGT 602 A 1 HETATM 4 C C45 PGT . . . E 3 -13.839 -15.587 33.893 1 36.67 ? C45 PGT 602 A 1 HETATM 5 C C44 PGT . . . E 3 -12.961 -14.489 34.402 0.18 40.56 ? C44 PGT 602 A 1 HETATM 6 C C43 PGT . . . E 3 -13.405 -13.082 34.152 1 44.01 ? C43 PGT 602 A 1 HETATM 7 C C42 PGT . . . E 3 -12.391 -11.979 34.298 0.79 46 ? C42 PGT 602 A 1 HETATM 8 C C41 PGT . . . E 3 -11.814 -11.686 35.66 0.23 47.53 ? C41 PGT 602 A 1 HETATM 9 C C40 PGT . . . E 3 -12.309 -10.471 36.394 0.86 50.18 ? C40 PGT 602 A 1 HETATM 10 C C39 PGT . . . E 3 -11.306 -9.506 36.964 0.34 51 ? C39 PGT 602 A 1 HETATM 11 C C38 PGT . . . E 3 -11.822 -8.289 37.685 0.82 52.95 ? C38 PGT 602 A 1 HETATM 12 C C37 PGT . . . E 3 -10.905 -7.124 37.878 0.6 53.39 ? C37 PGT 602 A 1 HETATM 13 C C36 PGT . . . E 3 -11.508 -5.775 38.151 0.98 52.28 ? C36 PGT 602 A 1 HETATM 14 C C35 PGT . . . E 3 -10.723 -4.547 37.796 0.85 52.71 ? C35 PGT 602 A 1 HETATM 15 C C34 PGT . . . E 3 -11.246 -3.207 38.253 1 55.94 ? C34 PGT 602 A 1 HETATM 16 C C33 PGT . . . E 3 -10.363 -1.99 38.115 1 60.36 ? C33 PGT 602 A 1 HETATM 17 C C32 PGT . . . E 3 -10.35 -0.989 39.251 0 63.93 ? C32 PGT 602 A 1 HETATM 18 C C31 PGT . . . E 3 -11.08 0.316 39.053 0 69.12 ? C31 PGT 602 A 1 HETATM 19 O O31 PGT . . . E 3 -12.144 0.323 38.374 0.76 73.23 ? O31 PGT 602 A 1 HETATM 20 O O2 PGT . . . E 3 -10.663 1.396 39.614 0.87 68.71 ? O2 PGT 602 A 1 HETATM 21 C C2 PGT . . . E 3 -11.344 2.588 39.395 0 65.11 ? C2 PGT 602 A 1 HETATM 22 C C1 PGT . . . E 3 -11.408 2.88 37.94 1 57.58 ? C1 PGT 602 A 1 HETATM 23 O O3P PGT . . . E 3 -10.477 3.763 37.431 0.35 50.15 ? O3P PGT 602 A 1 HETATM 24 P P PGT . . . E 3 -9.474 3.261 36.337 0.63 72.78 ? P PGT 602 A 1 HETATM 25 O O1P PGT . . . E 3 -9.584 4.149 35.124 0.29 73.07 ? O1P PGT 602 A 1 HETATM 26 O O2P PGT . . . E 3 -9.812 1.839 35.964 0.51 73.5 ? O2P PGT 602 A 1 HETATM 27 O O4P PGT . . . E 3 -8.021 3.319 36.9 0 40.86 ? O4P PGT 602 A 1 HETATM 28 C C4 PGT . . . E 3 -6.976 2.8 36.154 1 38.35 ? C4 PGT 602 A 1 HETATM 29 C C5 PGT . . . E 3 -5.683 2.612 36.892 0 37.19 ? C5 PGT 602 A 1 HETATM 30 O O5 PGT . . . E 3 -5.239 3.78 37.486 0.66 35.18 ? O5 PGT 602 A 1 HETATM 31 C C6 PGT . . . E 3 -4.648 2.173 35.934 1 35.63 ? C6 PGT 602 A 1 HETATM 32 O O6 PGT . . . E 3 -3.816 3.151 35.411 0.61 35.38 ? O6 PGT 602 A 1 HETATM 33 C C3 PGT . . . E 3 -10.656 3.754 40.091 0.86 64.11 ? C3 PGT 602 A 1 HETATM 34 O O3 PGT . . . E 3 -10.028 3.488 41.306 0.25 60.38 ? O3 PGT 602 A 1 HETATM 35 C C11 PGT . . . E 3 -8.923 4.08 41.593 1 57.85 ? C11 PGT 602 A 1 HETATM 36 O O11 PGT . . . E 3 -8.296 4.713 40.712 1 56.51 ? O11 PGT 602 A 1 HETATM 37 C C12 PGT . . . E 3 -8.26 3.788 42.916 1 54.32 ? C12 PGT 602 A 1 HETATM 38 C C13 PGT . . . E 3 -8.343 2.366 43.411 0.3 49.93 ? C13 PGT 602 A 1 HETATM 39 C C14 PGT . . . E 3 -8.137 1.265 42.386 1 49.98 ? C14 PGT 602 A 1 HETATM 40 C C15 PGT . . . E 3 -8.097 -0.152 42.913 1 47.78 ? C15 PGT 602 A 1 HETATM 41 C C16 PGT . . . E 3 -7.313 -1.198 42.118 0.82 45.66 ? C16 PGT 602 A 1 HETATM 42 C C17 PGT . . . E 3 -6.991 -2.501 42.826 1 42.8 ? C17 PGT 602 A 1 HETATM 43 C C18 PGT . . . E 3 -5.883 -3.361 42.245 0.37 42.42 ? C18 PGT 602 A 1 HETATM 44 C C19 PGT . . . E 3 -6.283 -4.611 41.507 0.84 42.13 ? C19 PGT 602 A 1 HETATM 45 C C20 PGT . . . E 3 -5.264 -5.711 41.377 1 40.54 ? C20 PGT 602 A 1 HETATM 46 C C21 PGT . . . E 3 -5.767 -7.12 41.537 0.68 41.28 ? C21 PGT 602 A 1 HETATM 47 C C22 PGT . . . E 3 -5.159 -8.184 40.663 0.72 45.66 ? C22 PGT 602 A 1 HETATM 48 C C23 PGT . . . E 3 -3.767 -7.938 40.173 0.94 46.83 ? C23 PGT 602 A 1 HETATM 49 C C24 PGT . . . E 3 -3.147 -8.916 39.227 1 41.83 ? C24 PGT 602 A 1 HETATM 50 C C25 PGT . . . E 3 -2.625 -10.212 39.799 1 37.25 ? C25 PGT 602 A 1 HETATM 51 C C26 PGT . . . E 3 -3.626 -11.305 40.033 0.99 33.78 ? C26 PGT 602 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 51 #