data_7F59 # _model_server_result.job_id g-rOKqghk0ovBRqIGhvhnA _model_server_result.datetime_utc '2025-02-17 14:25:44' _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 7f59 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1101}' # _entry.id 7F59 # _exptl.entry_id 7F59 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 751.023 _entity.id 5 _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,L,M,N,O,P,Q _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 ? _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 5 _struct_asym.id N _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n F NAG 1 F 1 NAG F 1 NAG 3 n F NAG 2 F 2 NAG F 2 NAG 3 n F BMA 3 F 3 BMA F 3 BMA 3 n G NAG 1 G 1 NAG G 1 NAG 3 n G NAG 2 G 2 NAG G 2 NAG 3 n G BMA 3 G 3 BMA G 3 BMA 3 n H NAG 1 H 1 NAG H 1 NAG 3 n H NAG 2 H 2 NAG H 2 NAG 3 n H BMA 3 H 3 BMA H 3 BMA 3 n I NAG 1 I 1 NAG I 1 NAG 3 n I NAG 2 I 2 NAG I 2 NAG 3 n I BMA 3 I 3 BMA I 3 BMA # 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 disulf ? disulf1 A SG CYS 96 A CYS 96 1_555 A SG CYS 347 A CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? disulf ? disulf2 B SG CYS 96 B CYS 96 1_555 B SG CYS 347 B CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? disulf ? disulf3 C SG CYS 96 C CYS 96 1_555 C SG CYS 347 C CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? disulf ? disulf4 D SG CYS 96 D CYS 96 1_555 D SG CYS 347 D CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? disulf ? disulf5 E SG CYS 45 E CYS 45 1_555 E SG CYS 72 E CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? disulf ? disulf6 E SG CYS 177 E CYS 177 1_555 E SG CYS 207 E CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 E SG CYS 234 E CYS 234 1_555 E SG CYS 256 E CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? disulf ? disulf8 E SG CYS 297 E CYS 297 1_555 E SG CYS 309 E CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 E SG CYS 304 E CYS 304 1_555 E SG CYS 322 E CYS 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? disulf ? disulf10 E SG CYS 316 E CYS 316 1_555 E SG CYS 331 E CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 275 A ASN 275 1_555 J C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 378 A ASN 378 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale3 B ND2 ASN 275 B ASN 275 1_555 K C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale4 B ND2 ASN 378 B ASN 378 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 412 B ASN 412 1_555 L C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale6 B ND2 ASN 546 B ASN 546 1_555 M C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale7 C ND2 ASN 378 C ASN 378 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 D ND2 ASN 275 D ASN 275 1_555 O C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale9 D ND2 ASN 378 D ASN 378 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 D ND2 ASN 412 D ASN 412 1_555 P C1 NAG . D NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D ND2 ASN 546 D ASN 546 1_555 Q C1 NAG . D NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale15 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale17 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale19 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 289 n n C48 H481 PGT sing 290 n n C48 H482 PGT sing 291 n n C48 H483 PGT sing 292 n n C47 C46 PGT sing 293 n n C47 H471 PGT sing 294 n n C47 H472 PGT sing 295 n n C46 C45 PGT sing 296 n n C46 H461 PGT sing 297 n n C46 H462 PGT sing 298 n n C45 C44 PGT sing 299 n n C45 H451 PGT sing 300 n n C45 H452 PGT sing 301 n n C44 C43 PGT sing 302 n n C44 H441 PGT sing 303 n n C44 H442 PGT sing 304 n n C43 C42 PGT sing 305 n n C43 H431 PGT sing 306 n n C43 H432 PGT sing 307 n n C42 C41 PGT sing 308 n n C42 H421 PGT sing 309 n n C42 H422 PGT sing 310 n n C41 C40 PGT sing 311 n n C41 H411 PGT sing 312 n n C41 H412 PGT sing 313 n n C40 C39 PGT sing 314 n n C40 H401 PGT sing 315 n n C40 H402 PGT sing 316 n n C39 C38 PGT sing 317 n n C39 H391 PGT sing 318 n n C39 H392 PGT sing 319 n n C38 C37 PGT sing 320 n n C38 H381 PGT sing 321 n n C38 H382 PGT sing 322 n n C37 C36 PGT sing 323 n n C37 H371 PGT sing 324 n n C37 H372 PGT sing 325 n n C36 C35 PGT sing 326 n n C36 H361 PGT sing 327 n n C36 H362 PGT sing 328 n n C35 C34 PGT sing 329 n n C35 H351 PGT sing 330 n n C35 H352 PGT sing 331 n n C34 C33 PGT sing 332 n n C34 H341 PGT sing 333 n n C34 H342 PGT sing 334 n n C33 C32 PGT sing 335 n n C33 H331 PGT sing 336 n n C33 H332 PGT sing 337 n n C32 C31 PGT sing 338 n n C32 H321 PGT sing 339 n n C32 H322 PGT sing 340 n n C31 O31 PGT doub 341 n n C31 O2 PGT sing 342 n n O2 C2 PGT sing 343 n n C2 C1 PGT sing 344 n n C2 C3 PGT sing 345 n n C2 H2 PGT sing 346 n n C1 O3P PGT sing 347 n n C1 H11 PGT sing 348 n n C1 H12 PGT sing 349 n n O3P P PGT sing 350 n n P O1P PGT doub 351 n n P O2P PGT sing 352 n n P O4P PGT sing 353 n n O2P HO2P PGT sing 354 n n O4P C4 PGT sing 355 n n C4 C5 PGT sing 356 n n C4 H41 PGT sing 357 n n C4 H42 PGT sing 358 n n C5 O5 PGT sing 359 n n C5 C6 PGT sing 360 n n C5 H5 PGT sing 361 n n O5 HO5 PGT sing 362 n n C6 O6 PGT sing 363 n n C6 H61 PGT sing 364 n n C6 H62 PGT sing 365 n n O6 HO6 PGT sing 366 n n C3 O3 PGT sing 367 n n C3 H31 PGT sing 368 n n C3 H32 PGT sing 369 n n O3 C11 PGT sing 370 n n C11 O11 PGT doub 371 n n C11 C12 PGT sing 372 n n C12 C13 PGT sing 373 n n C12 H121 PGT sing 374 n n C12 H122 PGT sing 375 n n C13 C14 PGT sing 376 n n C13 H131 PGT sing 377 n n C13 H132 PGT sing 378 n n C14 C15 PGT sing 379 n n C14 H141 PGT sing 380 n n C14 H142 PGT sing 381 n n C15 C16 PGT sing 382 n n C15 H151 PGT sing 383 n n C15 H152 PGT sing 384 n n C16 C17 PGT sing 385 n n C16 H161 PGT sing 386 n n C16 H162 PGT sing 387 n n C17 C18 PGT sing 388 n n C17 H171 PGT sing 389 n n C17 H172 PGT sing 390 n n C18 C19 PGT sing 391 n n C18 H181 PGT sing 392 n n C18 H182 PGT sing 393 n n C19 C20 PGT sing 394 n n C19 H191 PGT sing 395 n n C19 H192 PGT sing 396 n n C20 C21 PGT sing 397 n n C20 H201 PGT sing 398 n n C20 H202 PGT sing 399 n n C21 C22 PGT sing 400 n n C21 H211 PGT sing 401 n n C21 H212 PGT sing 402 n n C22 C23 PGT sing 403 n n C22 H221 PGT sing 404 n n C22 H222 PGT sing 405 n n C23 C24 PGT sing 406 n n C23 H231 PGT sing 407 n n C23 H232 PGT sing 408 n n C24 C25 PGT sing 409 n n C24 H241 PGT sing 410 n n C24 H242 PGT sing 411 n n C25 C26 PGT sing 412 n n C25 H251 PGT sing 413 n n C25 H252 PGT sing 414 n n C26 H261 PGT sing 415 n n C26 H262 PGT sing 416 n n C26 H263 PGT sing 417 n n # _atom_sites.entry_id 7F59 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 J 4 NAG A 1 1001 1001 NAG NAG . K 4 NAG B 1 1001 1001 NAG NAG . L 4 NAG B 1 1002 1002 NAG NAG . M 4 NAG B 1 1003 1003 NAG NAG . N 5 PGT C 1 1101 1101 PGT PGT . O 4 NAG D 1 1001 1001 NAG NAG . P 4 NAG D 1 1002 1002 NAG NAG . Q 4 NAG D 1 1003 1003 NAG NAG . # 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 . . . N 5 149.667 159.329 128.616 1 130.55 ? C48 PGT 1101 C 1 HETATM 2 C C47 PGT . . . N 5 150.528 159.198 127.393 1 130.55 ? C47 PGT 1101 C 1 HETATM 3 C C46 PGT . . . N 5 151.139 157.843 127.239 1 130.55 ? C46 PGT 1101 C 1 HETATM 4 C C45 PGT . . . N 5 151.937 157.72 125.956 1 130.55 ? C45 PGT 1101 C 1 HETATM 5 C C44 PGT . . . N 5 151.202 158.234 124.751 1 130.55 ? C44 PGT 1101 C 1 HETATM 6 C C43 PGT . . . N 5 151.716 157.727 123.431 1 130.55 ? C43 PGT 1101 C 1 HETATM 7 C C42 PGT . . . N 5 150.836 158.123 122.277 1 130.55 ? C42 PGT 1101 C 1 HETATM 8 C C41 PGT . . . N 5 150.978 157.277 121.037 1 130.55 ? C41 PGT 1101 C 1 HETATM 9 C C40 PGT . . . N 5 152.275 157.442 120.295 1 130.55 ? C40 PGT 1101 C 1 HETATM 10 C C39 PGT . . . N 5 152.163 157.134 118.824 1 130.55 ? C39 PGT 1101 C 1 HETATM 11 C C38 PGT . . . N 5 151.167 158.007 118.099 1 130.55 ? C38 PGT 1101 C 1 HETATM 12 C C37 PGT . . . N 5 150.937 157.673 116.642 1 130.55 ? C37 PGT 1101 C 1 HETATM 13 C C36 PGT . . . N 5 152.157 157.729 115.75 1 130.55 ? C36 PGT 1101 C 1 HETATM 14 C C35 PGT . . . N 5 152.877 156.409 115.585 1 130.55 ? C35 PGT 1101 C 1 HETATM 15 C C34 PGT . . . N 5 153.954 156.375 114.531 1 130.55 ? C34 PGT 1101 C 1 HETATM 16 C C33 PGT . . . N 5 153.433 156.527 113.124 1 130.55 ? C33 PGT 1101 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #