data_5BKJ # _model_server_result.job_id CufBSlAYv68NNAVz91XaCw _model_server_result.datetime_utc '2024-11-12 21:29:42' _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 5bkj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":401}' # _entry.id 5BKJ # _exptl.entry_id 5BKJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 749.007 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' _entity.pdbx_number_of_molecules 4 _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 5BKJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BKJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,R,S _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 M N N ? 2 N N N ? 2 O 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 metalc ? metalc1 A O THR 59 A THR 59 1_555 J K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc2 A OG1 THR 59 A THR 59 1_555 J K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.344 ? metalc ? metalc3 J K K . A K 402 1_555 F O THR 59 C THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc4 J K K . A K 402 1_555 F OG1 THR 59 C THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.376 ? metalc ? metalc5 J K K . A K 402 1_555 G O THR 59 E THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc6 J K K . A K 402 1_555 G OG1 THR 59 E THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.367 ? metalc ? metalc7 J K K . A K 402 1_555 H O THR 59 G THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc8 J K K . A K 402 1_555 H OG1 THR 59 G THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.361 ? # _chem_comp.formula 'C40 H77 O10 P' _chem_comp.formula_weight 749.007 _chem_comp.id PGW _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)];PHOSPHATIDYLGLYCEROL # 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 CAD C05 PGW sing 237 n n CAD HAD PGW sing 238 n n CAD HADA PGW sing 239 n n OAE CAD PGW sing 240 n n OAE HOAE PGW sing 241 n n OAF C05 PGW sing 242 n n OAF HOAF PGW sing 243 n n P O13 PGW sing 244 n n P O11 PGW sing 245 n n C01 O03 PGW sing 246 n n C01 C02 PGW sing 247 n n C01 H01 PGW sing 248 n n C01 H01A PGW sing 249 n n C1 C2 PGW sing 250 n n O01 C1 PGW sing 251 n n C02 O01 PGW sing 252 n n C02 H02 PGW sing 253 n n C2 C3 PGW sing 254 n n C2 H2 PGW sing 255 n n C2 H2A PGW sing 256 n n O02 C1 PGW doub 257 n n C03 C02 PGW sing 258 n n C03 H03 PGW sing 259 n n C03 H03A PGW sing 260 n n C3 C4 PGW sing 261 n n C3 H3 PGW sing 262 n n C3 H3A PGW sing 263 n n C04 C05 PGW sing 264 n n C04 O12 PGW sing 265 n n C04 H04 PGW sing 266 n n C04 H04A PGW sing 267 n n C4 C5 PGW sing 268 n n C4 H4 PGW sing 269 n n C4 H4A PGW sing 270 n n O04 C19 PGW doub 271 n n C05 H05 PGW sing 272 n n C5 C6 PGW sing 273 n n C5 H5 PGW sing 274 n n C5 H5A PGW sing 275 n n C06 C07 PGW sing 276 n n C06 H06 PGW sing 277 n n C06 H06A PGW sing 278 n n C6 C7 PGW sing 279 n n C6 H6 PGW sing 280 n n C6 H6A PGW sing 281 n n C07 H07 PGW sing 282 n n C07 H07A PGW sing 283 n n C7 C8 PGW sing 284 n n C7 H7 PGW sing 285 n n C7 H7A PGW sing 286 n n C08 C07 PGW sing 287 n n C08 H08 PGW sing 288 n n C08 H08A PGW sing 289 n n C8 C9 PGW sing 290 n n C8 H8 PGW sing 291 n n C8 H8A PGW sing 292 n n C09 C08 PGW sing 293 n n C09 C11 PGW sing 294 n n C09 H09 PGW sing 295 n n C09 H09A PGW sing 296 n n C9 C10 PGW doub 297 z n C10 C06 PGW sing 298 n n C11 H11 PGW sing 299 n n C11 H11A PGW sing 300 n n O11 C03 PGW sing 301 n n C12 C11 PGW sing 302 n n C12 H12 PGW sing 303 n n C12 H12A PGW sing 304 n n O12 P PGW sing 305 n n C13 C12 PGW sing 306 n n C13 C14 PGW sing 307 n n C13 H13 PGW sing 308 n n C13 H13A PGW sing 309 n n O13 HO13 PGW sing 310 n n C14 H14 PGW sing 311 n n C14 H14A PGW sing 312 n n C14 H14B PGW sing 313 n n O14 P PGW doub 314 n n C15 C16 PGW sing 315 n n C15 H15 PGW sing 316 n n C15 H15A PGW sing 317 n n C16 H16 PGW sing 318 n n C16 H16A PGW sing 319 n n C17 C16 PGW sing 320 n n C17 C18 PGW sing 321 n n C17 H17 PGW sing 322 n n C17 H17A PGW sing 323 n n C18 C28 PGW sing 324 n n C18 H18 PGW sing 325 n n C18 H18A PGW sing 326 n n C19 O03 PGW sing 327 n n C19 C20 PGW sing 328 n n C20 C21 PGW sing 329 n n C20 H20 PGW sing 330 n n C20 H20A PGW sing 331 n n C21 C22 PGW sing 332 n n C21 H21 PGW sing 333 n n C21 H21A PGW sing 334 n n C22 C23 PGW sing 335 n n C22 H22 PGW sing 336 n n C22 H22A PGW sing 337 n n C23 C24 PGW sing 338 n n C23 H23 PGW sing 339 n n C23 H23A PGW sing 340 n n C24 C25 PGW sing 341 n n C24 H24 PGW sing 342 n n C24 H24A PGW sing 343 n n C25 C26 PGW sing 344 n n C25 H25 PGW sing 345 n n C25 H25A PGW sing 346 n n C26 C27 PGW sing 347 n n C26 H26 PGW sing 348 n n C26 H26A PGW sing 349 n n C27 C15 PGW sing 350 n n C27 H27 PGW sing 351 n n C27 H27A PGW sing 352 n n C28 H28 PGW sing 353 n n C28 H28A PGW sing 354 n n C29 H29 PGW sing 355 n n C29 H29A PGW sing 356 n n C29 H29B PGW sing 357 n n C30 C28 PGW sing 358 n n C30 C29 PGW sing 359 n n C30 H30 PGW sing 360 n n C30 H30A PGW sing 361 n n C9 H9 PGW sing 362 n n C10 H10 PGW sing 363 n n # _atom_sites.entry_id 5BKJ _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 I 2 PGW A 1 401 401 PGW PGW . J 3 K A 1 402 1 K K . K 3 K A 1 403 5 K K . L 4 YQ1 A 1 404 501 YQ1 TPA . M 2 PGW C 1 401 401 PGW PGW . N 2 PGW E 1 401 401 PGW PGW . O 2 PGW G 1 401 401 PGW PGW . P 5 HOH A 1 501 338 HOH HOH . Q 5 HOH C 1 501 338 HOH HOH . R 5 HOH E 1 501 338 HOH HOH . S 5 HOH G 1 501 338 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 P P PGW . . . M 2 125.814 146.666 118.184 1 74.88 ? P PGW 401 C 1 HETATM 2 C C01 PGW . . . M 2 123.358 142.906 116.006 1 74.88 ? C01 PGW 401 C 1 HETATM 3 C C1 PGW . . . M 2 126.465 142.72 114.794 1 74.88 ? C1 PGW 401 C 1 HETATM 4 O O01 PGW . . . M 2 125.857 142.485 116.013 1 74.88 ? O01 PGW 401 C 1 HETATM 5 C C02 PGW . . . M 2 124.76 143.288 116.583 1 74.88 ? C02 PGW 401 C 1 HETATM 6 C C2 PGW . . . M 2 126.031 141.837 113.664 1 74.88 ? C2 PGW 401 C 1 HETATM 7 O O02 PGW . . . M 2 127.327 143.583 114.641 1 74.88 ? O02 PGW 401 C 1 HETATM 8 C C03 PGW . . . M 2 125.015 144.808 116.573 1 74.88 ? C03 PGW 401 C 1 HETATM 9 C C3 PGW . . . M 2 127.01 142.026 112.518 1 74.88 ? C3 PGW 401 C 1 HETATM 10 O O03 PGW . . . M 2 123.319 141.526 115.616 1 74.88 ? O03 PGW 401 C 1 HETATM 11 C C04 PGW . . . M 2 123.645 147.041 119.617 1 74.88 ? C04 PGW 401 C 1 HETATM 12 C C4 PGW . . . M 2 126.277 142.126 111.208 1 74.88 ? C4 PGW 401 C 1 HETATM 13 O O04 PGW . . . M 2 121.716 140.165 114.875 1 74.88 ? O04 PGW 401 C 1 HETATM 14 C C05 PGW . . . M 2 123.121 147.832 120.823 1 74.88 ? C05 PGW 401 C 1 HETATM 15 C C5 PGW . . . M 2 126.946 141.263 110.178 1 74.88 ? C5 PGW 401 C 1 HETATM 16 C C06 PGW . . . M 2 130.336 142.194 105.212 1 74.88 ? C06 PGW 401 C 1 HETATM 17 C C6 PGW . . . M 2 126.731 141.873 108.819 1 74.88 ? C6 PGW 401 C 1 HETATM 18 C C07 PGW . . . M 2 130.465 141.58 103.837 1 74.88 ? C07 PGW 401 C 1 HETATM 19 C C7 PGW . . . M 2 127.823 141.441 107.869 1 74.88 ? C7 PGW 401 C 1 HETATM 20 C C8 PGW . . . M 2 128.756 142.602 107.635 1 74.88 ? C8 PGW 401 C 1 HETATM 21 C C9 PGW . . . M 2 128.434 143.266 106.356 1 74.88 ? C9 PGW 401 C 1 HETATM 22 C C10 PGW . . . M 2 129.148 143.084 105.251 1 74.88 ? C10 PGW 401 C 1 HETATM 23 O O11 PGW . . . M 2 124.859 145.349 117.813 1 74.88 ? O11 PGW 401 C 1 HETATM 24 O O12 PGW . . . M 2 124.992 147.295 119.521 1 74.88 ? O12 PGW 401 C 1 HETATM 25 O O13 PGW . . . M 2 125.662 147.655 117.057 1 74.88 ? O13 PGW 401 C 1 HETATM 26 O O14 PGW . . . M 2 127.068 146.124 118.701 1 74.88 ? O14 PGW 401 C 1 HETATM 27 C C15 PGW . . . M 2 124.334 144.057 104.826 1 74.88 ? C15 PGW 401 C 1 HETATM 28 C C16 PGW . . . M 2 125.687 144.367 104.228 1 74.88 ? C16 PGW 401 C 1 HETATM 29 C C17 PGW . . . M 2 125.764 143.801 102.822 1 74.88 ? C17 PGW 401 C 1 HETATM 30 C C18 PGW . . . M 2 126.823 144.54 102.029 1 74.88 ? C18 PGW 401 C 1 HETATM 31 C C19 PGW . . . M 2 122.408 141.148 114.665 1 74.88 ? C19 PGW 401 C 1 HETATM 32 C C20 PGW . . . M 2 122.316 141.975 113.416 1 74.88 ? C20 PGW 401 C 1 HETATM 33 C C21 PGW . . . M 2 121.853 141.104 112.264 1 74.88 ? C21 PGW 401 C 1 HETATM 34 C C22 PGW . . . M 2 122.599 141.473 111.004 1 74.88 ? C22 PGW 401 C 1 HETATM 35 C C23 PGW . . . M 2 121.66 142.027 109.961 1 74.88 ? C23 PGW 401 C 1 HETATM 36 C C24 PGW . . . M 2 122.327 143.148 109.209 1 74.88 ? C24 PGW 401 C 1 HETATM 37 C C25 PGW . . . M 2 123.123 142.604 108.053 1 74.88 ? C25 PGW 401 C 1 HETATM 38 C C26 PGW . . . M 2 123.044 143.526 106.862 1 74.88 ? C26 PGW 401 C 1 HETATM 39 C C27 PGW . . . M 2 124.428 143.807 106.315 1 74.88 ? C27 PGW 401 C 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #