data_3PV0 # _model_server_result.job_id UMZrFHwlHYo-Bw_mU5Rqqw _model_server_result.datetime_utc '2024-11-18 16:30:30' _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 3pv0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":4001}' # _entry.id 3PV0 # _exptl.entry_id 3PV0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 749.007 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90.48 _cell.angle_beta 102.13 _cell.angle_gamma 104.21 _cell.entry_id 3PV0 _cell.length_a 78.543 _cell.length_b 92.63 _cell.length_c 119.132 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PV0 _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 6 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 5 n F GLC 1 C 1 GLC X 2002 MAL 5 n F GLC 2 C 2 GLC X 2002 MAL 5 n G GLC 1 D 1 GLC X 2001 MAL 5 n G GLC 2 D 2 GLC X 2001 MAL # 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 69 E CYS 69 1_555 A SG CYS 337 E CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 F O4 GLC . C GLC 1 1_555 F C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 sing covale ? covale2 G O4 GLC . D GLC 1 1_555 G C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 sing # _chem_comp.formula 'C40 H77 O10 P' _chem_comp.formula_weight 749.007 _chem_comp.id PGV _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PHOSPHATIDYLGLYCEROL;2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL # 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 P O11 PGV sing 259 n n P O12 PGV sing 260 n n P O13 PGV doub 261 n n P O14 PGV sing 262 n n C01 C02 PGV sing 263 n n C01 O03 PGV sing 264 n n C01 H011 PGV sing 265 n n C01 H012 PGV sing 266 n n C02 C03 PGV sing 267 n n C02 O01 PGV sing 268 n n C02 H02 PGV sing 269 n n C03 O11 PGV sing 270 n n C03 H031 PGV sing 271 n n C03 H032 PGV sing 272 n n C04 C05 PGV sing 273 n n C04 O12 PGV sing 274 n n C04 H041 PGV sing 275 n n C04 H042 PGV sing 276 n n C05 C06 PGV sing 277 n n C05 O05 PGV sing 278 n n C05 H05 PGV sing 279 n n C06 O06 PGV sing 280 n n C06 H061 PGV sing 281 n n C06 H062 PGV sing 282 n n O01 C1 PGV sing 283 n n O02 C1 PGV doub 284 n n O03 C19 PGV sing 285 n n O04 C19 PGV doub 286 n n O05 H1 PGV sing 287 n n O06 H06 PGV sing 288 n n O14 H14 PGV sing 289 n n C1 C2 PGV sing 290 n n C2 C3 PGV sing 291 n n C2 H21 PGV sing 292 n n C2 H22 PGV sing 293 n n C3 C4 PGV sing 294 n n C3 H31 PGV sing 295 n n C3 H32 PGV sing 296 n n C4 C5 PGV sing 297 n n C4 H41 PGV sing 298 n n C4 H42 PGV sing 299 n n C5 C6 PGV sing 300 n n C5 H51 PGV sing 301 n n C5 H52 PGV sing 302 n n C6 C7 PGV sing 303 n n C6 H61 PGV sing 304 n n C6 H62 PGV sing 305 n n C7 C8 PGV sing 306 n n C7 H71 PGV sing 307 n n C7 H72 PGV sing 308 n n C8 C9 PGV sing 309 n n C8 H81 PGV sing 310 n n C8 H82 PGV sing 311 n n C9 C10 PGV sing 312 n n C9 H91 PGV sing 313 n n C9 H92 PGV sing 314 n n C10 C11 PGV sing 315 n n C10 H101 PGV sing 316 n n C10 H102 PGV sing 317 n n C11 C12 PGV doub 318 z n C11 H11 PGV sing 319 n n C12 C13 PGV sing 320 n n C12 H12 PGV sing 321 n n C13 C14 PGV sing 322 n n C13 H131 PGV sing 323 n n C13 H132 PGV sing 324 n n C14 C15 PGV sing 325 n n C14 H141 PGV sing 326 n n C14 H142 PGV sing 327 n n C15 C16 PGV sing 328 n n C15 H151 PGV sing 329 n n C15 H152 PGV sing 330 n n C16 C17 PGV sing 331 n n C16 H161 PGV sing 332 n n C16 H162 PGV sing 333 n n C17 C18 PGV sing 334 n n C17 H171 PGV sing 335 n n C17 H172 PGV sing 336 n n C18 H181 PGV sing 337 n n C18 H182 PGV sing 338 n n C18 H183 PGV sing 339 n n C19 C20 PGV sing 340 n n C20 C21 PGV sing 341 n n C20 H201 PGV sing 342 n n C20 H202 PGV sing 343 n n C21 C22 PGV sing 344 n n C21 H211 PGV sing 345 n n C21 H212 PGV sing 346 n n C22 C23 PGV sing 347 n n C22 H221 PGV sing 348 n n C22 H222 PGV sing 349 n n C23 C24 PGV sing 350 n n C23 H231 PGV sing 351 n n C23 H232 PGV sing 352 n n C24 C25 PGV sing 353 n n C24 H241 PGV sing 354 n n C24 H242 PGV sing 355 n n C25 C26 PGV sing 356 n n C25 H251 PGV sing 357 n n C25 H252 PGV sing 358 n n C26 C27 PGV sing 359 n n C26 H261 PGV sing 360 n n C26 H262 PGV sing 361 n n C27 C28 PGV sing 362 n n C27 H271 PGV sing 363 n n C27 H272 PGV sing 364 n n C28 C29 PGV sing 365 n n C28 H281 PGV sing 366 n n C28 H282 PGV sing 367 n n C29 C30 PGV sing 368 n n C29 H291 PGV sing 369 n n C29 H292 PGV sing 370 n n C30 C31 PGV sing 371 n n C30 H301 PGV sing 372 n n C30 H302 PGV sing 373 n n C31 C32 PGV sing 374 n n C31 H311 PGV sing 375 n n C31 H312 PGV sing 376 n n C32 C33 PGV sing 377 n n C32 H321 PGV sing 378 n n C32 H322 PGV sing 379 n n C33 C34 PGV sing 380 n n C33 H331 PGV sing 381 n n C33 H332 PGV sing 382 n n C34 H341 PGV sing 383 n n C34 H342 PGV sing 384 n n C34 H343 PGV sing 385 n n # _atom_sites.entry_id 3PV0 _atom_sites.fract_transf_matrix[1][1] 0.012732 _atom_sites.fract_transf_matrix[1][2] 0.003224 _atom_sites.fract_transf_matrix[1][3] 0.002946 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011136 _atom_sites.fract_transf_matrix[2][3] 0.000706 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008603 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id H _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id PGV _pdbx_nonpoly_scheme.pdb_strand_id F _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 4001 _pdbx_nonpoly_scheme.auth_seq_num 4001 _pdbx_nonpoly_scheme.pdb_mon_id PGV _pdbx_nonpoly_scheme.auth_mon_id PGV _pdbx_nonpoly_scheme.pdb_ins_code . # 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 PGV . . . H 6 16.653 -50.2 40.666 1 88.84 ? P PGV 4001 F 1 HETATM 2 C C01 PGV . . . H 6 14.886 -52.361 37.562 1 88.1 ? C01 PGV 4001 F 1 HETATM 3 C C02 PGV . . . H 6 15.091 -53.279 38.761 1 88.49 ? C02 PGV 4001 F 1 HETATM 4 C C03 PGV . . . H 6 16.071 -52.628 39.735 1 88.65 ? C03 PGV 4001 F 1 HETATM 5 C C04 PGV . . . H 6 17.591 -47.993 39.539 1 88.39 ? C04 PGV 4001 F 1 HETATM 6 C C05 PGV . . . H 6 17.549 -47.739 38.035 1 88.22 ? C05 PGV 4001 F 1 HETATM 7 C C06 PGV . . . H 6 17.598 -46.238 37.777 1 88.08 ? C06 PGV 4001 F 1 HETATM 8 O O01 PGV . . . H 6 15.606 -54.53 38.304 1 88.83 ? O01 PGV 4001 F 1 HETATM 9 O O02 PGV . . . H 6 15.323 -55.791 40.22 1 89.29 ? O02 PGV 4001 F 1 HETATM 10 O O03 PGV . . . H 6 13.7 -51.594 37.753 1 87.72 ? O03 PGV 4001 F 1 HETATM 11 O O04 PGV . . . H 6 12.189 -52.577 36.314 1 87.52 ? O04 PGV 4001 F 1 HETATM 12 O O05 PGV . . . H 6 16.343 -48.275 37.477 1 88.27 ? O05 PGV 4001 F 1 HETATM 13 O O06 PGV . . . H 6 18.731 -45.927 36.961 1 87.91 ? O06 PGV 4001 F 1 HETATM 14 O O11 PGV . . . H 6 16.07 -51.21 39.549 1 88.82 ? O11 PGV 4001 F 1 HETATM 15 O O12 PGV . . . H 6 16.462 -48.768 39.945 1 88.63 ? O12 PGV 4001 F 1 HETATM 16 O O13 PGV . . . H 6 18.134 -50.469 40.822 1 88.83 ? O13 PGV 4001 F 1 HETATM 17 O O14 PGV . . . H 6 15.751 -50.251 41.878 1 88.75 ? O14 PGV 4001 F 1 HETATM 18 C C1 PGV . . . H 6 15.072 -55.674 39.031 1 89.14 ? C1 PGV 4001 F 1 HETATM 19 C C2 PGV . . . H 6 14.232 -56.705 38.309 1 89.27 ? C2 PGV 4001 F 1 HETATM 20 C C3 PGV . . . H 6 12.989 -57.071 39.117 1 89.47 ? C3 PGV 4001 F 1 HETATM 21 C C4 PGV . . . H 6 12.16 -58.137 38.402 1 89.59 ? C4 PGV 4001 F 1 HETATM 22 C C5 PGV . . . H 6 10.845 -57.563 37.881 1 89.68 ? C5 PGV 4001 F 1 HETATM 23 C C6 PGV . . . H 6 10.102 -58.567 37.005 1 89.7 ? C6 PGV 4001 F 1 HETATM 24 C C7 PGV . . . H 6 9.023 -57.889 36.164 1 89.69 ? C7 PGV 4001 F 1 HETATM 25 C C8 PGV . . . H 6 8.464 -58.831 35.099 1 89.67 ? C8 PGV 4001 F 1 HETATM 26 C C9 PGV . . . H 6 9.25 -58.726 33.794 1 89.61 ? C9 PGV 4001 F 1 HETATM 27 C C10 PGV . . . H 6 8.751 -59.716 32.745 1 89.49 ? C10 PGV 4001 F 1 HETATM 28 C C11 PGV . . . H 6 8.865 -59.13 31.342 1 89.32 ? C11 PGV 4001 F 1 HETATM 29 C C12 PGV . . . H 6 7.493 -58.988 30.694 1 89.27 ? C12 PGV 4001 F 1 HETATM 30 C C13 PGV . . . H 6 6.862 -57.639 31.016 1 89.24 ? C13 PGV 4001 F 1 HETATM 31 C C14 PGV . . . H 6 5.349 -57.759 31.146 1 89.26 ? C14 PGV 4001 F 1 HETATM 32 C C15 PGV . . . H 6 4.733 -56.431 31.569 1 89.35 ? C15 PGV 4001 F 1 HETATM 33 C C16 PGV . . . H 6 3.55 -56.649 32.507 1 89.42 ? C16 PGV 4001 F 1 HETATM 34 C C17 PGV . . . H 6 2.54 -55.512 32.397 1 89.39 ? C17 PGV 4001 F 1 HETATM 35 C C18 PGV . . . H 6 1.265 -55.979 31.727 1 89.36 ? C18 PGV 4001 F 1 HETATM 36 C C19 PGV . . . H 6 12.404 -52.178 37.446 1 87.39 ? C19 PGV 4001 F 1 HETATM 37 C C20 PGV . . . H 6 11.342 -52.288 38.514 1 86.95 ? C20 PGV 4001 F 1 HETATM 38 C C21 PGV . . . H 6 10.437 -53.474 38.204 1 86.42 ? C21 PGV 4001 F 1 HETATM 39 C C22 PGV . . . H 6 9.119 -53.007 37.599 1 86.01 ? C22 PGV 4001 F 1 HETATM 40 C C23 PGV . . . H 6 7.944 -53.715 38.262 1 85.69 ? C23 PGV 4001 F 1 HETATM 41 C C24 PGV . . . H 6 6.613 -53.227 37.7 1 85.36 ? C24 PGV 4001 F 1 HETATM 42 C C25 PGV . . . H 6 5.546 -54.31 37.817 1 85.05 ? C25 PGV 4001 F 1 HETATM 43 C C26 PGV . . . H 6 4.154 -53.764 37.516 1 84.78 ? C26 PGV 4001 F 1 HETATM 44 C C27 PGV . . . H 6 4.19 -52.732 36.394 1 84.51 ? C27 PGV 4001 F 1 HETATM 45 C C28 PGV . . . H 6 2.831 -52.599 35.717 1 84.25 ? C28 PGV 4001 F 1 HETATM 46 C C29 PGV . . . H 6 2.319 -51.165 35.796 1 84.03 ? C29 PGV 4001 F 1 HETATM 47 C C30 PGV . . . H 6 2.479 -50.452 34.458 1 83.83 ? C30 PGV 4001 F 1 HETATM 48 C C31 PGV . . . H 6 2.155 -48.968 34.583 1 83.65 ? C31 PGV 4001 F 1 HETATM 49 C C32 PGV . . . H 6 0.794 -48.642 33.979 1 83.52 ? C32 PGV 4001 F 1 HETATM 50 C C33 PGV . . . H 6 0.872 -47.407 33.086 1 83.39 ? C33 PGV 4001 F 1 HETATM 51 C C34 PGV . . . H 6 -0.416 -46.613 33.123 1 83.25 ? C34 PGV 4001 F 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 388 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 51 #