data_3PUY # _model_server_result.job_id Gj5TqrzI6VVOf-XZiJ91QA _model_server_result.datetime_utc '2024-11-18 15:32:15' _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 3puy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":4001}' # _entry.id 3PUY # _exptl.entry_id 3PUY _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 86.91 _cell.angle_beta 80.87 _cell.angle_gamma 74.32 _cell.entry_id 3PUY _cell.length_a 76.55 _cell.length_b 96.283 _cell.length_c 112.283 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PUY _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 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,K,L,M,N _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 G _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 2001 MAL 5 n F GLC 2 C 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 covale ? covale1 F O4 GLC . C GLC 1 1_555 F C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 sing metalc ? metalc1 D OG SER 43 A SER 43 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc2 D OE1 GLN 82 A GLN 82 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc3 M O HOH . A HOH 382 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc4 M O HOH . A HOH 383 1_555 H MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc5 H MG MG . A MG 1501 1_555 I O2B ANP . A ANP 2501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc6 H MG MG . A MG 1501 1_555 I O1G ANP . A ANP 2501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc7 E OG SER 43 B SER 43 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc8 E OE1 GLN 82 B GLN 82 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc9 N O HOH . B HOH 382 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc10 N O HOH . B HOH 383 1_555 J MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc11 J MG MG . B MG 1502 1_555 K O2B ANP . B ANP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc12 J MG MG . B MG 1502 1_555 K O1G ANP . B ANP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? # _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 311 n n P O12 PGV sing 312 n n P O13 PGV doub 313 n n P O14 PGV sing 314 n n C01 C02 PGV sing 315 n n C01 O03 PGV sing 316 n n C01 H011 PGV sing 317 n n C01 H012 PGV sing 318 n n C02 C03 PGV sing 319 n n C02 O01 PGV sing 320 n n C02 H02 PGV sing 321 n n C03 O11 PGV sing 322 n n C03 H031 PGV sing 323 n n C03 H032 PGV sing 324 n n C04 C05 PGV sing 325 n n C04 O12 PGV sing 326 n n C04 H041 PGV sing 327 n n C04 H042 PGV sing 328 n n C05 C06 PGV sing 329 n n C05 O05 PGV sing 330 n n C05 H05 PGV sing 331 n n C06 O06 PGV sing 332 n n C06 H061 PGV sing 333 n n C06 H062 PGV sing 334 n n O01 C1 PGV sing 335 n n O02 C1 PGV doub 336 n n O03 C19 PGV sing 337 n n O04 C19 PGV doub 338 n n O05 H1 PGV sing 339 n n O06 H06 PGV sing 340 n n O14 H14 PGV sing 341 n n C1 C2 PGV sing 342 n n C2 C3 PGV sing 343 n n C2 H21 PGV sing 344 n n C2 H22 PGV sing 345 n n C3 C4 PGV sing 346 n n C3 H31 PGV sing 347 n n C3 H32 PGV sing 348 n n C4 C5 PGV sing 349 n n C4 H41 PGV sing 350 n n C4 H42 PGV sing 351 n n C5 C6 PGV sing 352 n n C5 H51 PGV sing 353 n n C5 H52 PGV sing 354 n n C6 C7 PGV sing 355 n n C6 H61 PGV sing 356 n n C6 H62 PGV sing 357 n n C7 C8 PGV sing 358 n n C7 H71 PGV sing 359 n n C7 H72 PGV sing 360 n n C8 C9 PGV sing 361 n n C8 H81 PGV sing 362 n n C8 H82 PGV sing 363 n n C9 C10 PGV sing 364 n n C9 H91 PGV sing 365 n n C9 H92 PGV sing 366 n n C10 C11 PGV sing 367 n n C10 H101 PGV sing 368 n n C10 H102 PGV sing 369 n n C11 C12 PGV doub 370 z n C11 H11 PGV sing 371 n n C12 C13 PGV sing 372 n n C12 H12 PGV sing 373 n n C13 C14 PGV sing 374 n n C13 H131 PGV sing 375 n n C13 H132 PGV sing 376 n n C14 C15 PGV sing 377 n n C14 H141 PGV sing 378 n n C14 H142 PGV sing 379 n n C15 C16 PGV sing 380 n n C15 H151 PGV sing 381 n n C15 H152 PGV sing 382 n n C16 C17 PGV sing 383 n n C16 H161 PGV sing 384 n n C16 H162 PGV sing 385 n n C17 C18 PGV sing 386 n n C17 H171 PGV sing 387 n n C17 H172 PGV sing 388 n n C18 H181 PGV sing 389 n n C18 H182 PGV sing 390 n n C18 H183 PGV sing 391 n n C19 C20 PGV sing 392 n n C20 C21 PGV sing 393 n n C20 H201 PGV sing 394 n n C20 H202 PGV sing 395 n n C21 C22 PGV sing 396 n n C21 H211 PGV sing 397 n n C21 H212 PGV sing 398 n n C22 C23 PGV sing 399 n n C22 H221 PGV sing 400 n n C22 H222 PGV sing 401 n n C23 C24 PGV sing 402 n n C23 H231 PGV sing 403 n n C23 H232 PGV sing 404 n n C24 C25 PGV sing 405 n n C24 H241 PGV sing 406 n n C24 H242 PGV sing 407 n n C25 C26 PGV sing 408 n n C25 H251 PGV sing 409 n n C25 H252 PGV sing 410 n n C26 C27 PGV sing 411 n n C26 H261 PGV sing 412 n n C26 H262 PGV sing 413 n n C27 C28 PGV sing 414 n n C27 H271 PGV sing 415 n n C27 H272 PGV sing 416 n n C28 C29 PGV sing 417 n n C28 H281 PGV sing 418 n n C28 H282 PGV sing 419 n n C29 C30 PGV sing 420 n n C29 H291 PGV sing 421 n n C29 H292 PGV sing 422 n n C30 C31 PGV sing 423 n n C30 H301 PGV sing 424 n n C30 H302 PGV sing 425 n n C31 C32 PGV sing 426 n n C31 H311 PGV sing 427 n n C31 H312 PGV sing 428 n n C32 C33 PGV sing 429 n n C32 H321 PGV sing 430 n n C32 H322 PGV sing 431 n n C33 C34 PGV sing 432 n n C33 H331 PGV sing 433 n n C33 H332 PGV sing 434 n n C34 H341 PGV sing 435 n n C34 H342 PGV sing 436 n n C34 H343 PGV sing 437 n n # _atom_sites.entry_id 3PUY _atom_sites.fract_transf_matrix[1][1] 0.013063 _atom_sites.fract_transf_matrix[1][2] -0.003667 _atom_sites.fract_transf_matrix[1][3] -0.002057 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010787 _atom_sites.fract_transf_matrix[2][3] -0.000125 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009021 _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 G 6 PGV F 1 4001 4001 PGV PGV . H 7 MG A 1 1501 1501 MG MG . I 8 ANP A 1 2501 2501 ANP ANP . J 7 MG B 1 1502 1502 MG MG . K 8 ANP B 1 2502 2502 ANP ANP . L 9 HOH F 1 515 10 HOH HOH . L 9 HOH F 2 516 11 HOH HOH . M 9 HOH A 1 382 1 HOH HOH . M 9 HOH A 2 383 2 HOH HOH . M 9 HOH A 3 384 6 HOH HOH . M 9 HOH A 4 385 7 HOH HOH . M 9 HOH A 5 386 8 HOH HOH . M 9 HOH A 6 387 9 HOH HOH . N 9 HOH B 1 382 3 HOH HOH . N 9 HOH B 2 383 4 HOH HOH . N 9 HOH B 3 384 5 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 PGV . . . G 6 60.863 36.766 10.769 1 111.42 ? P PGV 4001 F 1 HETATM 2 C C01 PGV . . . G 6 58.871 40.045 13.111 1 108.22 ? C01 PGV 4001 F 1 HETATM 3 C C02 PGV . . . G 6 59.448 40.353 11.735 1 110.36 ? C02 PGV 4001 F 1 HETATM 4 C C03 PGV . . . G 6 60.551 39.344 11.418 1 110.93 ? C03 PGV 4001 F 1 HETATM 5 C C04 PGV . . . G 6 61.432 34.544 12.143 1 111.06 ? C04 PGV 4001 F 1 HETATM 6 C C05 PGV . . . G 6 62.415 34.81 13.289 1 110.8 ? C05 PGV 4001 F 1 HETATM 7 C C06 PGV . . . G 6 62.55 33.562 14.159 1 110.15 ? C06 PGV 4001 F 1 HETATM 8 O O01 PGV . . . G 6 59.977 41.683 11.732 1 111.44 ? O01 PGV 4001 F 1 HETATM 9 O O02 PGV . . . G 6 59.698 42.538 9.59 1 114.41 ? O02 PGV 4001 F 1 HETATM 10 O O03 PGV . . . G 6 57.765 39.155 12.971 1 107.27 ? O03 PGV 4001 F 1 HETATM 11 O O04 PGV . . . G 6 56.289 40.177 14.422 1 106.45 ? O04 PGV 4001 F 1 HETATM 12 O O05 PGV . . . G 6 61.976 35.907 14.105 1 110.19 ? O05 PGV 4001 F 1 HETATM 13 O O06 PGV . . . G 6 63.795 32.901 13.895 1 110.59 ? O06 PGV 4001 F 1 HETATM 14 O O11 PGV . . . G 6 60.003 38.027 11.293 1 110.97 ? O11 PGV 4001 F 1 HETATM 15 O O12 PGV . . . G 6 60.566 35.659 11.905 1 110.6 ? O12 PGV 4001 F 1 HETATM 16 O O13 PGV . . . G 6 62.331 37.12 10.8 1 112.05 ? O13 PGV 4001 F 1 HETATM 17 O O14 PGV . . . G 6 60.244 36.298 9.476 1 112.51 ? O14 PGV 4001 F 1 HETATM 18 C C1 PGV . . . G 6 59.363 42.598 10.766 1 113.15 ? C1 PGV 4001 F 1 HETATM 19 C C2 PGV . . . G 6 58.349 43.632 11.22 1 113.29 ? C2 PGV 4001 F 1 HETATM 20 C C3 PGV . . . G 6 57.18 43.76 10.243 1 114.35 ? C3 PGV 4001 F 1 HETATM 21 C C4 PGV . . . G 6 56.325 44.985 10.554 1 115.05 ? C4 PGV 4001 F 1 HETATM 22 C C5 PGV . . . G 6 55.007 44.604 11.224 1 114.34 ? C5 PGV 4001 F 1 HETATM 23 C C6 PGV . . . G 6 54.213 45.839 11.644 1 115.04 ? C6 PGV 4001 F 1 HETATM 24 C C7 PGV . . . G 6 53.517 45.632 12.986 1 113.6 ? C7 PGV 4001 F 1 HETATM 25 C C8 PGV . . . G 6 53.339 46.95 13.736 1 113.95 ? C8 PGV 4001 F 1 HETATM 26 C C9 PGV . . . G 6 53.882 46.861 15.16 1 112.4 ? C9 PGV 4001 F 1 HETATM 27 C C10 PGV . . . G 6 53.317 47.95 16.07 1 112.3 ? C10 PGV 4001 F 1 HETATM 28 C C11 PGV . . . G 6 53.063 47.417 17.478 1 110.35 ? C11 PGV 4001 F 1 HETATM 29 C C12 PGV . . . G 6 51.604 47.594 17.887 1 110.2 ? C12 PGV 4001 F 1 HETATM 30 C C13 PGV . . . G 6 50.837 46.273 17.878 1 109.55 ? C13 PGV 4001 F 1 HETATM 31 C C14 PGV . . . G 6 49.853 46.218 16.713 1 111.24 ? C14 PGV 4001 F 1 HETATM 32 C C15 PGV . . . G 6 48.746 45.191 16.933 1 110.92 ? C15 PGV 4001 F 1 HETATM 33 C C16 PGV . . . G 6 47.382 45.787 16.587 1 112.59 ? C16 PGV 4001 F 1 HETATM 34 C C17 PGV . . . G 6 46.351 44.717 16.235 1 112.86 ? C17 PGV 4001 F 1 HETATM 35 C C18 PGV . . . G 6 44.941 45.272 16.281 1 113.49 ? C18 PGV 4001 F 1 HETATM 36 C C19 PGV . . . G 6 56.431 39.575 13.371 1 106.88 ? C19 PGV 4001 F 1 HETATM 37 C C20 PGV . . . G 6 55.235 39.273 12.501 1 107.35 ? C20 PGV 4001 F 1 HETATM 38 C C21 PGV . . . G 6 54.449 40.554 12.251 1 107.99 ? C21 PGV 4001 F 1 HETATM 39 C C22 PGV . . . G 6 52.971 40.332 12.531 1 108.09 ? C22 PGV 4001 F 1 HETATM 40 C C23 PGV . . . G 6 52.112 40.996 11.461 1 109.86 ? C23 PGV 4001 F 1 HETATM 41 C C24 PGV . . . G 6 50.63 40.737 11.708 1 110.11 ? C24 PGV 4001 F 1 HETATM 42 C C25 PGV . . . G 6 49.966 41.939 12.371 1 110.19 ? C25 PGV 4001 F 1 HETATM 43 C C26 PGV . . . G 6 48.451 41.879 12.224 1 111.23 ? C26 PGV 4001 F 1 HETATM 44 C C27 PGV . . . G 6 47.788 41.471 13.534 1 110.01 ? C27 PGV 4001 F 1 HETATM 45 C C28 PGV . . . G 6 46.819 40.321 13.304 1 110.52 ? C28 PGV 4001 F 1 HETATM 46 C C29 PGV . . . G 6 47.155 39.136 14.198 1 108.89 ? C29 PGV 4001 F 1 HETATM 47 C C30 PGV . . . G 6 45.915 38.678 14.956 1 108.95 ? C30 PGV 4001 F 1 HETATM 48 C C31 PGV . . . G 6 46.118 37.304 15.587 1 108.1 ? C31 PGV 4001 F 1 HETATM 49 C C32 PGV . . . G 6 44.79 36.723 16.061 1 108.51 ? C32 PGV 4001 F 1 HETATM 50 C C33 PGV . . . G 6 44.965 35.82 17.277 1 106.84 ? C33 PGV 4001 F 1 HETATM 51 C C34 PGV . . . G 6 43.824 34.83 17.376 1 107.84 ? C34 PGV 4001 F 1 # _model_server_stats.io_time_ms 151 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 51 #