data_3PUZ # _model_server_result.job_id ganv24ER7MoJoRq-sVxmvQ _model_server_result.datetime_utc '2024-11-13 21:31:32' _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 3puz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":4001}' # _entry.id 3PUZ # _exptl.entry_id 3PUZ _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 90.05 _cell.angle_beta 102.57 _cell.angle_gamma 105.01 _cell.entry_id 3PUZ _cell.length_a 80.021 _cell.length_b 93.36 _cell.length_c 119.761 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PUZ _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,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 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 F O4 GLC . C GLC 1 1_555 F C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 sing covale ? covale2 G O4 GLC . D GLC 1 1_555 G C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 sing metalc ? metalc1 D OG SER 43 A SER 43 1_555 I MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc2 D OE1 GLN 82 A GLN 82 1_555 I MG MG . A MG 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc3 I MG MG . A MG 1501 1_555 J O2B ANP . A ANP 2501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc4 E OG SER 43 B SER 43 1_555 K MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc5 E OE1 GLN 82 B GLN 82 1_555 K MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc6 K MG MG . B MG 1502 1_555 L O2B ANP . B ANP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? # _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 3PUZ _atom_sites.fract_transf_matrix[1][1] 0.012497 _atom_sites.fract_transf_matrix[1][2] 0.003351 _atom_sites.fract_transf_matrix[1][3] 0.002995 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01109 _atom_sites.fract_transf_matrix[2][3] 0.000675 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008571 _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 H 6 PGV F 1 4001 4001 PGV PGV . I 7 MG A 1 1501 1501 MG MG . J 8 ANP A 1 2501 2501 ANP ANP . K 7 MG B 1 1502 1502 MG MG . L 8 ANP B 1 2502 2502 ANP ANP . M 9 HOH A 1 382 1 HOH HOH . M 9 HOH A 2 383 3 HOH HOH . M 9 HOH A 3 384 7 HOH HOH . N 9 HOH B 1 382 2 HOH HOH . N 9 HOH B 2 383 4 HOH HOH . N 9 HOH B 3 384 5 HOH HOH . N 9 HOH B 4 385 6 HOH HOH . N 9 HOH B 5 386 8 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 . . . H 6 19.868 -50.316 38.863 1 101.77 ? P PGV 4001 F 1 HETATM 2 C C01 PGV . . . H 6 18.193 -52.709 35.471 1 96.78 ? C01 PGV 4001 F 1 HETATM 3 C C02 PGV . . . H 6 18.393 -53.401 36.813 1 99.5 ? C02 PGV 4001 F 1 HETATM 4 C C03 PGV . . . H 6 19.44 -52.648 37.633 1 101.11 ? C03 PGV 4001 F 1 HETATM 5 C C04 PGV . . . H 6 20.569 -47.896 38.007 1 100.49 ? C04 PGV 4001 F 1 HETATM 6 C C05 PGV . . . H 6 21.151 -47.96 36.599 1 99.43 ? C05 PGV 4001 F 1 HETATM 7 C C06 PGV . . . H 6 21.635 -46.568 36.202 1 99.34 ? C06 PGV 4001 F 1 HETATM 8 O O01 PGV . . . H 6 18.839 -54.738 36.578 1 100.96 ? O01 PGV 4001 F 1 HETATM 9 O O02 PGV . . . H 6 18.115 -55.989 38.378 1 104.68 ? O02 PGV 4001 F 1 HETATM 10 O O03 PGV . . . H 6 17.091 -51.81 35.567 1 95.32 ? O03 PGV 4001 F 1 HETATM 11 O O04 PGV . . . H 6 15.585 -52.47 33.949 1 92.66 ? O04 PGV 4001 F 1 HETATM 12 O O05 PGV . . . H 6 20.157 -48.42 35.673 1 97.6 ? O05 PGV 4001 F 1 HETATM 13 O O06 PGV . . . H 6 21.761 -46.47 34.778 1 97.99 ? O06 PGV 4001 F 1 HETATM 14 O O11 PGV . . . H 6 19.027 -51.304 37.9 1 100.5 ? O11 PGV 4001 F 1 HETATM 15 O O12 PGV . . . H 6 19.557 -48.89 38.177 1 99.98 ? O12 PGV 4001 F 1 HETATM 16 O O13 PGV . . . H 6 21.345 -50.617 38.737 1 102.97 ? O13 PGV 4001 F 1 HETATM 17 O O14 PGV . . . H 6 19.228 -50.338 40.23 1 102.9 ? O14 PGV 4001 F 1 HETATM 18 C C1 PGV . . . H 6 17.997 -55.764 37.183 1 102.63 ? C1 PGV 4001 F 1 HETATM 19 C C2 PGV . . . H 6 17.015 -56.54 36.327 1 102.11 ? C2 PGV 4001 F 1 HETATM 20 C C3 PGV . . . H 6 16.074 -57.414 37.157 1 104.31 ? C3 PGV 4001 F 1 HETATM 21 C C4 PGV . . . H 6 15.363 -58.454 36.295 1 104.12 ? C4 PGV 4001 F 1 HETATM 22 C C5 PGV . . . H 6 13.896 -58.094 36.08 1 103.42 ? C5 PGV 4001 F 1 HETATM 23 C C6 PGV . . . H 6 13.251 -58.98 35.019 1 103.02 ? C6 PGV 4001 F 1 HETATM 24 C C7 PGV . . . H 6 12.76 -58.152 33.836 1 100.91 ? C7 PGV 4001 F 1 HETATM 25 C C8 PGV . . . H 6 12.228 -59.034 32.711 1 100.62 ? C8 PGV 4001 F 1 HETATM 26 C C9 PGV . . . H 6 13.21 -59.105 31.543 1 99.7 ? C9 PGV 4001 F 1 HETATM 27 C C10 PGV . . . H 6 12.61 -59.829 30.34 1 98.84 ? C10 PGV 4001 F 1 HETATM 28 C C11 PGV . . . H 6 12.53 -58.911 29.126 1 96.45 ? C11 PGV 4001 F 1 HETATM 29 C C12 PGV . . . H 6 11.118 -58.892 28.55 1 95.76 ? C12 PGV 4001 F 1 HETATM 30 C C13 PGV . . . H 6 10.423 -57.562 28.814 1 95.11 ? C13 PGV 4001 F 1 HETATM 31 C C14 PGV . . . H 6 8.907 -57.719 28.752 1 95.68 ? C14 PGV 4001 F 1 HETATM 32 C C15 PGV . . . H 6 8.237 -57.109 29.978 1 97.33 ? C15 PGV 4001 F 1 HETATM 33 C C16 PGV . . . H 6 6.72 -57.074 29.821 1 97.87 ? C16 PGV 4001 F 1 HETATM 34 C C17 PGV . . . H 6 6.073 -56.217 30.905 1 98.99 ? C17 PGV 4001 F 1 HETATM 35 C C18 PGV . . . H 6 4.573 -56.142 30.716 1 99.6 ? C18 PGV 4001 F 1 HETATM 36 C C19 PGV . . . H 6 15.767 -52.22 35.129 1 94.08 ? C19 PGV 4001 F 1 HETATM 37 C C20 PGV . . . H 6 14.638 -52.324 36.126 1 94.86 ? C20 PGV 4001 F 1 HETATM 38 C C21 PGV . . . H 6 13.963 -53.688 36.029 1 95.23 ? C21 PGV 4001 F 1 HETATM 39 C C22 PGV . . . H 6 12.605 -53.564 35.351 1 93.88 ? C22 PGV 4001 F 1 HETATM 40 C C23 PGV . . . H 6 11.534 -54.322 36.127 1 95.5 ? C23 PGV 4001 F 1 HETATM 41 C C24 PGV . . . H 6 10.17 -53.656 35.982 1 95.05 ? C24 PGV 4001 F 1 HETATM 42 C C25 PGV . . . H 6 9.269 -54.438 35.033 1 94.49 ? C25 PGV 4001 F 1 HETATM 43 C C26 PGV . . . H 6 7.801 -54.106 35.27 1 95.19 ? C26 PGV 4001 F 1 HETATM 44 C C27 PGV . . . H 6 7.138 -53.618 33.986 1 93.43 ? C27 PGV 4001 F 1 HETATM 45 C C28 PGV . . . H 6 5.666 -53.289 34.211 1 94.41 ? C28 PGV 4001 F 1 HETATM 46 C C29 PGV . . . H 6 5.452 -51.782 34.307 1 93.97 ? C29 PGV 4001 F 1 HETATM 47 C C30 PGV . . . H 6 4.666 -51.261 33.111 1 92.64 ? C30 PGV 4001 F 1 HETATM 48 C C31 PGV . . . H 6 5.242 -49.943 32.607 1 91.19 ? C31 PGV 4001 F 1 HETATM 49 C C32 PGV . . . H 6 4.145 -48.892 32.476 1 91.56 ? C32 PGV 4001 F 1 HETATM 50 C C33 PGV . . . H 6 4.306 -48.073 31.2 1 89.5 ? C33 PGV 4001 F 1 HETATM 51 C C34 PGV . . . H 6 3.19 -47.059 31.066 1 90.1 ? C34 PGV 4001 F 1 # _model_server_stats.io_time_ms 133 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 51 #