data_5Z39 # _model_server_result.job_id YFtHnBPeg5bEWb5E46guOw _model_server_result.datetime_utc '2024-11-18 03:19:24' _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 5z39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5Z39 # _exptl.entry_id 5Z39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 691.959 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE _entity.pdbx_number_of_molecules 1 _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 5Z39 _cell.length_a 33.468 _cell.length_b 43.618 _cell.length_c 101.681 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z39 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id O _struct_conn.ptnr1_label_comp_id GLU _struct_conn.ptnr1_label_seq_id 146 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id GLU _struct_conn.ptnr1_auth_seq_id 288 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id NA _struct_conn.ptnr2_label_comp_id NA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NA _struct_conn.ptnr2_auth_seq_id 403 _struct_conn.ptnr2_symmetry 1_555 _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 2.876 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C37 H74 N O8 P' _chem_comp.formula_weight 691.959 _chem_comp.id PEF _chem_comp.mon_nstd_flag . _chem_comp.name DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL # 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 C2 C1 PEF sing 347 n n C2 C3 PEF sing 348 n n C2 O2 PEF sing 349 n n C2 H21 PEF sing 350 n n C1 O3P PEF sing 351 n n C1 H11 PEF sing 352 n n C1 H12 PEF sing 353 n n N C5 PEF sing 354 n n N HN1 PEF sing 355 n n N HN2 PEF sing 356 n n C3 O3 PEF sing 357 n n C3 H31 PEF sing 358 n n C3 H32 PEF sing 359 n n C4 C5 PEF sing 360 n n C4 O4P PEF sing 361 n n C4 H41 PEF sing 362 n n C4 H42 PEF sing 363 n n C5 H51 PEF sing 364 n n C5 H52 PEF sing 365 n n C10 C11 PEF sing 366 n n C10 O4 PEF doub 367 n n C10 O2 PEF sing 368 n n C11 C12 PEF sing 369 n n C11 H112 PEF sing 370 n n C11 H111 PEF sing 371 n n C12 C13 PEF sing 372 n n C12 H122 PEF sing 373 n n C12 H121 PEF sing 374 n n C13 C14 PEF sing 375 n n C13 H132 PEF sing 376 n n C13 H131 PEF sing 377 n n C14 C15 PEF sing 378 n n C14 H142 PEF sing 379 n n C14 H141 PEF sing 380 n n C15 C16 PEF sing 381 n n C15 H152 PEF sing 382 n n C15 H151 PEF sing 383 n n C16 C17 PEF sing 384 n n C16 H162 PEF sing 385 n n C16 H161 PEF sing 386 n n C17 C18 PEF sing 387 n n C17 H172 PEF sing 388 n n C17 H171 PEF sing 389 n n C18 C19 PEF sing 390 n n C18 H182 PEF sing 391 n n C18 H181 PEF sing 392 n n C19 C20 PEF sing 393 n n C19 H192 PEF sing 394 n n C19 H191 PEF sing 395 n n C20 C21 PEF sing 396 n n C20 H202 PEF sing 397 n n C20 H201 PEF sing 398 n n C21 C22 PEF sing 399 n n C21 H212 PEF sing 400 n n C21 H211 PEF sing 401 n n C22 C23 PEF sing 402 n n C22 H222 PEF sing 403 n n C22 H221 PEF sing 404 n n C23 C24 PEF sing 405 n n C23 H232 PEF sing 406 n n C23 H231 PEF sing 407 n n C24 C25 PEF sing 408 n n C24 H242 PEF sing 409 n n C24 H241 PEF sing 410 n n C25 H252 PEF sing 411 n n C25 H251 PEF sing 412 n n C25 H253 PEF sing 413 n n C30 C31 PEF sing 414 n n C30 O5 PEF doub 415 n n C30 O3 PEF sing 416 n n C31 C32 PEF sing 417 n n C31 H312 PEF sing 418 n n C31 H311 PEF sing 419 n n C32 C33 PEF sing 420 n n C32 H322 PEF sing 421 n n C32 H321 PEF sing 422 n n C33 C34 PEF sing 423 n n C33 H332 PEF sing 424 n n C33 H331 PEF sing 425 n n C34 C35 PEF sing 426 n n C34 H342 PEF sing 427 n n C34 H341 PEF sing 428 n n C35 C36 PEF sing 429 n n C35 H352 PEF sing 430 n n C35 H351 PEF sing 431 n n C36 C37 PEF sing 432 n n C36 H362 PEF sing 433 n n C36 H361 PEF sing 434 n n C37 C38 PEF sing 435 n n C37 H372 PEF sing 436 n n C37 H371 PEF sing 437 n n C38 C39 PEF sing 438 n n C38 H382 PEF sing 439 n n C38 H381 PEF sing 440 n n C39 C40 PEF sing 441 n n C39 H392 PEF sing 442 n n C39 H391 PEF sing 443 n n C40 C41 PEF sing 444 n n C40 H402 PEF sing 445 n n C40 H401 PEF sing 446 n n C41 C42 PEF sing 447 n n C41 H412 PEF sing 448 n n C41 H411 PEF sing 449 n n C42 C43 PEF sing 450 n n C42 H422 PEF sing 451 n n C42 H421 PEF sing 452 n n C43 C44 PEF sing 453 n n C43 H432 PEF sing 454 n n C43 H431 PEF sing 455 n n C44 C45 PEF sing 456 n n C44 H442 PEF sing 457 n n C44 H441 PEF sing 458 n n C45 H452 PEF sing 459 n n C45 H451 PEF sing 460 n n C45 H453 PEF sing 461 n n O1P P PEF doub 462 n n O2P P PEF sing 463 n n O2P HOP2 PEF sing 464 n n O3P P PEF sing 465 n n O4P P PEF sing 466 n n # _atom_sites.entry_id 5Z39 _atom_sites.fract_transf_matrix[1][1] 0.029879 _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] 0.022926 _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] 0.009835 _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 B 2 PEF A 1 401 1 PEF PEF . C 3 LHG A 1 402 2 LHG LHG . D 4 NA A 1 403 1 NA NA . E 5 HOH A 1 501 5 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 1 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 3 HOH HOH . E 5 HOH A 6 506 6 HOH HOH . E 5 HOH A 7 507 7 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 C C2 PEF . A . B 2 0.126 -4.662 -20.962 1 61.03 ? C2 PEF 401 A 1 HETATM 2 C C1 PEF . A . B 2 0.211 -5.366 -22.316 1 61.07 ? C1 PEF 401 A 1 HETATM 3 N N PEF . A . B 2 4.455 -3.727 -25.882 0.5 50.38 ? N PEF 401 A 1 HETATM 4 C C3 PEF . A . B 2 1.528 -4.455 -20.403 1 69.07 ? C3 PEF 401 A 1 HETATM 5 C C4 PEF . A . B 2 2.36 -4.836 -25.311 0.5 54.47 ? C4 PEF 401 A 1 HETATM 6 C C5 PEF . A . B 2 3.2 -4.21 -26.42 0.5 50.32 ? C5 PEF 401 A 1 HETATM 7 C C10 PEF . A . B 2 -1.121 -3.014 -19.773 1 61.04 ? C10 PEF 401 A 1 HETATM 8 C C11 PEF . A . B 2 -0.989 -1.603 -19.25 1 58.74 ? C11 PEF 401 A 1 HETATM 9 C C12 PEF . A . B 2 -1.282 -1.572 -17.753 1 48.44 ? C12 PEF 401 A 1 HETATM 10 C C13 PEF . A . B 2 -0.866 -0.24 -17.136 1 44.08 ? C13 PEF 401 A 1 HETATM 11 C C14 PEF . A . B 2 -0.629 -0.38 -15.636 1 52.75 ? C14 PEF 401 A 1 HETATM 12 C C15 PEF . A . B 2 -1.695 0.34 -14.817 1 48.81 ? C15 PEF 401 A 1 HETATM 13 C C16 PEF . A . B 2 -1.156 1.64 -14.231 1 46.91 ? C16 PEF 401 A 1 HETATM 14 C C17 PEF . A . B 2 -2.024 2.126 -13.074 1 57.66 ? C17 PEF 401 A 1 HETATM 15 C C18 PEF . A . B 2 -1.767 1.314 -11.809 1 47.14 ? C18 PEF 401 A 1 HETATM 16 C C19 PEF . A . B 2 -2.768 1.67 -10.715 1 43.56 ? C19 PEF 401 A 1 HETATM 17 C C20 PEF . A . B 2 -2.722 0.644 -9.588 1 47.99 ? C20 PEF 401 A 1 HETATM 18 C C21 PEF . A . B 2 -1.59 0.937 -8.612 1 35.39 ? C21 PEF 401 A 1 HETATM 19 C C22 PEF . A . B 2 -2.129 1.659 -7.386 1 39.05 ? C22 PEF 401 A 1 HETATM 20 C C23 PEF . A . B 2 -3.079 0.775 -6.586 1 34.38 ? C23 PEF 401 A 1 HETATM 21 C C24 PEF . A . B 2 -3.674 1.562 -5.421 1 39.81 ? C24 PEF 401 A 1 HETATM 22 C C25 PEF . A . B 2 -4.308 0.657 -4.387 1 36.82 ? C25 PEF 401 A 1 HETATM 23 C C30 PEF . A . B 2 2.501 -2.279 -21.087 1 68.57 ? C30 PEF 401 A 1 HETATM 24 C C31 PEF . A . B 2 3.864 -1.728 -20.746 1 60.27 ? C31 PEF 401 A 1 HETATM 25 C C32 PEF . A . B 2 3.663 -0.351 -20.125 1 51.18 ? C32 PEF 401 A 1 HETATM 26 C C33 PEF . A . B 2 4.445 -0.214 -18.825 1 43.83 ? C33 PEF 401 A 1 HETATM 27 C C34 PEF . A . B 2 3.759 0.753 -17.866 1 43.99 ? C34 PEF 401 A 1 HETATM 28 C C35 PEF . A . B 2 3.41 2.078 -18.536 1 42.9 ? C35 PEF 401 A 1 HETATM 29 C C36 PEF . A . B 2 3.92 3.258 -17.713 1 41.68 ? C36 PEF 401 A 1 HETATM 30 C C37 PEF . A . B 2 2.844 4.323 -17.528 1 42.59 ? C37 PEF 401 A 1 HETATM 31 C C38 PEF . A . B 2 1.79 3.861 -16.528 1 42.41 ? C38 PEF 401 A 1 HETATM 32 C C39 PEF . A . B 2 0.615 4.832 -16.462 1 38.45 ? C39 PEF 401 A 1 HETATM 33 C C40 PEF . A . B 2 0.869 5.964 -15.473 1 46.49 ? C40 PEF 401 A 1 HETATM 34 C C41 PEF . A . B 2 -0.003 5.839 -14.225 1 46.01 ? C41 PEF 401 A 1 HETATM 35 C C42 PEF . A . B 2 0.498 4.744 -13.288 1 45.52 ? C42 PEF 401 A 1 HETATM 36 C C43 PEF . A . B 2 0.032 4.977 -11.853 1 45.85 ? C43 PEF 401 A 1 HETATM 37 C C44 PEF . A . B 2 0.596 3.915 -10.915 1 42.28 ? C44 PEF 401 A 1 HETATM 38 C C45 PEF . A . B 2 0.434 4.315 -9.465 1 33.67 ? C45 PEF 401 A 1 HETATM 39 O O4 PEF . A . B 2 -1.742 -3.848 -19.136 1 61.41 ? O4 PEF 401 A 1 HETATM 40 O O5 PEF . A . B 2 1.544 -1.528 -21.178 1 62.21 ? O5 PEF 401 A 1 HETATM 41 O O2 PEF . A . B 2 -0.513 -3.386 -21.046 1 65.75 ? O2 PEF 401 A 1 HETATM 42 O O3 PEF . A . B 2 2.308 -3.701 -21.327 1 73.4 ? O3 PEF 401 A 1 HETATM 43 O O1P PEF . A . B 2 -1.452 -4.686 -25.69 1 58.33 ? O1P PEF 401 A 1 HETATM 44 O O2P PEF . A . B 2 0.051 -6.636 -24.855 1 50.98 ? O2P PEF 401 A 1 HETATM 45 O O3P PEF . A . B 2 -0.395 -4.619 -23.373 1 64.13 ? O3P PEF 401 A 1 HETATM 46 O O4P PEF . A . B 2 1.022 -4.375 -25.472 1 48.02 ? O4P PEF 401 A 1 HETATM 47 P P PEF . A . B 2 -0.259 -5.156 -24.891 1 63.57 ? P PEF 401 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 47 #