data_5JDF # _model_server_result.job_id LgHsZy2gpdohzwgY4ydTsA _model_server_result.datetime_utc '2024-11-23 02:27:39' _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 5jdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 5JDF # _exptl.entry_id 5JDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.54 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' _entity.pdbx_number_of_molecules 5 _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 5JDF _cell.length_a 49.801 _cell.length_b 72.258 _cell.length_c 95.803 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDF _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,F,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 50 A THR 50 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A OE1 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 A OE2 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.202 ? metalc ? metalc4 A OE2 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.45 ? metalc ? metalc5 A O ILE 118 A ILE 118 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc6 A OD1 ASP 121 A ASP 121 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc7 A O GLY 122 A GLY 122 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc8 A OD2 ASP 127 A ASP 127 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc9 A O THR 209 A THR 209 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.352 ? metalc ? metalc10 A OE1 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.408 ? metalc ? metalc11 A OE2 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.104 ? metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.348 ? metalc ? metalc13 A OD1 ASP 240 A ASP 240 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 3.096 ? metalc ? metalc14 A OD2 ASP 240 A ASP 240 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.807 ? metalc ? metalc15 B CA CA . A CA 401 1_555 H O25 OLC . A OLC 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc16 B CA CA . A CA 401 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? # _chem_comp.formula 'C21 H40 O4' _chem_comp.formula_weight 356.54 _chem_comp.id OLC _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-Oleoyl-R-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 C18 C17 OLC sing 320 n n C10 C9 OLC doub 321 n n C10 C11 OLC sing 322 n n C9 C8 OLC sing 323 n n C17 C16 OLC sing 324 z n C11 C12 OLC sing 325 n n C8 C7 OLC sing 326 n n C24 C22 OLC sing 327 n n C24 O25 OLC sing 328 n n C16 C15 OLC sing 329 n n C12 C13 OLC sing 330 n n C7 C6 OLC sing 331 n n C15 C14 OLC sing 332 n n C13 C14 OLC sing 333 n n C6 C5 OLC sing 334 n n C5 C4 OLC sing 335 n n C4 C3 OLC sing 336 n n C3 C2 OLC sing 337 n n C2 C1 OLC sing 338 n n C21 C22 OLC sing 339 n n C21 O20 OLC sing 340 n n C1 O19 OLC doub 341 n n C1 O20 OLC sing 342 n n C22 O23 OLC sing 343 n n C18 H18 OLC sing 344 n n C18 H18A OLC sing 345 n n C18 H18B OLC sing 346 n n C10 H10 OLC sing 347 n n C9 H9 OLC sing 348 n n C17 H17 OLC sing 349 n n C17 H17A OLC sing 350 n n C11 H11 OLC sing 351 n n C11 H11A OLC sing 352 n n C8 H8 OLC sing 353 n n C8 H8A OLC sing 354 n n C24 H24 OLC sing 355 n n C24 H24A OLC sing 356 n n C16 H16 OLC sing 357 n n C16 H16A OLC sing 358 n n C12 H12 OLC sing 359 n n C12 H12A OLC sing 360 n n C7 H7 OLC sing 361 n n C7 H7A OLC sing 362 n n C15 H15 OLC sing 363 n n C15 H15A OLC sing 364 n n C13 H13 OLC sing 365 n n C13 H13A OLC sing 366 n n C6 H6 OLC sing 367 n n C6 H6A OLC sing 368 n n C14 H14 OLC sing 369 n n C14 H14A OLC sing 370 n n C5 H5 OLC sing 371 n n C5 H5A OLC sing 372 n n C4 H4 OLC sing 373 n n C4 H4A OLC sing 374 n n C3 H3 OLC sing 375 n n C3 H3A OLC sing 376 n n C2 H2 OLC sing 377 n n C2 H2A OLC sing 378 n n C21 H21 OLC sing 379 n n C21 H21A OLC sing 380 n n C22 H22 OLC sing 381 n n O25 HO25 OLC sing 382 n n O23 HO23 OLC sing 383 n n # _atom_sites.entry_id 5JDF _atom_sites.fract_transf_matrix[1][1] 0.02008 _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] 0.013839 _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] 0.010438 _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 CA A 1 401 1 CA CA . C 2 CA A 1 402 2 CA CA . D 3 OLC A 1 403 1 OLC MON . E 3 OLC A 1 404 3 OLC MON . F 3 OLC A 1 405 4 OLC MON . G 3 OLC A 1 406 5 OLC MON . H 3 OLC A 1 407 6 OLC MON . I 4 MYS A 1 408 15 MYS FAT . J 4 MYS A 1 409 20 MYS FAT . K 4 MYS A 1 410 24 MYS FAT . L 4 MYS A 1 411 25 MYS FAT . M 4 MYS A 1 412 26 MYS FAT . N 4 MYS A 1 413 28 MYS FAT . O 5 1PE A 1 414 1 1PE PEG . P 6 HOH A 1 501 10 HOH HOH . P 6 HOH A 2 502 21 HOH HOH . P 6 HOH A 3 503 12 HOH HOH . P 6 HOH A 4 504 8 HOH HOH . P 6 HOH A 5 505 14 HOH HOH . P 6 HOH A 6 506 24 HOH HOH . P 6 HOH A 7 507 3 HOH HOH . P 6 HOH A 8 508 16 HOH HOH . P 6 HOH A 9 509 5 HOH HOH . P 6 HOH A 10 510 2 HOH HOH . P 6 HOH A 11 511 9 HOH HOH . P 6 HOH A 12 512 11 HOH HOH . P 6 HOH A 13 513 19 HOH HOH . P 6 HOH A 14 514 23 HOH HOH . P 6 HOH A 15 515 17 HOH HOH . P 6 HOH A 16 516 18 HOH HOH . P 6 HOH A 17 517 22 HOH HOH . P 6 HOH A 18 518 20 HOH HOH . P 6 HOH A 19 519 4 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 C24 OLC . . . F 3 13.214 23.57 28.893 1 82.26 ? C24 OLC 405 A 1 HETATM 2 C C21 OLC . . . F 3 14.633 21.619 28.228 1 88.01 ? C21 OLC 405 A 1 HETATM 3 C C1 OLC . . . F 3 15.904 19.84 27.589 1 108.05 ? C1 OLC 405 A 1 HETATM 4 C C22 OLC . . . F 3 13.487 22.537 27.797 1 85.01 ? C22 OLC 405 A 1 HETATM 5 O O19 OLC . . . F 3 15.921 18.625 27.397 1 92.26 ? O19 OLC 405 A 1 HETATM 6 O O25 OLC . . . F 3 12.142 24.425 28.487 1 80.03 ? O25 OLC 405 A 1 HETATM 7 O O23 OLC . . . F 3 13.838 23.203 26.582 1 74.99 ? O23 OLC 405 A 1 HETATM 8 O O20 OLC . . . F 3 14.888 20.657 27.202 1 95.66 ? O20 OLC 405 A 1 # _model_server_stats.io_time_ms 111 _model_server_stats.parse_time_ms 137 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 8 #