data_5JDM # _model_server_result.job_id bwhLHXKxbnkoakxbcA_0yw _model_server_result.datetime_utc '2024-11-15 04:13:05' _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 5jdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 5JDM # _exptl.entry_id 5JDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.54 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' _entity.pdbx_number_of_molecules 2 _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 5JDM _cell.length_a 49.802 _cell.length_b 72.267 _cell.length_c 94.839 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDM _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,Q,R,S _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 ? 4 E N N ? 4 F 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 ALA 47 A ALA 47 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc3 A O THR 50 A THR 50 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc7 A O ILE 118 A ILE 118 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc8 A OD1 ASP 121 A ASP 121 1_555 D SR SR . A SR 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc9 A OD2 ASP 121 A ASP 121 1_555 D SR SR . A SR 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc10 A OD2 ASP 127 A ASP 127 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc11 A O THR 209 A THR 209 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc13 A OE1 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc14 A OE2 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc15 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? # _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 5JDM _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] 0.013838 _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] 0.010544 _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 NA A 1 401 1 NA NA . C 2 NA A 1 402 2 NA NA . D 3 SR A 1 403 1 SR SR . E 4 OLC A 1 404 1 OLC MON . F 4 OLC A 1 405 2 OLC MON . G 5 MYS A 1 406 1 MYS FAT . H 5 MYS A 1 407 3 MYS FAT . I 5 MYS A 1 408 4 MYS FAT . J 5 MYS A 1 409 5 MYS FAT . K 5 MYS A 1 410 6 MYS FAT . L 5 MYS A 1 411 7 MYS FAT . M 5 MYS A 1 412 8 MYS FAT . N 5 MYS A 1 413 9 MYS FAT . O 5 MYS A 1 414 11 MYS FAT . P 6 1PE A 1 415 1 1PE PEG . Q 7 P3G A 1 416 2 P3G PEG . R 6 1PE A 1 417 3 1PE PEG . S 8 HOH A 1 501 1 HOH HOH . S 8 HOH A 2 502 5 HOH HOH . S 8 HOH A 3 503 4 HOH HOH . S 8 HOH A 4 504 3 HOH HOH . S 8 HOH A 5 505 2 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 C10 OLC . . . F 4 13.515 31.793 40.261 1 87.27 ? C10 OLC 405 A 1 HETATM 2 C C9 OLC . . . F 4 13.762 30.323 40.665 1 91.24 ? C9 OLC 405 A 1 HETATM 3 C C11 OLC . . . F 4 12.788 32.132 38.995 1 87.53 ? C11 OLC 405 A 1 HETATM 4 C C8 OLC . . . F 4 13.262 29.167 39.802 1 96.75 ? C8 OLC 405 A 1 HETATM 5 C C24 OLC . . . F 4 14.547 22.843 36.98 1 100.29 ? C24 OLC 405 A 1 HETATM 6 C C7 OLC . . . F 4 14.059 29.02 38.491 1 96.06 ? C7 OLC 405 A 1 HETATM 7 C C6 OLC . . . F 4 13.576 27.794 37.692 1 90.66 ? C6 OLC 405 A 1 HETATM 8 C C5 OLC . . . F 4 14.358 27.713 36.378 1 94.59 ? C5 OLC 405 A 1 HETATM 9 C C4 OLC . . . F 4 13.998 26.454 35.578 1 98.7 ? C4 OLC 405 A 1 HETATM 10 C C3 OLC . . . F 4 14.761 26.504 34.245 1 96.74 ? C3 OLC 405 A 1 HETATM 11 C C2 OLC . . . F 4 14.552 25.272 33.343 1 103.42 ? C2 OLC 405 A 1 HETATM 12 C C21 OLC . . . F 4 13.126 23.167 34.903 1 102.93 ? C21 OLC 405 A 1 HETATM 13 C C1 OLC . . . F 4 15.109 23.982 33.978 1 106.92 ? C1 OLC 405 A 1 HETATM 14 C C22 OLC . . . F 4 13.28 22.407 36.231 1 100.02 ? C22 OLC 405 A 1 HETATM 15 O O19 OLC . . . F 4 16.275 23.933 34.375 1 106.74 ? O19 OLC 405 A 1 HETATM 16 O O25 OLC . . . F 4 14.658 22.117 38.209 1 99.99 ? O25 OLC 405 A 1 HETATM 17 O O23 OLC . . . F 4 12.144 22.678 37.053 1 101.44 ? O23 OLC 405 A 1 HETATM 18 O O20 OLC . . . F 4 14.255 22.919 34.058 1 105.52 ? O20 OLC 405 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #