data_5JDL # _model_server_result.job_id 9wDpRGuFU5cE-OL3SV0aSw _model_server_result.datetime_utc '2024-11-15 03:37:12' _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 5jdl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":407}' # _entry.id 5JDL # _exptl.entry_id 5JDL _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 4 _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 5JDL _cell.length_a 49.764 _cell.length_b 72.622 _cell.length_c 95.616 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDL _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 _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 ? 4 G N N ? 4 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 SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc2 A OE1 GLU 54 A GLU 54 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc3 A OE2 GLU 54 A GLU 54 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc4 A O ILE 118 A ILE 118 1_555 B SR SR . A SR 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc5 A O GLY 122 A GLY 122 1_555 B SR SR . A SR 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc6 A OD2 ASP 127 A ASP 127 1_555 B SR SR . A SR 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc7 A O THR 209 A THR 209 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc8 A OE1 GLU 213 A GLU 213 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc9 A OE2 GLU 213 A GLU 213 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc10 B SR SR . A SR 401 1_555 E O23 OLC . A OLC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc11 B SR SR . A SR 401 1_555 M O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? # _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 5JDL _atom_sites.fract_transf_matrix[1][1] 0.020095 _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] 0.01377 _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] 0.010459 _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 SR A 1 401 2 SR SR . C 2 SR A 1 402 3 SR SR . D 3 CL A 1 403 1 CL CL . E 4 OLC A 1 404 1 OLC MON . F 4 OLC A 1 405 2 OLC MON . G 4 OLC A 1 406 3 OLC MON . H 4 OLC A 1 407 4 OLC MON . I 5 MYS A 1 408 5 MYS FAT . J 5 MYS A 1 409 7 MYS FAT . K 5 MYS A 1 410 8 MYS FAT . L 6 1PE A 1 411 1 1PE PEG . M 7 HOH A 1 501 2 HOH HOH . M 7 HOH A 2 502 1 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 . . . H 4 3.577 1.803 35.05 1 57.6 ? C10 OLC 407 A 1 HETATM 2 C C9 OLC . . . H 4 2.784 2.146 36.325 1 50.82 ? C9 OLC 407 A 1 HETATM 3 C C11 OLC . . . H 4 5.053 2.19 35.154 1 63.88 ? C11 OLC 407 A 1 HETATM 4 C C8 OLC . . . H 4 3.652 2.782 37.416 1 59.64 ? C8 OLC 407 A 1 HETATM 5 C C24 OLC . . . H 4 -6.305 1.42 39.845 1 85.18 ? C24 OLC 407 A 1 HETATM 6 C C12 OLC . . . H 4 5.946 1.6 34.054 1 70.92 ? C12 OLC 407 A 1 HETATM 7 C C7 OLC . . . H 4 3.356 2.284 38.836 1 66.9 ? C7 OLC 407 A 1 HETATM 8 C C15 OLC . . . H 4 6.239 1.903 30.235 1 63.52 ? C15 OLC 407 A 1 HETATM 9 C C13 OLC . . . H 4 5.565 2.079 32.655 1 63.6 ? C13 OLC 407 A 1 HETATM 10 C C6 OLC . . . H 4 1.918 2.574 39.271 1 62.93 ? C6 OLC 407 A 1 HETATM 11 C C14 OLC . . . H 4 6.55 1.448 31.662 1 59.67 ? C14 OLC 407 A 1 HETATM 12 C C5 OLC . . . H 4 1.741 2.074 40.711 1 63.04 ? C5 OLC 407 A 1 HETATM 13 C C4 OLC . . . H 4 0.319 2.337 41.227 1 67.38 ? C4 OLC 407 A 1 HETATM 14 C C3 OLC . . . H 4 0.21 1.835 42.672 1 71.64 ? C3 OLC 407 A 1 HETATM 15 C C2 OLC . . . H 4 -1.188 2.079 43.265 1 78.4 ? C2 OLC 407 A 1 HETATM 16 C C21 OLC . . . H 4 -4.333 1.36 41.4 1 84.56 ? C21 OLC 407 A 1 HETATM 17 C C1 OLC . . . H 4 -2.306 1.343 42.511 1 82.85 ? C1 OLC 407 A 1 HETATM 18 C C22 OLC . . . H 4 -5.182 2.247 40.478 1 85.88 ? C22 OLC 407 A 1 HETATM 19 O O19 OLC . . . H 4 -2.292 0.117 42.403 1 62.43 ? O19 OLC 407 A 1 HETATM 20 O O25 OLC . . . H 4 -7.086 2.256 38.985 1 86.76 ? O25 OLC 407 A 1 HETATM 21 O O23 OLC . . . H 4 -5.73 3.347 41.211 1 103.33 ? O23 OLC 407 A 1 HETATM 22 O O20 OLC . . . H 4 -3.288 2.141 42.001 1 95.99 ? O20 OLC 407 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 22 #