data_8EX6 # _model_server_result.job_id 06_Z8Js-4b2akffBF0e_gQ _model_server_result.datetime_utc '2024-11-29 14:25:49' _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 8ex6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8EX6 # _exptl.entry_id 8EX6 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 379.472 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate' _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 8EX6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EX6 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 ? _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 # _chem_comp.formula 'C18 H38 N O5 P' _chem_comp.formula_weight 379.472 _chem_comp.id S1P _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'sphingosine 1-phosphate' # 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 S1P sing 275 n n O1 C1 S1P sing 276 n n C1 H1 S1P sing 277 n n C1 H1A S1P sing 278 n n O1 P22 S1P sing 279 n n C3 C2 S1P sing 280 n n N2 C2 S1P sing 281 n n C2 H2 S1P sing 282 n n N2 HN2 S1P sing 283 n n N2 HN2A S1P sing 284 n n C4 C3 S1P sing 285 n n C3 O3 S1P sing 286 n n C3 H3 S1P sing 287 n n O3 HO3 S1P sing 288 n n C5 C4 S1P doub 289 n n C4 H4 S1P sing 290 e n C6 C5 S1P sing 291 n n C5 H5 S1P sing 292 n n C7 C6 S1P sing 293 n n C6 H6 S1P sing 294 n n C6 H6A S1P sing 295 n n C8 C7 S1P sing 296 n n C7 H7 S1P sing 297 n n C7 H7A S1P sing 298 n n C8 C9 S1P sing 299 n n C8 H8 S1P sing 300 n n C8 H8A S1P sing 301 n n C10 C9 S1P sing 302 n n C9 H9 S1P sing 303 n n C9 H9A S1P sing 304 n n C11 C10 S1P sing 305 n n C10 H10 S1P sing 306 n n C10 H10A S1P sing 307 n n C12 C11 S1P sing 308 n n C11 H11 S1P sing 309 n n C11 H11A S1P sing 310 n n C12 C13 S1P sing 311 n n C12 H12 S1P sing 312 n n C12 H12A S1P sing 313 n n C14 C13 S1P sing 314 n n C13 H13 S1P sing 315 n n C13 H13A S1P sing 316 n n C14 C15 S1P sing 317 n n C14 H14 S1P sing 318 n n C14 H14A S1P sing 319 n n C15 C16 S1P sing 320 n n C15 H15 S1P sing 321 n n C15 H15A S1P sing 322 n n C16 C17 S1P sing 323 n n C16 H16 S1P sing 324 n n C16 H16A S1P sing 325 n n C17 C18 S1P sing 326 n n C17 H17 S1P sing 327 n n C17 H17A S1P sing 328 n n C18 H18 S1P sing 329 n n C18 H18A S1P sing 330 n n C18 H18B S1P sing 331 n n O25 P22 S1P doub 332 n n O24 P22 S1P sing 333 n n P22 O23 S1P sing 334 n n O23 HO23 S1P sing 335 n n O24 HO24 S1P sing 336 n n # _atom_sites.entry_id 8EX6 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id S1P _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 601 _pdbx_nonpoly_scheme.auth_seq_num 601 _pdbx_nonpoly_scheme.pdb_mon_id S1P _pdbx_nonpoly_scheme.auth_mon_id S1P _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C1 S1P . . . B 2 126.883 131.096 116.91 1 48.15 ? C1 S1P 601 A 1 HETATM 2 O O1 S1P . . . B 2 125.642 130.622 117.348 1 48.15 ? O1 S1P 601 A 1 HETATM 3 C C2 S1P . . . B 2 127.454 130.136 115.869 1 48.15 ? C2 S1P 601 A 1 HETATM 4 N N2 S1P . . . B 2 128.867 130.412 115.677 1 48.15 ? N2 S1P 601 A 1 HETATM 5 C C3 S1P . . . B 2 126.718 130.322 114.546 1 48.15 ? C3 S1P 601 A 1 HETATM 6 O O3 S1P . . . B 2 125.958 129.18 114.266 1 48.15 ? O3 S1P 601 A 1 HETATM 7 C C4 S1P . . . B 2 127.74 130.554 113.435 1 48.15 ? C4 S1P 601 A 1 HETATM 8 C C5 S1P . . . B 2 127.536 130.057 112.235 1 48.15 ? C5 S1P 601 A 1 HETATM 9 C C6 S1P . . . B 2 128.56 130.292 111.129 1 48.15 ? C6 S1P 601 A 1 HETATM 10 C C7 S1P . . . B 2 128.209 129.414 109.931 1 48.15 ? C7 S1P 601 A 1 HETATM 11 C C8 S1P . . . B 2 129.411 129.34 108.995 1 48.15 ? C8 S1P 601 A 1 HETATM 12 C C9 S1P . . . B 2 129.256 128.145 108.058 1 48.15 ? C9 S1P 601 A 1 HETATM 13 C C10 S1P . . . B 2 130.586 127.892 107.354 1 48.15 ? C10 S1P 601 A 1 HETATM 14 C C11 S1P . . . B 2 130.324 127.484 105.909 1 48.15 ? C11 S1P 601 A 1 HETATM 15 C C12 S1P . . . B 2 131.628 127.549 105.122 1 48.15 ? C12 S1P 601 A 1 HETATM 16 C C13 S1P . . . B 2 131.317 128.007 103.703 1 48.15 ? C13 S1P 601 A 1 HETATM 17 C C14 S1P . . . B 2 131.727 129.467 103.555 1 48.15 ? C14 S1P 601 A 1 HETATM 18 C C15 S1P . . . B 2 130.786 130.178 102.587 1 48.15 ? C15 S1P 601 A 1 HETATM 19 C C16 S1P . . . B 2 131.626 130.993 101.61 1 48.15 ? C16 S1P 601 A 1 HETATM 20 C C17 S1P . . . B 2 130.89 132.272 101.227 1 48.15 ? C17 S1P 601 A 1 HETATM 21 C C18 S1P . . . B 2 131.795 133.107 100.325 1 48.15 ? C18 S1P 601 A 1 HETATM 22 P P22 S1P . . . B 2 125.165 130.97 118.886 1 48.15 ? P22 S1P 601 A 1 HETATM 23 O O23 S1P . . . B 2 125.028 132.464 119.05 1 48.15 ? O23 S1P 601 A 1 HETATM 24 O O24 S1P . . . B 2 123.837 130.309 119.162 1 48.15 ? O24 S1P 601 A 1 HETATM 25 O O25 S1P . . . B 2 126.194 130.458 119.864 1 48.15 ? O25 S1P 601 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #