data_7EW3 # _model_server_result.job_id rjuevcLQofY4rUkZpB_lgg _model_server_result.datetime_utc '2024-11-26 21:17:48' _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 7ew3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 7EW3 # _exptl.entry_id 7EW3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 379.472 _entity.id 6 _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 7EW3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EW3 _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 D SG CYS 212 R CYS 178 1_555 D SG CYS 219 R CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 D SG CYS 303 R CYS 269 1_555 D SG CYS 308 R CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 E SG CYS 159 S CYS 159 1_555 E SG CYS 229 S CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _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 324 n n O1 C1 S1P sing 325 n n C1 H1 S1P sing 326 n n C1 H1A S1P sing 327 n n O1 P22 S1P sing 328 n n C3 C2 S1P sing 329 n n N2 C2 S1P sing 330 n n C2 H2 S1P sing 331 n n N2 HN2 S1P sing 332 n n N2 HN2A S1P sing 333 n n C4 C3 S1P sing 334 n n C3 O3 S1P sing 335 n n C3 H3 S1P sing 336 n n O3 HO3 S1P sing 337 n n C5 C4 S1P doub 338 n n C4 H4 S1P sing 339 e n C6 C5 S1P sing 340 n n C5 H5 S1P sing 341 n n C7 C6 S1P sing 342 n n C6 H6 S1P sing 343 n n C6 H6A S1P sing 344 n n C8 C7 S1P sing 345 n n C7 H7 S1P sing 346 n n C7 H7A S1P sing 347 n n C8 C9 S1P sing 348 n n C8 H8 S1P sing 349 n n C8 H8A S1P sing 350 n n C10 C9 S1P sing 351 n n C9 H9 S1P sing 352 n n C9 H9A S1P sing 353 n n C11 C10 S1P sing 354 n n C10 H10 S1P sing 355 n n C10 H10A S1P sing 356 n n C12 C11 S1P sing 357 n n C11 H11 S1P sing 358 n n C11 H11A S1P sing 359 n n C12 C13 S1P sing 360 n n C12 H12 S1P sing 361 n n C12 H12A S1P sing 362 n n C14 C13 S1P sing 363 n n C13 H13 S1P sing 364 n n C13 H13A S1P sing 365 n n C14 C15 S1P sing 366 n n C14 H14 S1P sing 367 n n C14 H14A S1P sing 368 n n C15 C16 S1P sing 369 n n C15 H15 S1P sing 370 n n C15 H15A S1P sing 371 n n C16 C17 S1P sing 372 n n C16 H16 S1P sing 373 n n C16 H16A S1P sing 374 n n C17 C18 S1P sing 375 n n C17 H17 S1P sing 376 n n C17 H17A S1P sing 377 n n C18 H18 S1P sing 378 n n C18 H18A S1P sing 379 n n C18 H18B S1P sing 380 n n O25 P22 S1P doub 381 n n O24 P22 S1P sing 382 n n P22 O23 S1P sing 383 n n O23 HO23 S1P sing 384 n n O24 HO24 S1P sing 385 n n # _atom_sites.entry_id 7EW3 _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 # 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 F 6 S1P R 1 401 401 S1P S1P . G 7 PLM R 1 402 1 PLM PLM . H 7 PLM R 1 403 2 PLM PLM . I 7 PLM R 1 404 3 PLM PLM . J 7 PLM R 1 405 4 PLM PLM . # 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 . . . F 6 129.819 114.075 79.915 1 83.8 ? C1 S1P 401 R 1 HETATM 2 O O1 S1P . . . F 6 131.153 113.978 79.49 1 83.8 ? O1 S1P 401 R 1 HETATM 3 C C2 S1P . . . F 6 129.708 113.885 81.409 1 83.8 ? C2 S1P 401 R 1 HETATM 4 N N2 S1P . . . F 6 128.948 112.694 81.586 1 83.8 ? N2 S1P 401 R 1 HETATM 5 C C3 S1P . . . F 6 128.765 114.861 82.021 1 83.8 ? C3 S1P 401 R 1 HETATM 6 O O3 S1P . . . F 6 129.094 116.102 81.553 1 83.8 ? O3 S1P 401 R 1 HETATM 7 C C4 S1P . . . F 6 128.973 114.735 83.509 1 83.8 ? C4 S1P 401 R 1 HETATM 8 C C5 S1P . . . F 6 128.049 114.755 84.431 1 83.8 ? C5 S1P 401 R 1 HETATM 9 C C6 S1P . . . F 6 126.607 114.957 84.116 1 83.8 ? C6 S1P 401 R 1 HETATM 10 C C7 S1P . . . F 6 125.931 115.105 85.435 1 83.8 ? C7 S1P 401 R 1 HETATM 11 C C8 S1P . . . F 6 124.975 116.233 85.323 1 83.8 ? C8 S1P 401 R 1 HETATM 12 C C9 S1P . . . F 6 123.94 115.857 86.269 1 83.8 ? C9 S1P 401 R 1 HETATM 13 C C10 S1P . . . F 6 123.898 116.893 87.324 1 83.8 ? C10 S1P 401 R 1 HETATM 14 C C11 S1P . . . F 6 122.455 117.26 87.362 1 83.8 ? C11 S1P 401 R 1 HETATM 15 C C12 S1P . . . F 6 121.868 117.061 88.705 1 83.8 ? C12 S1P 401 R 1 HETATM 16 C C13 S1P . . . F 6 120.414 116.996 88.615 1 83.8 ? C13 S1P 401 R 1 HETATM 17 C C14 S1P . . . F 6 119.992 116.791 89.988 1 83.8 ? C14 S1P 401 R 1 HETATM 18 C C15 S1P . . . F 6 118.576 117.067 89.949 1 83.8 ? C15 S1P 401 R 1 HETATM 19 C C16 S1P . . . F 6 117.997 116.87 91.269 1 83.8 ? C16 S1P 401 R 1 HETATM 20 C C17 S1P . . . F 6 116.58 117.21 91.045 1 83.8 ? C17 S1P 401 R 1 HETATM 21 C C18 S1P . . . F 6 115.725 116.534 92.069 1 83.8 ? C18 S1P 401 R 1 HETATM 22 P P22 S1P . . . F 6 131.714 113.213 78.171 1 83.8 ? P22 S1P 401 R 1 HETATM 23 O O23 S1P . . . F 6 131.8 113.996 76.949 1 83.8 ? O23 S1P 401 R 1 HETATM 24 O O24 S1P . . . F 6 133.093 113.046 78.574 1 83.8 ? O24 S1P 401 R 1 HETATM 25 O O25 S1P . . . F 6 131.025 111.948 77.99 1 83.8 ? O25 S1P 401 R 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #