data_7TD3 # _model_server_result.job_id USu5nD-KiN44T6NYtt5M3Q _model_server_result.datetime_utc '2024-11-21 14:25:53' _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 7td3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 7TD3 # _exptl.entry_id 7TD3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 379.472 _entity.id 5 _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 7TD3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TD3 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 5 _struct_asym.id E _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 194 R CYS 184 1_555 D SG CYS 201 R CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 D SG CYS 292 R CYS 282 1_555 D SG CYS 297 R CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? covale ? covale1 D ND2 ASN 40 R ASN 30 1_555 F C1 NAG . R NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 305 n n O1 C1 S1P sing 306 n n C1 H1 S1P sing 307 n n C1 H1A S1P sing 308 n n O1 P22 S1P sing 309 n n C3 C2 S1P sing 310 n n N2 C2 S1P sing 311 n n C2 H2 S1P sing 312 n n N2 HN2 S1P sing 313 n n N2 HN2A S1P sing 314 n n C4 C3 S1P sing 315 n n C3 O3 S1P sing 316 n n C3 H3 S1P sing 317 n n O3 HO3 S1P sing 318 n n C5 C4 S1P doub 319 n n C4 H4 S1P sing 320 e n C6 C5 S1P sing 321 n n C5 H5 S1P sing 322 n n C7 C6 S1P sing 323 n n C6 H6 S1P sing 324 n n C6 H6A S1P sing 325 n n C8 C7 S1P sing 326 n n C7 H7 S1P sing 327 n n C7 H7A S1P sing 328 n n C8 C9 S1P sing 329 n n C8 H8 S1P sing 330 n n C8 H8A S1P sing 331 n n C10 C9 S1P sing 332 n n C9 H9 S1P sing 333 n n C9 H9A S1P sing 334 n n C11 C10 S1P sing 335 n n C10 H10 S1P sing 336 n n C10 H10A S1P sing 337 n n C12 C11 S1P sing 338 n n C11 H11 S1P sing 339 n n C11 H11A S1P sing 340 n n C12 C13 S1P sing 341 n n C12 H12 S1P sing 342 n n C12 H12A S1P sing 343 n n C14 C13 S1P sing 344 n n C13 H13 S1P sing 345 n n C13 H13A S1P sing 346 n n C14 C15 S1P sing 347 n n C14 H14 S1P sing 348 n n C14 H14A S1P sing 349 n n C15 C16 S1P sing 350 n n C15 H15 S1P sing 351 n n C15 H15A S1P sing 352 n n C16 C17 S1P sing 353 n n C16 H16 S1P sing 354 n n C16 H16A S1P sing 355 n n C17 C18 S1P sing 356 n n C17 H17 S1P sing 357 n n C17 H17A S1P sing 358 n n C18 H18 S1P sing 359 n n C18 H18A S1P sing 360 n n C18 H18B S1P sing 361 n n O25 P22 S1P doub 362 n n O24 P22 S1P sing 363 n n P22 O23 S1P sing 364 n n O23 HO23 S1P sing 365 n n O24 HO24 S1P sing 366 n n # _atom_sites.entry_id 7TD3 _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 E 5 S1P R 1 401 401 S1P S1P . F 6 NAG R 1 402 402 NAG NAG . # 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 . . . E 5 137.536 136.422 170.941 1 48.4 ? C1 S1P 401 R 1 HETATM 2 O O1 S1P . . . E 5 136.454 136.916 171.561 1 48.4 ? O1 S1P 401 R 1 HETATM 3 C C2 S1P . . . E 5 137.34 136.735 169.415 1 48.4 ? C2 S1P 401 R 1 HETATM 4 N N2 S1P . . . E 5 136.465 135.74 168.84 1 48.4 ? N2 S1P 401 R 1 HETATM 5 C C3 S1P . . . E 5 138.711 136.737 168.694 1 48.4 ? C3 S1P 401 R 1 HETATM 6 O O3 S1P . . . E 5 139.428 137.918 168.872 1 48.4 ? O3 S1P 401 R 1 HETATM 7 C C4 S1P . . . E 5 138.464 136.446 167.257 1 48.4 ? C4 S1P 401 R 1 HETATM 8 C C5 S1P . . . E 5 139.019 135.387 166.683 1 48.4 ? C5 S1P 401 R 1 HETATM 9 C C6 S1P . . . E 5 138.755 135.112 165.264 1 48.4 ? C6 S1P 401 R 1 HETATM 10 C C7 S1P . . . E 5 140.027 134.746 164.533 1 48.4 ? C7 S1P 401 R 1 HETATM 11 C C8 S1P . . . E 5 141.142 135.769 164.8 1 48.4 ? C8 S1P 401 R 1 HETATM 12 C C9 S1P . . . E 5 142.403 135.456 164.001 1 48.4 ? C9 S1P 401 R 1 HETATM 13 C C10 S1P . . . E 5 142.124 135.274 162.522 1 48.4 ? C10 S1P 401 R 1 HETATM 14 C C11 S1P . . . E 5 143.426 135.255 161.745 1 48.4 ? C11 S1P 401 R 1 HETATM 15 C C12 S1P . . . E 5 143.331 134.292 160.581 1 48.4 ? C12 S1P 401 R 1 HETATM 16 C C13 S1P . . . E 5 144.664 134.156 159.88 1 48.4 ? C13 S1P 401 R 1 HETATM 17 C C14 S1P . . . E 5 144.458 133.633 158.477 1 48.4 ? C14 S1P 401 R 1 HETATM 18 C C15 S1P . . . E 5 145.704 132.936 157.972 1 48.4 ? C15 S1P 401 R 1 HETATM 19 C C16 S1P . . . E 5 145.814 133.103 156.475 1 48.4 ? C16 S1P 401 R 1 HETATM 20 C C17 S1P . . . E 5 146.624 131.977 155.875 1 48.4 ? C17 S1P 401 R 1 HETATM 21 C C18 S1P . . . E 5 146.706 132.151 154.378 1 48.4 ? C18 S1P 401 R 1 HETATM 22 P P22 S1P . . . E 5 136.056 136.446 173.264 1 48.4 ? P22 S1P 401 R 1 HETATM 23 O O23 S1P . . . E 5 135.317 135.157 173.047 1 48.4 ? O23 S1P 401 R 1 HETATM 24 O O24 S1P . . . E 5 137.386 136.463 173.936 1 48.4 ? O24 S1P 401 R 1 HETATM 25 O O25 S1P . . . E 5 135.133 137.651 173.521 1 48.4 ? O25 S1P 401 R 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 428 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #