data_7YUB # _model_server_result.job_id EKVfVKkQgDjqeAAIoK8wfg _model_server_result.datetime_utc '2024-11-22 20:48:25' _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 7yub # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 7YUB # _exptl.entry_id 7YUB _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # _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 A SG CYS 26 H CYS 26 1_555 A SG CYS 100 H CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 159 H CYS 159 1_555 A SG CYS 215 H CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 25 L CYS 25 1_555 B SG CYS 90 L CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 136 L CYS 136 1_555 B SG CYS 196 L CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 C SG CYS 22 N CYS 22 1_555 C SG CYS 97 N CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _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 7YUB _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 E _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id S1P _pdbx_nonpoly_scheme.pdb_strand_id R _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 . . . E 5 137.405 137.793 122.208 1 61.97 ? C1 S1P 601 R 1 HETATM 2 O O1 S1P . . . E 5 136.457 137.583 123.135 1 61.97 ? O1 S1P 601 R 1 HETATM 3 C C2 S1P . . . E 5 138.578 138.497 122.969 1 61.97 ? C2 S1P 601 R 1 HETATM 4 N N2 S1P . . . E 5 138.132 139.78 123.486 1 61.97 ? N2 S1P 601 R 1 HETATM 5 C C3 S1P . . . E 5 139.798 138.667 122.015 1 61.97 ? C3 S1P 601 R 1 HETATM 6 O O3 S1P . . . E 5 140.337 137.44 121.631 1 61.97 ? O3 S1P 601 R 1 HETATM 7 C C4 S1P . . . E 5 140.8 139.559 122.705 1 61.97 ? C4 S1P 601 R 1 HETATM 8 C C5 S1P . . . E 5 141.944 139.949 122.131 1 61.97 ? C5 S1P 601 R 1 HETATM 9 C C6 S1P . . . E 5 142.369 139.55 120.765 1 61.97 ? C6 S1P 601 R 1 HETATM 10 C C7 S1P . . . E 5 143.838 139.136 120.798 1 61.97 ? C7 S1P 601 R 1 HETATM 11 C C8 S1P . . . E 5 144.445 139.145 119.403 1 61.97 ? C8 S1P 601 R 1 HETATM 12 C C9 S1P . . . E 5 145.966 139.158 119.499 1 61.97 ? C9 S1P 601 R 1 HETATM 13 C C10 S1P . . . E 5 146.602 139.031 118.121 1 61.97 ? C10 S1P 601 R 1 HETATM 14 C C11 S1P . . . E 5 148.115 139.181 118.214 1 61.97 ? C11 S1P 601 R 1 HETATM 15 C C12 S1P . . . E 5 148.771 138.724 116.922 1 61.97 ? C12 S1P 601 R 1 HETATM 16 C C13 S1P . . . E 5 150.144 139.358 116.754 1 61.97 ? C13 S1P 601 R 1 HETATM 17 C C14 S1P . . . E 5 150.008 140.837 116.429 1 61.97 ? C14 S1P 601 R 1 HETATM 18 C C15 S1P . . . E 5 151.282 141.363 115.796 1 61.97 ? C15 S1P 601 R 1 HETATM 19 C C16 S1P . . . E 5 151.207 142.868 115.612 1 61.97 ? C16 S1P 601 R 1 HETATM 20 C C17 S1P . . . E 5 152.431 143.361 114.857 1 61.97 ? C17 S1P 601 R 1 HETATM 21 C C18 S1P . . . E 5 152.604 144.852 115.041 1 61.97 ? C18 S1P 601 R 1 HETATM 22 P P22 S1P . . . E 5 134.698 137.85 122.77 1 61.97 ? P22 S1P 601 R 1 HETATM 23 O O23 S1P . . . E 5 134.415 136.723 121.809 1 61.97 ? O23 S1P 601 R 1 HETATM 24 O O24 S1P . . . E 5 134.653 139.271 122.315 1 61.97 -1 O24 S1P 601 R 1 HETATM 25 O O25 S1P . . . E 5 134.216 137.575 124.207 1 61.97 ? O25 S1P 601 R 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #