data_7C4S # _model_server_result.job_id NmGbU_4PjYQHmbNAQCNClQ _model_server_result.datetime_utc '2024-11-18 01:30:10' _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 7c4s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 7C4S # _exptl.entry_id 7C4S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 379.472 _entity.id 4 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.37 _cell.angle_gamma 90 _cell.entry_id 7C4S _cell.length_a 79.48 _cell.length_b 247.08 _cell.length_c 98.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7C4S _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G 1 1 D,E,F,H 2 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 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 disulf ? disulf1 A SG CYS 23 L CYS 23 1_555 A SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 134 L CYS 134 1_555 A SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 146 H CYS 146 1_555 B SG CYS 201 H CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 C SG CYS 178 A CYS 178 1_555 C SG CYS 185 A CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 C SG CYS 269 A CYS 269 1_555 C SG CYS 274 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf7 D SG CYS 23 K CYS 23 1_555 D SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf8 D SG CYS 134 K CYS 134 1_555 D SG CYS 194 K CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 E SG CYS 22 J CYS 22 1_555 E SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 E SG CYS 146 J CYS 146 1_555 E SG CYS 201 J CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 F SG CYS 178 B CYS 178 1_555 F SG CYS 185 B CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 F SG CYS 269 B CYS 269 1_555 F SG CYS 274 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? # _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 7C4S _atom_sites.fract_transf_matrix[1][1] 0.012582 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001627 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004047 _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] 0.010225 _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 G 4 S1P A 1 1001 1001 S1P S1P . H 4 S1P B 1 401 1002 S1P S1P . # 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 . . . H 4 3.728 49.908 18.512 1 82.69 ? C1 S1P 401 B 1 HETATM 2 O O1 S1P . . . H 4 3.803 49.24 17.258 1 83.27 ? O1 S1P 401 B 1 HETATM 3 C C2 S1P . . . H 4 3.919 51.395 18.255 1 81.27 ? C2 S1P 401 B 1 HETATM 4 N N2 S1P . . . H 4 5.277 51.774 18.661 1 81.72 ? N2 S1P 401 B 1 HETATM 5 C C3 S1P . . . H 4 2.874 52.154 19.069 1 77.24 ? C3 S1P 401 B 1 HETATM 6 O O3 S1P . . . H 4 1.727 52.385 18.253 1 77.93 ? O3 S1P 401 B 1 HETATM 7 C C4 S1P . . . H 4 3.45 53.47 19.507 1 79.92 ? C4 S1P 401 B 1 HETATM 8 C C5 S1P . . . H 4 2.943 54.075 20.543 1 80.7 ? C5 S1P 401 B 1 HETATM 9 C C6 S1P . . . H 4 3.521 55.387 20.989 1 79.9 ? C6 S1P 401 B 1 HETATM 10 C C7 S1P . . . H 4 2.9 55.746 22.336 1 79.44 ? C7 S1P 401 B 1 HETATM 11 C C8 S1P . . . H 4 2.633 57.246 22.33 1 82.14 ? C8 S1P 401 B 1 HETATM 12 C C9 S1P . . . H 4 1.603 57.585 23.401 1 80.35 ? C9 S1P 401 B 1 HETATM 13 C C10 S1P . . . H 4 1.858 59.038 23.792 1 81.37 ? C10 S1P 401 B 1 HETATM 14 C C11 S1P . . . H 4 1.203 59.344 25.134 1 80.06 ? C11 S1P 401 B 1 HETATM 15 C C12 S1P . . . H 4 1.603 60.764 25.521 1 79.58 ? C12 S1P 401 B 1 HETATM 16 C C13 S1P . . . H 4 1.418 60.923 27.023 1 76.16 ? C13 S1P 401 B 1 HETATM 17 C C14 S1P . . . H 4 1.188 62.397 27.331 1 75.08 ? C14 S1P 401 B 1 HETATM 18 C C15 S1P . . . H 4 1.783 62.653 28.711 1 76.35 ? C15 S1P 401 B 1 HETATM 19 C C16 S1P . . . H 4 0.975 63.735 29.423 1 80.83 ? C16 S1P 401 B 1 HETATM 20 C C17 S1P . . . H 4 1.266 63.63 30.92 1 84.33 ? C17 S1P 401 B 1 HETATM 21 C C18 S1P . . . H 4 0.682 64.834 31.655 1 87.27 ? C18 S1P 401 B 1 HETATM 22 P P22 S1P . . . H 4 3.968 47.649 17.207 1 80.87 ? P22 S1P 401 B 1 HETATM 23 O O23 S1P . . . H 4 2.964 47.042 18.31 1 80.92 ? O23 S1P 401 B 1 HETATM 24 O O24 S1P . . . H 4 3.587 47.125 15.734 1 84.38 ? O24 S1P 401 B 1 HETATM 25 O O25 S1P . . . H 4 5.364 47.287 17.548 1 80.2 ? O25 S1P 401 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #