data_3D9S # _model_server_result.job_id PVFyhWHrEZsrhOtfXlrjkg _model_server_result.datetime_utc '2025-07-05 03:52:01' _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 3d9s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":266}' # _entry.id 3D9S # _exptl.entry_id 3D9S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 567.65 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description O-[(S)-{[(2S)-2-(hexanoyloxy)-3-(tetradecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-D-serine _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 3D9S _cell.length_a 90.477 _cell.length_b 90.644 _cell.length_c 184.395 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D9S _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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,F,G,H,I _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 2 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C26 H50 N O10 P' _chem_comp.formula_weight 567.65 _chem_comp.id PS6 _chem_comp.mon_nstd_flag . _chem_comp.name O-[(S)-{[(2S)-2-(hexanoyloxy)-3-(tetradecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-D-serine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P O2 PS6 sing 277 n n O2 C2 PS6 sing 278 n n CB O1 PS6 sing 279 n n O1 P PS6 sing 280 n n O4 P PS6 doub 281 n n O3 P PS6 sing 282 n n O3 HO3 PS6 sing 283 n n C2 C3 PS6 sing 284 n n C2 H2 PS6 sing 285 n n C2 H2A PS6 sing 286 n n C3 O11 PS6 sing 287 n n C3 C4 PS6 sing 288 n n C3 H3 PS6 sing 289 n n C1 O11 PS6 sing 290 n n O12 C1 PS6 doub 291 n n C13 C1 PS6 sing 292 n n C4 O52 PS6 sing 293 n n C4 H4 PS6 sing 294 n n C4 H4A PS6 sing 295 n n O52 C5 PS6 sing 296 n n C5 O51 PS6 doub 297 n n C5 C6 PS6 sing 298 n n C13 C14 PS6 sing 299 n n C13 H13 PS6 sing 300 n n C13 H13A PS6 sing 301 n n C15 C14 PS6 sing 302 n n C14 H14 PS6 sing 303 n n C14 H14A PS6 sing 304 n n C15 C16 PS6 sing 305 n n C15 H15 PS6 sing 306 n n C15 H15A PS6 sing 307 n n N CA PS6 sing 308 n n N HN PS6 sing 309 n n N HNA PS6 sing 310 n n CB CA PS6 sing 311 n n CA C PS6 sing 312 n n CA HA PS6 sing 313 n n CB HB PS6 sing 314 n n CB HBA PS6 sing 315 n n OXT C PS6 doub 316 n n C O PS6 sing 317 n n O HO PS6 sing 318 n n C17 C16 PS6 sing 319 n n C16 H16 PS6 sing 320 n n C16 H16A PS6 sing 321 n n C17 H17 PS6 sing 322 n n C17 H17A PS6 sing 323 n n C17 H17B PS6 sing 324 n n C6 C7 PS6 sing 325 n n C6 H6 PS6 sing 326 n n C6 H6A PS6 sing 327 n n C7 C8 PS6 sing 328 n n C7 H7 PS6 sing 329 n n C7 H7A PS6 sing 330 n n C8 C9 PS6 sing 331 n n C8 H8 PS6 sing 332 n n C8 H8A PS6 sing 333 n n C9 C10 PS6 sing 334 n n C9 H9 PS6 sing 335 n n C9 H9A PS6 sing 336 n n C10 C18 PS6 sing 337 n n C10 H10 PS6 sing 338 n n C10 H10A PS6 sing 339 n n C18 C19 PS6 sing 340 n n C18 H18 PS6 sing 341 n n C18 H18A PS6 sing 342 n n C19 C20 PS6 sing 343 n n C19 H19 PS6 sing 344 n n C19 H19A PS6 sing 345 n n C20 C21 PS6 sing 346 n n C20 H20 PS6 sing 347 n n C20 H20A PS6 sing 348 n n C21 C22 PS6 sing 349 n n C21 H21 PS6 sing 350 n n C21 H21A PS6 sing 351 n n C22 C23 PS6 sing 352 n n C22 H22 PS6 sing 353 n n C22 H22A PS6 sing 354 n n C23 C24 PS6 sing 355 n n C23 H23 PS6 sing 356 n n C23 H23A PS6 sing 357 n n C24 C25 PS6 sing 358 n n C24 H24 PS6 sing 359 n n C24 H24A PS6 sing 360 n n C25 H25 PS6 sing 361 n n C25 H25A PS6 sing 362 n n C25 H25B PS6 sing 363 n n # _atom_sites.entry_id 3D9S _atom_sites.fract_transf_matrix[1][1] 0.011053 _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] 0.011032 _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] 0.005423 _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 2 PS6 D 1 266 1 PS6 PS6 . F 3 HOH A 1 266 13 HOH HOH . F 3 HOH A 2 267 14 HOH HOH . F 3 HOH A 3 268 15 HOH HOH . F 3 HOH A 4 269 16 HOH HOH . F 3 HOH A 5 270 17 HOH HOH . F 3 HOH A 6 271 18 HOH HOH . F 3 HOH A 7 272 19 HOH HOH . F 3 HOH A 8 273 28 HOH HOH . F 3 HOH A 9 274 29 HOH HOH . F 3 HOH A 10 275 30 HOH HOH . F 3 HOH A 11 276 39 HOH HOH . F 3 HOH A 12 277 46 HOH HOH . F 3 HOH A 13 278 48 HOH HOH . F 3 HOH A 14 279 50 HOH HOH . F 3 HOH A 15 280 51 HOH HOH . F 3 HOH A 16 281 91 HOH HOH . F 3 HOH A 17 282 92 HOH HOH . F 3 HOH A 18 283 93 HOH HOH . F 3 HOH A 19 284 99 HOH HOH . F 3 HOH A 20 285 100 HOH HOH . F 3 HOH A 21 286 112 HOH HOH . F 3 HOH A 22 287 113 HOH HOH . F 3 HOH A 23 288 114 HOH HOH . F 3 HOH A 24 289 115 HOH HOH . F 3 HOH A 25 290 116 HOH HOH . F 3 HOH A 26 291 117 HOH HOH . G 3 HOH B 1 266 7 HOH HOH . G 3 HOH B 2 267 8 HOH HOH . G 3 HOH B 3 268 9 HOH HOH . G 3 HOH B 4 269 10 HOH HOH . G 3 HOH B 5 270 11 HOH HOH . G 3 HOH B 6 271 12 HOH HOH . G 3 HOH B 7 272 31 HOH HOH . G 3 HOH B 8 273 49 HOH HOH . G 3 HOH B 9 274 52 HOH HOH . G 3 HOH B 10 275 53 HOH HOH . G 3 HOH B 11 276 54 HOH HOH . G 3 HOH B 12 277 55 HOH HOH . G 3 HOH B 13 278 58 HOH HOH . G 3 HOH B 14 279 68 HOH HOH . G 3 HOH B 15 280 72 HOH HOH . G 3 HOH B 16 281 74 HOH HOH . G 3 HOH B 17 282 75 HOH HOH . G 3 HOH B 18 283 81 HOH HOH . G 3 HOH B 19 284 82 HOH HOH . G 3 HOH B 20 285 83 HOH HOH . G 3 HOH B 21 286 84 HOH HOH . G 3 HOH B 22 287 85 HOH HOH . G 3 HOH B 23 288 86 HOH HOH . G 3 HOH B 24 289 87 HOH HOH . G 3 HOH B 25 290 88 HOH HOH . G 3 HOH B 26 291 89 HOH HOH . G 3 HOH B 27 292 110 HOH HOH . H 3 HOH C 1 266 20 HOH HOH . H 3 HOH C 2 267 21 HOH HOH . H 3 HOH C 3 268 23 HOH HOH . H 3 HOH C 4 269 24 HOH HOH . H 3 HOH C 5 270 25 HOH HOH . H 3 HOH C 6 271 26 HOH HOH . H 3 HOH C 7 272 27 HOH HOH . H 3 HOH C 8 273 34 HOH HOH . H 3 HOH C 9 274 35 HOH HOH . H 3 HOH C 10 275 36 HOH HOH . H 3 HOH C 11 276 45 HOH HOH . H 3 HOH C 12 277 59 HOH HOH . H 3 HOH C 13 278 60 HOH HOH . H 3 HOH C 14 279 61 HOH HOH . H 3 HOH C 15 280 62 HOH HOH . H 3 HOH C 16 281 63 HOH HOH . H 3 HOH C 17 282 64 HOH HOH . H 3 HOH C 18 283 65 HOH HOH . H 3 HOH C 19 284 66 HOH HOH . H 3 HOH C 20 285 69 HOH HOH . H 3 HOH C 21 286 70 HOH HOH . H 3 HOH C 22 287 71 HOH HOH . H 3 HOH C 23 288 76 HOH HOH . H 3 HOH C 24 289 77 HOH HOH . H 3 HOH C 25 290 78 HOH HOH . H 3 HOH C 26 291 79 HOH HOH . H 3 HOH C 27 292 80 HOH HOH . H 3 HOH C 28 293 101 HOH HOH . H 3 HOH C 29 294 102 HOH HOH . H 3 HOH C 30 295 103 HOH HOH . H 3 HOH C 31 296 104 HOH HOH . H 3 HOH C 32 297 111 HOH HOH . I 3 HOH D 1 267 1 HOH HOH . I 3 HOH D 2 268 2 HOH HOH . I 3 HOH D 3 269 3 HOH HOH . I 3 HOH D 4 270 4 HOH HOH . I 3 HOH D 5 271 5 HOH HOH . I 3 HOH D 6 272 6 HOH HOH . I 3 HOH D 7 273 32 HOH HOH . I 3 HOH D 8 274 37 HOH HOH . I 3 HOH D 9 275 40 HOH HOH . I 3 HOH D 10 276 41 HOH HOH . I 3 HOH D 11 277 42 HOH HOH . I 3 HOH D 12 278 43 HOH HOH . I 3 HOH D 13 279 44 HOH HOH . I 3 HOH D 14 280 47 HOH HOH . I 3 HOH D 15 281 56 HOH HOH . I 3 HOH D 16 282 57 HOH HOH . I 3 HOH D 17 283 94 HOH HOH . I 3 HOH D 18 284 95 HOH HOH . I 3 HOH D 19 285 96 HOH HOH . I 3 HOH D 20 286 97 HOH HOH . I 3 HOH D 21 287 98 HOH HOH . I 3 HOH D 22 288 105 HOH HOH . I 3 HOH D 23 289 106 HOH HOH . I 3 HOH D 24 290 107 HOH HOH . I 3 HOH D 25 291 108 HOH HOH . I 3 HOH D 26 292 109 HOH HOH . # 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 O O2 PS6 . . . E 2 20.465 1.154 11.098 1 102.93 ? O2 PS6 266 D 1 HETATM 2 O O1 PS6 . . . E 2 19.839 2.338 8.928 1 125.15 ? O1 PS6 266 D 1 HETATM 3 P P PS6 . . . E 2 20.32 0.939 9.528 1 121.12 ? P PS6 266 D 1 HETATM 4 O O4 PS6 . . . E 2 21.56 0.48 8.889 1 154.18 ? O4 PS6 266 D 1 HETATM 5 O O3 PS6 . . . E 2 19.113 -0.076 9.3 1 114.51 ? O3 PS6 266 D 1 HETATM 6 C C2 PS6 . . . E 2 20.177 0.167 12.09 1 84.11 ? C2 PS6 266 D 1 HETATM 7 C C3 PS6 . . . E 2 19.646 0.816 13.356 1 68.44 ? C3 PS6 266 D 1 HETATM 8 O O11 PS6 . . . E 2 18.22 0.786 13.428 1 75.56 ? O11 PS6 266 D 1 HETATM 9 O O12 PS6 . . . E 2 17.633 2.378 11.94 1 38.77 ? O12 PS6 266 D 1 HETATM 10 C C1 PS6 . . . E 2 17.631 1.189 12.276 1 85.89 ? C1 PS6 266 D 1 HETATM 11 C C4 PS6 . . . E 2 20.105 0.12 14.64 1 55.97 ? C4 PS6 266 D 1 HETATM 12 C C5 PS6 . . . E 2 19.425 0.056 16.847 1 33.46 ? C5 PS6 266 D 1 HETATM 13 O O51 PS6 . . . E 2 20.068 -0.995 16.87 1 74.71 ? O51 PS6 266 D 1 HETATM 14 O O52 PS6 . . . E 2 19.192 0.624 15.641 1 53.81 ? O52 PS6 266 D 1 HETATM 15 C C13 PS6 . . . E 2 16.944 0.106 11.433 1 100.05 ? C13 PS6 266 D 1 HETATM 16 C C14 PS6 . . . E 2 17.224 -1.288 12.023 1 103.9 ? C14 PS6 266 D 1 HETATM 17 C C15 PS6 . . . E 2 17.311 -2.325 10.906 1 114.37 ? C15 PS6 266 D 1 HETATM 18 N N PS6 . . . E 2 23.023 3.705 7.865 1 114.43 ? N PS6 266 D 1 HETATM 19 C CA PS6 . . . E 2 21.807 3.812 8.686 1 113.78 ? CA PS6 266 D 1 HETATM 20 C CB PS6 . . . E 2 20.643 3.097 8.005 1 121.59 ? CB PS6 266 D 1 HETATM 21 C C PS6 . . . E 2 21.48 5.281 8.956 1 99.85 ? C PS6 266 D 1 HETATM 22 O O PS6 . . . E 2 22.444 6.053 9.186 1 52.16 ? O PS6 266 D 1 HETATM 23 O OXT PS6 . . . E 2 20.272 5.616 8.933 1 73.81 ? OXT PS6 266 D 1 HETATM 24 C C16 PS6 . . . E 2 18.263 -3.467 11.28 1 122.91 ? C16 PS6 266 D 1 HETATM 25 C C17 PS6 . . . E 2 18.415 -4.441 10.086 1 138.58 ? C17 PS6 266 D 1 HETATM 26 C C6 PS6 . . . E 2 18.891 0.714 18.114 1 26.86 ? C6 PS6 266 D 1 HETATM 27 C C7 PS6 . . . E 2 19.497 0.085 19.374 1 30.93 ? C7 PS6 266 D 1 HETATM 28 C C8 PS6 . . . E 2 18.758 0.527 20.627 1 29.92 ? C8 PS6 266 D 1 HETATM 29 C C9 PS6 . . . E 2 19.255 -0.149 21.894 1 27.66 ? C9 PS6 266 D 1 HETATM 30 C C10 PS6 . . . E 2 19.425 0.835 23.046 1 32.35 ? C10 PS6 266 D 1 HETATM 31 C C18 PS6 . . . E 2 19.458 0.146 24.409 1 31.87 ? C18 PS6 266 D 1 HETATM 32 C C19 PS6 . . . E 2 18.622 0.956 25.406 1 35.57 ? C19 PS6 266 D 1 HETATM 33 C C20 PS6 . . . E 2 18.203 0.123 26.608 1 41.37 ? C20 PS6 266 D 1 HETATM 34 C C21 PS6 . . . E 2 18.539 0.823 27.93 1 50.79 ? C21 PS6 266 D 1 HETATM 35 C C22 PS6 . . . E 2 18.09 -0.015 29.127 1 54.5 ? C22 PS6 266 D 1 HETATM 36 C C23 PS6 . . . E 2 18.008 0.796 30.424 1 57.96 ? C23 PS6 266 D 1 HETATM 37 C C24 PS6 . . . E 2 18.358 -0.064 31.637 1 62.26 ? C24 PS6 266 D 1 HETATM 38 C C25 PS6 . . . E 2 19.171 0.699 32.69 1 70.21 ? C25 PS6 266 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 38 #