data_8SJX # _model_server_result.job_id gSWgLPePZOBJSfBu9VesOw _model_server_result.datetime_utc '2025-09-04 23:46:15' _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 8sjx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":306}' # _entry.id 8SJX # _exptl.entry_id 8SJX _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 703.028 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(E,2S,3R)-2-(hexadecanoylamino)-3-oxidanyl-octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate' _entity.pdbx_number_of_molecules 7 _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 8SJX _cell.length_a 65.5 _cell.length_b 65.5 _cell.length_c 200 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SJX _symmetry.cell_setting ? _symmetry.Int_Tables_number 89 _symmetry.space_group_name_Hall 'P 4 2' _symmetry.space_group_name_H-M 'P 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 131 0 0 3 'crystal symmetry operation' 3_645 -y+1,x-1,z 0 -1 0 1 0 0 0 0 1 65.5 -65.5 0 4 'crystal symmetry operation' 4_665 y+1,-x+1,z 0 1 0 -1 0 0 0 0 1 65.5 65.5 0 5 'crystal symmetry operation' 5_755 -x+2,y,-z -1 0 0 0 1 0 0 0 -1 131 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_645 y+1,x-1,-z 0 1 0 1 0 0 0 0 -1 65.5 -65.5 0 8 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 65.5 65.5 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C39 H79 N2 O6 P' _chem_comp.formula_weight 703.028 _chem_comp.id HWP _chem_comp.mon_nstd_flag . _chem_comp.name '[(E,2S,3R)-2-(hexadecanoylamino)-3-oxidanyl-octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-Palmitoylsphingomyelin # 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 C30 N28 HWP sing 229 n n O24 P22 HWP doub 230 n n N28 C31 HWP sing 231 n n N28 C27 HWP sing 232 n n N28 C29 HWP sing 233 n n C26 C27 HWP sing 234 n n C26 O25 HWP sing 235 n n O17 C16 HWP doub 236 n n C20 O21 HWP sing 237 n n C20 C19 HWP sing 238 n n O25 P22 HWP sing 239 n n P22 O21 HWP sing 240 n n P22 O23 HWP sing 241 n n C16 C15 HWP sing 242 n n C16 N18 HWP sing 243 n n C19 N18 HWP sing 244 n n C19 C32 HWP sing 245 n n C15 C14 HWP sing 246 n n C32 O48 HWP sing 247 n n C32 C33 HWP sing 248 n n C14 C13 HWP sing 249 n n C13 C12 HWP sing 250 n n C33 C34 HWP doub 251 e n C12 C11 HWP sing 252 n n C34 C35 HWP sing 253 n n C11 C10 HWP sing 254 n n C10 C9 HWP sing 255 n n C35 C36 HWP sing 256 n n C8 C9 HWP sing 257 n n C8 C7 HWP sing 258 n n C36 C37 HWP sing 259 n n C6 C7 HWP sing 260 n n C6 C5 HWP sing 261 n n C37 C38 HWP sing 262 n n C5 C4 HWP sing 263 n n C38 C39 HWP sing 264 n n C4 C3 HWP sing 265 n n C39 C40 HWP sing 266 n n C1 C2 HWP sing 267 n n C3 C2 HWP sing 268 n n C40 C41 HWP sing 269 n n C41 C42 HWP sing 270 n n C42 C43 HWP sing 271 n n C43 C44 HWP sing 272 n n C44 C45 HWP sing 273 n n C45 C46 HWP sing 274 n n C46 C47 HWP sing 275 n n C10 H1 HWP sing 276 n n C10 H2 HWP sing 277 n n C13 H3 HWP sing 278 n n C13 H4 HWP sing 279 n n C15 H5 HWP sing 280 n n C15 H6 HWP sing 281 n n C20 H7 HWP sing 282 n n C20 H8 HWP sing 283 n n C26 H9 HWP sing 284 n n C26 H10 HWP sing 285 n n C1 H11 HWP sing 286 n n C1 H12 HWP sing 287 n n C1 H13 HWP sing 288 n n C2 H14 HWP sing 289 n n C2 H15 HWP sing 290 n n C3 H16 HWP sing 291 n n C3 H17 HWP sing 292 n n C4 H18 HWP sing 293 n n C4 H19 HWP sing 294 n n C5 H20 HWP sing 295 n n C5 H21 HWP sing 296 n n C6 H22 HWP sing 297 n n C6 H23 HWP sing 298 n n C7 H24 HWP sing 299 n n C7 H25 HWP sing 300 n n C8 H26 HWP sing 301 n n C8 H27 HWP sing 302 n n C9 H28 HWP sing 303 n n C9 H29 HWP sing 304 n n C11 H30 HWP sing 305 n n C11 H31 HWP sing 306 n n C12 H32 HWP sing 307 n n C12 H33 HWP sing 308 n n C14 H34 HWP sing 309 n n C14 H35 HWP sing 310 n n N18 H36 HWP sing 311 n n C19 H37 HWP sing 312 n n C27 H39 HWP sing 313 n n C27 H40 HWP sing 314 n n C29 H41 HWP sing 315 n n C29 H42 HWP sing 316 n n C29 H43 HWP sing 317 n n C30 H44 HWP sing 318 n n C30 H45 HWP sing 319 n n C30 H46 HWP sing 320 n n C31 H47 HWP sing 321 n n C31 H48 HWP sing 322 n n C31 H49 HWP sing 323 n n C32 H50 HWP sing 324 n n C33 H51 HWP sing 325 n n C34 H52 HWP sing 326 n n C35 H53 HWP sing 327 n n C35 H54 HWP sing 328 n n C36 H55 HWP sing 329 n n C36 H56 HWP sing 330 n n C37 H57 HWP sing 331 n n C37 H58 HWP sing 332 n n C38 H59 HWP sing 333 n n C38 H60 HWP sing 334 n n C39 H61 HWP sing 335 n n C39 H62 HWP sing 336 n n C40 H63 HWP sing 337 n n C40 H64 HWP sing 338 n n C41 H65 HWP sing 339 n n C41 H66 HWP sing 340 n n C42 H67 HWP sing 341 n n C42 H68 HWP sing 342 n n C43 H69 HWP sing 343 n n C43 H70 HWP sing 344 n n C44 H71 HWP sing 345 n n C44 H72 HWP sing 346 n n C45 H73 HWP sing 347 n n C45 H74 HWP sing 348 n n C46 H75 HWP sing 349 n n C46 H76 HWP sing 350 n n C47 H77 HWP sing 351 n n C47 H78 HWP sing 352 n n C47 H79 HWP sing 353 n n O48 H80 HWP sing 354 n n # _atom_sites.entry_id 8SJX _atom_sites.fract_transf_matrix[1][1] 0.015267 _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] 0.015267 _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] 0.005 _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 B 2 HWP A 1 301 301 HWP LSM . C 2 HWP A 1 302 302 HWP LSM . D 2 HWP A 1 303 303 HWP LSM . E 2 HWP A 1 304 304 HWP LSM . F 2 HWP A 1 305 305 HWP LSM . G 2 HWP A 1 306 306 HWP LSM . H 2 HWP A 1 307 307 HWP LSM . I 3 CLR A 1 308 401 CLR CLR . J 4 HOH A 1 401 949 HOH HOH . J 4 HOH A 2 402 932 HOH HOH . J 4 HOH A 3 403 916 HOH HOH . J 4 HOH A 4 404 950 HOH HOH . J 4 HOH A 5 405 969 HOH HOH . J 4 HOH A 6 406 968 HOH HOH . J 4 HOH A 7 407 965 HOH HOH . J 4 HOH A 8 408 925 HOH HOH . J 4 HOH A 9 409 915 HOH HOH . J 4 HOH A 10 410 967 HOH HOH . J 4 HOH A 11 411 970 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 C C10 HWP . . . G 2 49.669 30.352 29.373 1 81.23 ? C10 HWP 306 A 1 HETATM 2 C C13 HWP . . . G 2 47.127 31.101 32.184 1 109.29 ? C13 HWP 306 A 1 HETATM 3 C C15 HWP . . . G 2 46.065 32.788 33.705 1 108.59 ? C15 HWP 306 A 1 HETATM 4 C C20 HWP . . . G 2 49.326 36.149 34.54 1 104.61 ? C20 HWP 306 A 1 HETATM 5 C C26 HWP . . . G 2 48.256 34.071 38.411 1 119.51 ? C26 HWP 306 A 1 HETATM 6 P P22 HWP . . . G 2 50.174 35.64 37.068 1 121.64 ? P22 HWP 306 A 1 HETATM 7 C C3 HWP . . . G 2 58.086 31.08 27.861 1 75.4 ? C3 HWP 306 A 1 HETATM 8 C C4 HWP . . . G 2 56.692 31.141 27.234 1 78.36 ? C4 HWP 306 A 1 HETATM 9 C C5 HWP . . . G 2 55.725 30.302 28.065 1 73.94 ? C5 HWP 306 A 1 HETATM 10 C C6 HWP . . . G 2 54.284 30.491 27.577 1 67.44 ? C6 HWP 306 A 1 HETATM 11 C C7 HWP . . . G 2 53.361 29.84 28.594 1 67.61 ? C7 HWP 306 A 1 HETATM 12 C C8 HWP . . . G 2 51.913 30.209 28.3 1 80.51 ? C8 HWP 306 A 1 HETATM 13 C C9 HWP . . . G 2 51.07 29.773 29.485 1 71.87 ? C9 HWP 306 A 1 HETATM 14 C C11 HWP . . . G 2 48.944 30.138 30.723 1 93.71 ? C11 HWP 306 A 1 HETATM 15 C C12 HWP . . . G 2 47.67 30.999 30.738 1 99.42 ? C12 HWP 306 A 1 HETATM 16 C C14 HWP . . . G 2 46.274 32.368 32.246 1 111.05 ? C14 HWP 306 A 1 HETATM 17 C C16 HWP . . . G 2 46.019 34.316 33.705 1 118.05 ? C16 HWP 306 A 1 HETATM 18 O O17 HWP . . . G 2 45.064 34.936 33.232 1 115.18 ? O17 HWP 306 A 1 HETATM 19 N N18 HWP . . . G 2 47.124 34.972 34.247 1 118.06 ? N18 HWP 306 A 1 HETATM 20 C C19 HWP . . . G 2 48.142 35.812 33.538 1 108.17 ? C19 HWP 306 A 1 HETATM 21 O O21 HWP . . . G 2 49.185 35.403 35.696 1 112.74 ? O21 HWP 306 A 1 HETATM 22 O O23 HWP . . . G 2 49.793 36.898 37.742 1 106.61 ? O23 HWP 306 A 1 HETATM 23 O O24 HWP . . . G 2 51.584 35.381 36.713 1 104.21 ? O24 HWP 306 A 1 HETATM 24 O O25 HWP . . . G 2 49.509 34.255 37.943 1 111.9 ? O25 HWP 306 A 1 HETATM 25 C C27 HWP . . . G 2 47.465 33.146 37.431 1 118.77 ? C27 HWP 306 A 1 HETATM 26 N N28 HWP . . . G 2 46.972 31.829 38.057 1 104.36 ? N28 HWP 306 A 1 HETATM 27 C C29 HWP . . . G 2 48.063 31.223 38.911 1 93.71 ? C29 HWP 306 A 1 HETATM 28 C C30 HWP . . . G 2 46.601 30.856 36.949 1 95.72 ? C30 HWP 306 A 1 HETATM 29 C C31 HWP . . . G 2 45.755 32.103 38.91 1 101.07 ? C31 HWP 306 A 1 HETATM 30 C C32 HWP . . . G 2 48.745 35.057 32.313 1 102.42 ? C32 HWP 306 A 1 HETATM 31 C C33 HWP . . . G 2 47.824 35.139 31.133 1 106.93 ? C33 HWP 306 A 1 HETATM 32 C C34 HWP . . . G 2 47.167 36.264 30.927 1 107.7 ? C34 HWP 306 A 1 HETATM 33 C C35 HWP . . . G 2 46.307 36.146 29.71 1 109.17 ? C35 HWP 306 A 1 HETATM 34 C C36 HWP . . . G 2 47.192 35.521 28.644 1 109.12 ? C36 HWP 306 A 1 HETATM 35 C C37 HWP . . . G 2 46.345 34.805 27.622 1 111.46 ? C37 HWP 306 A 1 HETATM 36 C C38 HWP . . . G 2 47.262 34.121 26.623 1 108.29 ? C38 HWP 306 A 1 HETATM 37 C C39 HWP . . . G 2 46.424 33.28 25.658 1 117.41 ? C39 HWP 306 A 1 HETATM 38 C C40 HWP . . . G 2 47.348 32.804 24.524 1 102.2 ? C40 HWP 306 A 1 HETATM 39 C C41 HWP . . . G 2 46.506 32.098 23.454 1 106.79 ? C41 HWP 306 A 1 HETATM 40 C C42 HWP . . . G 2 47.366 31.913 22.198 1 95.95 ? C42 HWP 306 A 1 HETATM 41 O O48 HWP . . . G 2 50.029 35.535 32.026 1 101.15 ? O48 HWP 306 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #