data_8SJY # _model_server_result.job_id p8fWllL26n-oyPnqGz1gGQ _model_server_result.datetime_utc '2024-11-17 22:23:27' _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 8sjy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 8SJY # _exptl.entry_id 8SJY _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 5 _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 8SJY _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 8SJY _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 ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 1 A,B,C,D,E,F,G,H,I,J,K 1 2 A,B,C,D,E,F,G,H,I,J,K 1 3 A,B,C,D,E,F,G,H,I,J,K 1 4 A,B,C,D,E,F,G,H,I,J,K 1 5 A,B,C,D,E,F,G,H,I,J,K 1 6 A,B,C,D,E,F,G,H,I,J,K 1 7 A,B,C,D,E,F,G,H,I,J,K 1 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 # _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 8SJY _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 1 301 302 HWP LSM . C 2 HWP A 1 302 303 HWP LSM . D 2 HWP A 1 303 305 HWP LSM . E 2 HWP A 1 304 306 HWP LSM . F 2 HWP A 1 305 307 HWP LSM . G 3 CLR A 1 306 401 CLR CLR . H 3 CLR A 1 307 402 CLR CLR . I 3 CLR A 1 308 403 CLR CLR . J 3 CLR A 1 309 404 CLR CLR . K 4 HOH A 1 401 912 HOH HOH . K 4 HOH A 2 402 993 HOH HOH . K 4 HOH A 3 403 930 HOH HOH . K 4 HOH A 4 404 925 HOH HOH . K 4 HOH A 5 405 983 HOH HOH . K 4 HOH A 6 406 984 HOH HOH . K 4 HOH A 7 407 981 HOH HOH . K 4 HOH A 8 408 964 HOH HOH . K 4 HOH A 9 409 949 HOH HOH . K 4 HOH A 10 410 982 HOH HOH . K 4 HOH A 11 411 980 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 . . . C 2 50.959 32.287 13.951 1 53.9 ? C10 HWP 302 A 1 HETATM 2 C C13 HWP . . . C 2 50.078 31.34 10.356 1 45.02 ? C13 HWP 302 A 1 HETATM 3 C C15 HWP . . . C 2 49.88 30.49 8.076 1 74.96 ? C15 HWP 302 A 1 HETATM 4 C C20 HWP . . . C 2 52.52 31.542 4.259 1 104.85 ? C20 HWP 302 A 1 HETATM 5 C C26 HWP . . . C 2 51.976 28.484 0.872 1 75.95 ? C26 HWP 302 A 1 HETATM 6 P P22 HWP . . . C 2 53.533 29.329 3.054 1 128.23 ? P22 HWP 302 A 1 HETATM 7 C C1 HWP . . . C 2 45.998 28.158 22.875 1 68.32 ? C1 HWP 302 A 1 HETATM 8 C C2 HWP . . . C 2 47.177 28.947 22.373 1 74.64 ? C2 HWP 302 A 1 HETATM 9 C C3 HWP . . . C 2 47.06 29.113 20.857 1 58.75 ? C3 HWP 302 A 1 HETATM 10 C C4 HWP . . . C 2 48.311 29.804 20.353 1 79.42 ? C4 HWP 302 A 1 HETATM 11 C C5 HWP . . . C 2 48.165 30.159 18.904 1 70.47 ? C5 HWP 302 A 1 HETATM 12 C C6 HWP . . . C 2 49.44 30.869 18.442 1 81.11 ? C6 HWP 302 A 1 HETATM 13 C C7 HWP . . . C 2 49.157 31.381 17.069 1 77.78 ? C7 HWP 302 A 1 HETATM 14 C C8 HWP . . . C 2 50.404 31.853 16.358 1 43.24 ? C8 HWP 302 A 1 HETATM 15 C C9 HWP . . . C 2 49.891 32.198 14.993 1 60.28 ? C9 HWP 302 A 1 HETATM 16 C C11 HWP . . . C 2 50.142 32.017 12.689 1 46.11 ? C11 HWP 302 A 1 HETATM 17 C C12 HWP . . . C 2 51.022 31.82 11.465 1 54.85 ? C12 HWP 302 A 1 HETATM 18 C C14 HWP . . . C 2 50.837 31.178 9.057 1 50.08 ? C14 HWP 302 A 1 HETATM 19 C C16 HWP . . . C 2 50.518 30.502 6.709 1 79.09 ? C16 HWP 302 A 1 HETATM 20 O O17 HWP . . . C 2 50.115 29.778 5.794 1 64.02 ? O17 HWP 302 A 1 HETATM 21 N N18 HWP . . . C 2 51.572 31.369 6.541 1 92.53 ? N18 HWP 302 A 1 HETATM 22 C C19 HWP . . . C 2 52.78 31.117 5.763 1 86.42 ? C19 HWP 302 A 1 HETATM 23 O O21 HWP . . . C 2 52.288 30.404 3.517 1 103.16 ? O21 HWP 302 A 1 HETATM 24 O O23 HWP . . . C 2 54.033 28.58 4.225 1 86.64 ? O23 HWP 302 A 1 HETATM 25 O O24 HWP . . . C 2 54.477 30.019 2.152 1 111.73 ? O24 HWP 302 A 1 HETATM 26 O O25 HWP . . . C 2 52.44 28.309 2.124 1 78.54 ? O25 HWP 302 A 1 HETATM 27 C C27 HWP . . . C 2 50.624 27.712 0.688 1 86.04 ? C27 HWP 302 A 1 HETATM 28 N N28 HWP . . . C 2 50.732 26.172 0.783 1 86.81 ? N28 HWP 302 A 1 HETATM 29 C C29 HWP . . . C 2 52.042 25.706 0.191 1 89.98 ? C29 HWP 302 A 1 HETATM 30 C C30 HWP . . . C 2 49.584 25.536 0.019 1 79.79 ? C30 HWP 302 A 1 HETATM 31 C C31 HWP . . . C 2 50.647 25.743 2.226 1 69.57 ? C31 HWP 302 A 1 HETATM 32 C C32 HWP . . . C 2 53.962 31.93 6.365 1 74.52 ? C32 HWP 302 A 1 HETATM 33 C C33 HWP . . . C 2 55.133 30.994 6.558 1 74.07 ? C33 HWP 302 A 1 HETATM 34 C C34 HWP . . . C 2 55.42 30.615 7.794 1 65.51 ? C34 HWP 302 A 1 HETATM 35 C C35 HWP . . . C 2 54.564 31.156 8.913 1 51.84 ? C35 HWP 302 A 1 HETATM 36 C C36 HWP . . . C 2 55.459 31.37 10.123 1 52.37 ? C36 HWP 302 A 1 HETATM 37 C C37 HWP . . . C 2 54.638 31.905 11.286 1 49.99 ? C37 HWP 302 A 1 HETATM 38 C C38 HWP . . . C 2 55.524 31.969 12.524 1 31.03 ? C38 HWP 302 A 1 HETATM 39 C C39 HWP . . . C 2 54.664 32.283 13.754 1 45.61 ? C39 HWP 302 A 1 HETATM 40 C C40 HWP . . . C 2 55.527 32.021 14.997 1 46.38 ? C40 HWP 302 A 1 HETATM 41 C C41 HWP . . . C 2 54.667 32.147 16.258 1 62.94 ? C41 HWP 302 A 1 HETATM 42 C C42 HWP . . . C 2 55.509 31.691 17.453 1 66.25 ? C42 HWP 302 A 1 HETATM 43 C C43 HWP . . . C 2 54.677 31.742 18.733 1 57.15 ? C43 HWP 302 A 1 HETATM 44 C C44 HWP . . . C 2 55.59 31.373 19.904 1 61.88 ? C44 HWP 302 A 1 HETATM 45 C C45 HWP . . . C 2 54.89 31.698 21.226 1 48.69 ? C45 HWP 302 A 1 HETATM 46 C C46 HWP . . . C 2 55.883 31.49 22.373 1 47.58 ? C46 HWP 302 A 1 HETATM 47 C C47 HWP . . . C 2 55.277 32.014 23.661 1 39.68 ? C47 HWP 302 A 1 HETATM 48 O O48 HWP . . . C 2 54.253 33.019 5.544 1 87.68 ? O48 HWP 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 48 #