data_6ACU # _model_server_result.job_id zwAzU66H5vkTTVgTJH_ifw _model_server_result.datetime_utc '2025-03-01 14:06:20' _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 6acu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 6ACU # _exptl.entry_id 6ACU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPHINGOSINE _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 6ACU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ACU _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? 240-meric 240 'complete icosahedral assembly' 1 ? tetrameric 4 'icosahedral asymmetric unit' 2 ? eicosameric 20 'icosahedral pentamer' 3 ? 24-meric 24 'icosahedral 23 hexamer' 4 ? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 # 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 1 (1-60) A,B,C,D,E 2 1 A,B,C,D,E 3 (1-5) A,B,C,D,E 4 (1,2,6,10,23,24) A,B,C,D,E 5 P # 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] P 'transform to point frame' ? ? 0.809017 0.309017 0.5 -0.5 0.809017 0.309017 -0.309017 -0.5 0.809017 -440.14508 -168.12036 0.00003 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 440.14502 -168.12046 272.02466 3 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 712.16961 272.02459 440.14516 4 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 440.14503 712.16965 272.02468 5 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0 544.04921 0.00002 6 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 544.0492 544.04916 544.04922 7 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 544.04914 544.04922 8 'point symmetry operation' ? ? 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 -168.12045 272.02451 103.90417 9 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 272.02462 103.90406 -168.12043 10 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 712.16967 272.02454 103.90417 11 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 712.16963 272.02475 440.14511 12 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 544.04934 0.00009 0.00002 13 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0.00013 -0.00001 -0.00011 14 'point symmetry operation' ? ? 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 -168.12049 272.02459 440.14489 15 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 272.02447 440.14513 712.1696 16 'point symmetry operation' ? ? 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 -168.12039 272.02447 103.90402 17 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 103.90409 712.16962 272.02445 18 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 544.04916 544.0493 544.04913 19 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 544.04929 0.00009 544.0492 20 'point symmetry operation' ? ? -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 103.9043 -168.1205 272.02455 21 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 544.04929 -0.00005 0.00011 22 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 544.04929 544.04917 0.00004 23 'point symmetry operation' ? ? -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 103.9042 712.16966 272.02458 24 'point symmetry operation' ? ? 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 -168.12043 272.02462 440.14505 25 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 103.9042 -168.12046 272.02468 26 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 -0.00002 544.04926 544.04909 27 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 272.0246 103.90426 712.16967 28 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 440.14518 -168.1204 272.02469 29 'point symmetry operation' ? ? -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 272.02478 103.90411 -168.12045 30 'point symmetry operation' ? ? -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 0.00009 544.04917 -0.00012 31 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 103.90405 712.1696 272.02461 32 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 272.02455 440.14504 -168.12046 33 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 544.0492 0 -0.00003 34 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 544.04917 -0.00004 544.04918 35 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 272.02451 440.14498 712.16966 36 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 440.14513 -168.12042 272.02453 37 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0 -0.00008 544.04909 38 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 -0.00013 544.04913 544.0491 39 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 440.14492 712.1697 272.02456 40 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 712.16965 272.0247 103.90412 41 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 272.02472 440.14509 -168.12044 42 'point symmetry operation' ? ? 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 -168.1204 272.02464 103.90406 43 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 -0.00005 0.00006 544.04918 44 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 544.04916 0.00008 544.04931 45 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 712.16971 272.02467 103.90428 46 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 272.02448 103.90415 712.16963 47 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 544.04907 544.04925 544.04927 48 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 544.04918 544.04929 0.00005 49 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0.809017 0.309017 0.5 272.02466 103.90422 -168.12049 50 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 103.90415 -168.12044 272.02452 51 'point symmetry operation' ? ? -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 0.00009 -0.00003 544.04922 52 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0.00011 -0.00013 0.00001 53 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 272.02468 440.14494 -168.1205 54 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 440.14508 712.16964 272.02452 55 'point symmetry operation' ? ? -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 272.02463 440.14509 712.16962 56 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 544.04917 544.04918 -0.00007 57 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 712.16967 272.02462 440.145 58 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 272.02464 103.9041 712.16961 59 'point symmetry operation' ? ? 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 -168.12045 272.02446 440.145 60 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 -0.00004 544.04908 -0.00007 # _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 # _chem_comp.formula 'C18 H37 N O2' _chem_comp.formula_weight 299.492 _chem_comp.id SPH _chem_comp.mon_nstd_flag . _chem_comp.name SPHINGOSINE _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 C1 O1 SPH sing 288 n n C1 C2 SPH sing 289 n n C1 H11 SPH sing 290 n n C1 H12 SPH sing 291 n n O1 HO1 SPH sing 292 n n C2 N2 SPH sing 293 n n C2 C3 SPH sing 294 n n C2 H2 SPH sing 295 n n N2 HN21 SPH sing 296 n n N2 HN22 SPH sing 297 n n C3 O3 SPH sing 298 n n C3 C4 SPH sing 299 n n C3 H3 SPH sing 300 n n O3 HO3 SPH sing 301 n n C4 C5 SPH doub 302 z n C4 H4 SPH sing 303 n n C5 C6 SPH sing 304 n n C5 H5 SPH sing 305 n n C6 C7 SPH sing 306 n n C6 H61 SPH sing 307 n n C6 H62 SPH sing 308 n n C7 C8 SPH sing 309 n n C7 H71 SPH sing 310 n n C7 H72 SPH sing 311 n n C8 C9 SPH sing 312 n n C8 H81 SPH sing 313 n n C8 H82 SPH sing 314 n n C9 C10 SPH sing 315 n n C9 H91 SPH sing 316 n n C9 H92 SPH sing 317 n n C10 C11 SPH sing 318 n n C10 H101 SPH sing 319 n n C10 H102 SPH sing 320 n n C11 C12 SPH sing 321 n n C11 H111 SPH sing 322 n n C11 H112 SPH sing 323 n n C12 C13 SPH sing 324 n n C12 H121 SPH sing 325 n n C12 H122 SPH sing 326 n n C13 C14 SPH sing 327 n n C13 H131 SPH sing 328 n n C13 H132 SPH sing 329 n n C14 C15 SPH sing 330 n n C14 H141 SPH sing 331 n n C14 H142 SPH sing 332 n n C15 C16 SPH sing 333 n n C15 H151 SPH sing 334 n n C15 H152 SPH sing 335 n n C16 C17 SPH sing 336 n n C16 H161 SPH sing 337 n n C16 H162 SPH sing 338 n n C17 C18 SPH sing 339 n n C17 H171 SPH sing 340 n n C17 H172 SPH sing 341 n n C18 H181 SPH sing 342 n n C18 H182 SPH sing 343 n n C18 H183 SPH sing 344 n n # _atom_sites.entry_id 6ACU _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 SPH _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 300 _pdbx_nonpoly_scheme.auth_seq_num 300 _pdbx_nonpoly_scheme.pdb_mon_id SPH _pdbx_nonpoly_scheme.auth_mon_id SPH _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 SPH . . . E 5 234.453 266.224 402.153 1 12.97 ? C1 SPH 300 A 1 HETATM 2 O O1 SPH . . . E 5 235.72 265.619 402.257 1 12.97 ? O1 SPH 300 A 1 HETATM 3 C C2 SPH . . . E 5 234.268 266.852 400.778 1 12.97 ? C2 SPH 300 A 1 HETATM 4 N N2 SPH . . . E 5 235.411 266.632 399.926 1 12.97 ? N2 SPH 300 A 1 HETATM 5 C C3 SPH . . . E 5 233.079 266.211 400.105 1 12.97 ? C3 SPH 300 A 1 HETATM 6 O O3 SPH . . . E 5 231.991 266.365 400.98 1 12.97 ? O3 SPH 300 A 1 HETATM 7 C C4 SPH . . . E 5 232.798 266.876 398.796 1 12.97 ? C4 SPH 300 A 1 HETATM 8 C C5 SPH . . . E 5 232.873 268.331 398.714 1 12.97 ? C5 SPH 300 A 1 HETATM 9 C C6 SPH . . . E 5 231.595 269.088 398.505 1 12.97 ? C6 SPH 300 A 1 HETATM 10 C C7 SPH . . . E 5 231.025 268.823 397.12 1 12.97 ? C7 SPH 300 A 1 HETATM 11 C C8 SPH . . . E 5 231.289 269.989 396.176 1 12.97 ? C8 SPH 300 A 1 HETATM 12 C C9 SPH . . . E 5 230.843 271.331 396.753 1 12.97 ? C9 SPH 300 A 1 HETATM 13 C C10 SPH . . . E 5 229.33 271.447 396.907 1 12.97 ? C10 SPH 300 A 1 HETATM 14 C C11 SPH . . . E 5 228.94 272.842 397.364 1 12.97 ? C11 SPH 300 A 1 HETATM 15 C C12 SPH . . . E 5 227.751 273.361 396.568 1 12.97 ? C12 SPH 300 A 1 HETATM 16 C C13 SPH . . . E 5 226.409 273.023 397.202 1 12.97 ? C13 SPH 300 A 1 HETATM 17 C C14 SPH . . . E 5 225.322 273.9 396.596 1 12.97 ? C14 SPH 300 A 1 HETATM 18 C C15 SPH . . . E 5 223.993 273.672 397.291 1 12.97 ? C15 SPH 300 A 1 HETATM 19 C C16 SPH . . . E 5 223.238 274.983 397.45 1 12.97 ? C16 SPH 300 A 1 HETATM 20 C C17 SPH . . . E 5 222.598 275.413 396.142 1 12.97 ? C17 SPH 300 A 1 HETATM 21 C C18 SPH . . . E 5 221.517 276.454 396.382 1 12.97 ? C18 SPH 300 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 21 #