data_8X95 # _model_server_result.job_id 8iiFbL7yoWrh9WCgEh8L_g _model_server_result.datetime_utc '2025-01-23 03:19:46' _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 8x95 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 8X95 # _exptl.entry_id 8X95 _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 8X95 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X95 _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' ? ? 0.309017 -0.5 0.809017 -0.809017 0.309017 0.5 -0.5 -0.809017 -0.309017 -177.18477 0.5 465.68477 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 109.50621 -177.18477 287.30902 3 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 -0.30902 0.5 574.19098 4 'point symmetry operation' ? ? 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 -177.68477 287.5 464.18477 5 'point symmetry operation' ? ? 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 -177.49379 287.19098 109.31523 6 'point symmetry operation' ? ? -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 110.31523 -177.49379 286.19098 7 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 1 0 -1 8 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 288.30902 109.50621 -178.18477 9 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 575.19098 -0.30902 -0.5 10 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 465.18477 -177.68477 286.5 11 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 575.19098 576.30902 574.5 12 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 465.18477 753.68477 287.5 13 'point symmetry operation' ? ? -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 110.31523 753.49379 287.80902 14 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 1 576 575 15 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 288.30902 466.49379 752.18477 16 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 466.49379 753.18477 287.30902 17 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 576.30902 575.5 574.19099 18 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 753.68477 288.5 464.18477 19 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 753.49379 288.80902 109.31523 20 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 576 576 0 21 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 575 0 575 22 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 287.69098 109.50621 752.18477 23 'point symmetry operation' ? ? -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 0.80902 -0.30902 574.5 24 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 110.81523 -177.68477 287.5 25 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 465.68477 -177.49379 287.80902 26 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 288.80902 110.31523 752.49379 27 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 576 1 575 28 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 753.18477 288.30902 465.49379 29 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 575.5 575.19098 575.30902 30 'point symmetry operation' ? ? -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 288.5 465.18477 752.68477 31 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.5 575.19098 -1.30902 32 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 287.5 465.18477 -178.68477 33 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0.809017 0.309017 0.5 287.19098 110.31523 -178.49379 34 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 1 -1 35 'point symmetry operation' ? ? 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 -177.18477 288.30902 108.50621 36 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 287.69098 466.49379 -178.18477 37 'point symmetry operation' ? ? -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 0.80902 576.30902 -0.5 38 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 110.81523 753.68477 286.5 39 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 465.68477 753.49379 286.19098 40 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 575 576 -1 41 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 575 575 42 'point symmetry operation' ? ? 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 -177.18477 287.69098 465.49379 43 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.5 0.80902 575.30902 44 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 287.5 110.81523 752.68477 45 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 287.19098 465.68477 752.49379 46 'point symmetry operation' ? ? 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 -177.49379 288.80902 464.68477 47 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 576 574 48 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 109.50621 753.18477 286.69098 49 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 -0.30902 575.5 -0.19098 50 'point symmetry operation' ? ? 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 -177.68477 288.5 109.81523 51 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 576.30902 0.5 -0.19098 52 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 753.68477 287.5 109.81523 53 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 753.49379 287.19098 464.68477 54 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 576 0 574 55 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 466.49379 -177.18477 286.69098 56 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 753.18477 287.69098 108.50621 57 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 575.5 0.80902 -1.30902 58 'point symmetry operation' ? ? -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 288.5 110.81523 -178.68477 59 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 288.80902 465.68477 -178.49379 60 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 576 575 -1 # _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 8X95 _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 301 _pdbx_nonpoly_scheme.auth_seq_num 301 _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 5 193.886 189.482 303.427 1 36.93 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 193.998 188.631 304.552 1 36.93 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 193.075 190.736 303.732 1 36.93 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 192.549 190.737 305.104 1 36.93 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 193.897 191.987 303.45 1 36.93 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 193.601 192.432 302.161 1 36.93 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 193.647 193.174 304.302 1 36.93 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 193.165 194.266 303.86 1 36.93 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 193.889 195.231 302.984 1 36.93 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 193.011 195.814 301.944 1 36.93 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 192.537 197.207 302.263 1 36.93 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 191.563 197.277 303.391 1 36.93 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 190.409 198.188 303.118 1 36.93 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 189.931 198.961 304.308 1 36.93 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 189.06 200.141 303.974 1 36.93 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 187.825 199.806 303.184 1 36.93 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 186.538 200.301 303.784 1 36.93 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 186.121 201.666 303.324 1 36.93 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 184.635 201.853 303.228 1 36.93 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 184.086 202.972 304.056 1 36.93 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 183.336 204.007 303.276 1 36.93 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #