data_6AKS # _model_server_result.job_id kfjLC3HTeoSWu6VVp7WsNw _model_server_result.datetime_utc '2025-02-22 22:45:07' _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 6aks # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 6AKS # _exptl.entry_id 6AKS _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 6AKS _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AKS _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' ? ? 0.16246 -0.5 -0.850651 -0.951057 -0.309017 0 -0.262866 0.809017 -0.525731 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.67082 0.16246 0.723607 -0.688191 0.5 0.525731 -0.276393 -0.850651 0.447214 0 0 0 3 'point symmetry operation' ? ? 0.138197 -0.425325 0.894427 -0.951057 -0.309017 0 0.276393 -0.850651 -0.447214 0 0 0 4 'point symmetry operation' ? ? 0.138197 -0.951057 0.276393 -0.425325 -0.309017 -0.850651 0.894427 0 -0.447214 0 0 0 5 'point symmetry operation' ? ? 0.67082 -0.688191 -0.276393 0.16246 0.5 -0.850651 0.723607 0.525731 0.447214 0 0 0 6 'point symmetry operation' ? ? -0.861803 -0.425325 0.276393 -0.425325 0.309017 -0.850651 0.276393 -0.850651 -0.447214 0 0 0 7 'point symmetry operation' ? ? -0.361803 -0.587785 -0.723607 -0.262866 0.809017 -0.525731 0.894427 0 -0.447214 0 0 0 8 'point symmetry operation' ? ? 0.361803 0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 0.447214 0 0 0 9 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 0 0 0 10 'point symmetry operation' ? ? -0.447214 0.525731 0.723607 -0.850651 0 -0.525731 -0.276393 -0.850651 0.447214 0 0 0 11 'point symmetry operation' ? ? 0.809017 0.587785 0 0.587785 -0.809017 0 0 0 -1 0 0 0 12 'point symmetry operation' ? ? 0.138197 0.425325 0.894427 0.951057 -0.309017 0 0.276393 0.850651 -0.447214 0 0 0 13 'point symmetry operation' ? ? -0.447214 -0.525731 0.723607 0.850651 0 0.525731 -0.276393 0.850651 0.447214 0 0 0 14 'point symmetry operation' ? ? -0.138197 -0.951057 -0.276393 0.425325 -0.309017 0.850651 -0.894427 0 0.447214 0 0 0 15 'point symmetry operation' ? ? 0.638197 -0.262866 -0.723607 0.262866 -0.809017 0.525731 -0.723607 -0.525731 -0.447214 0 0 0 16 'point symmetry operation' ? ? -0.947214 -0.16246 -0.276393 -0.16246 -0.5 0.850651 -0.276393 0.850651 0.447214 0 0 0 17 'point symmetry operation' ? ? -0.447214 0 -0.894427 0 -1 0 -0.894427 0 0.447214 0 0 0 18 'point symmetry operation' ? ? -0.052786 0.688191 -0.723607 0.688191 -0.5 -0.525731 -0.723607 -0.525731 -0.447214 0 0 0 19 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0 0 0 -1 0 0 0 20 'point symmetry operation' ? ? -0.861803 0.425325 0.276393 0.425325 0.309017 0.850651 0.276393 0.850651 -0.447214 0 0 0 21 'point symmetry operation' ? ? 0.052786 0.688191 0.723607 -0.688191 -0.5 0.525731 0.723607 -0.525731 0.447214 0 0 0 22 'point symmetry operation' ? ? -0.638197 -0.262866 0.723607 -0.262866 -0.809017 -0.525731 0.723607 -0.525731 0.447214 0 0 0 23 'point symmetry operation' ? ? -0.447214 -0.850651 -0.276393 0.525731 0 -0.850651 0.723607 -0.525731 0.447214 0 0 0 24 'point symmetry operation' ? ? 0.361803 -0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 0.447214 0 0 0 25 'point symmetry operation' ? ? 0.67082 0.688191 -0.276393 -0.16246 0.5 0.850651 0.723607 -0.525731 0.447214 0 0 0 26 'point symmetry operation' ? ? -0.138197 -0.425325 -0.894427 0.951057 -0.309017 0 -0.276393 -0.850651 0.447214 0 0 0 27 'point symmetry operation' ? ? 0.447214 0.525731 -0.723607 0.850651 0 0.525731 0.276393 -0.850651 -0.447214 0 0 0 28 'point symmetry operation' ? ? 0.138197 0.951057 0.276393 0.425325 -0.309017 0.850651 0.894427 0 -0.447214 0 0 0 29 'point symmetry operation' ? ? -0.638197 0.262866 0.723607 0.262866 -0.809017 0.525731 0.723607 0.525731 0.447214 0 0 0 30 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 0 0 0 31 'point symmetry operation' ? ? 0.447214 -0.525731 -0.723607 -0.850651 0 -0.525731 0.276393 0.850651 -0.447214 0 0 0 32 'point symmetry operation' ? ? 0.861803 0.425325 -0.276393 -0.425325 0.309017 -0.850651 -0.276393 0.850651 0.447214 0 0 0 33 'point symmetry operation' ? ? 0.361803 0.587785 0.723607 -0.262866 0.809017 -0.525731 -0.894427 0 0.447214 0 0 0 34 'point symmetry operation' ? ? -0.361803 -0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 -0.447214 0 0 0 35 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 0 0 0 -1 0 0 0 36 'point symmetry operation' ? ? -0.361803 0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 -0.447214 0 0 0 37 'point symmetry operation' ? ? -0.67082 -0.688191 0.276393 -0.16246 0.5 0.850651 -0.723607 0.525731 -0.447214 0 0 0 38 'point symmetry operation' ? ? -0.052786 -0.688191 -0.723607 -0.688191 -0.5 0.525731 -0.723607 0.525731 -0.447214 0 0 0 39 'point symmetry operation' ? ? 0.638197 0.262866 -0.723607 -0.262866 -0.809017 -0.525731 -0.723607 0.525731 -0.447214 0 0 0 40 'point symmetry operation' ? ? 0.447214 0.850651 0.276393 0.525731 0 -0.850651 -0.723607 0.525731 -0.447214 0 0 0 41 'point symmetry operation' ? ? 0.052786 -0.688191 0.723607 0.688191 -0.5 -0.525731 0.723607 0.525731 0.447214 0 0 0 42 'point symmetry operation' ? ? 0.309017 -0.951057 0 0.951057 0.309017 0 0 0 1 0 0 0 43 'point symmetry operation' ? ? 0.861803 -0.425325 -0.276393 0.425325 0.309017 0.850651 -0.276393 -0.850651 0.447214 0 0 0 44 'point symmetry operation' ? ? 0.947214 0.16246 0.276393 -0.16246 -0.5 0.850651 0.276393 -0.850651 -0.447214 0 0 0 45 'point symmetry operation' ? ? 0.447214 0 0.894427 0 -1 0 0.894427 0 -0.447214 0 0 0 46 'point symmetry operation' ? ? 0.447214 -0.850651 0.276393 -0.525731 0 0.850651 -0.723607 -0.525731 -0.447214 0 0 0 47 'point symmetry operation' ? ? 0.809017 -0.587785 0 -0.587785 -0.809017 0 0 0 -1 0 0 0 48 'point symmetry operation' ? ? 0.947214 -0.16246 0.276393 0.16246 -0.5 -0.850651 0.276393 0.850651 -0.447214 0 0 0 49 'point symmetry operation' ? ? 0.67082 -0.16246 0.723607 0.688191 0.5 -0.525731 -0.276393 0.850651 0.447214 0 0 0 50 'point symmetry operation' ? ? 0.361803 -0.587785 0.723607 0.262866 0.809017 0.525731 -0.894427 0 0.447214 0 0 0 51 'point symmetry operation' ? ? -0.361803 0.587785 -0.723607 0.262866 0.809017 0.525731 0.894427 0 -0.447214 0 0 0 52 'point symmetry operation' ? ? -0.447214 0.850651 -0.276393 -0.525731 0 0.850651 0.723607 0.525731 0.447214 0 0 0 53 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 0 0 0 54 'point symmetry operation' ? ? -0.947214 0.16246 -0.276393 0.16246 -0.5 -0.850651 -0.276393 -0.850651 0.447214 0 0 0 55 'point symmetry operation' ? ? -0.67082 0.16246 -0.723607 0.688191 0.5 -0.525731 0.276393 -0.850651 -0.447214 0 0 0 56 'point symmetry operation' ? ? -0.138197 0.951057 -0.276393 -0.425325 -0.309017 -0.850651 -0.894427 0 0.447214 0 0 0 57 'point symmetry operation' ? ? -0.67082 0.688191 0.276393 0.16246 0.5 -0.850651 -0.723607 -0.525731 -0.447214 0 0 0 58 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 59 'point symmetry operation' ? ? -0.67082 -0.16246 -0.723607 -0.688191 0.5 0.525731 0.276393 0.850651 -0.447214 0 0 0 60 'point symmetry operation' ? ? -0.138197 0.425325 -0.894427 -0.951057 -0.309017 0 -0.276393 0.850651 0.447214 0 0 0 # _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 6AKS _atom_sites.fract_transf_matrix[1][1] 0.002058 _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] 0.002058 _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] 0.002058 _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 -78.482 62.261 -90.973 1 68.15 ? C1 SPH 300 A 1 HETATM 2 O O1 SPH . . . E 5 -78.484 62.277 -92.383 1 66.6 ? O1 SPH 300 A 1 HETATM 3 C C2 SPH . . . E 5 -77.108 62.699 -90.482 1 62.59 ? C2 SPH 300 A 1 HETATM 4 N N2 SPH . . . E 5 -76.624 63.646 -91.46 1 54.63 ? N2 SPH 300 A 1 HETATM 5 C C3 SPH . . . E 5 -77.183 63.346 -89.106 1 44.16 ? C3 SPH 300 A 1 HETATM 6 O O3 SPH . . . E 5 -78.506 63.759 -88.876 1 30.51 ? O3 SPH 300 A 1 HETATM 7 C C4 SPH . . . E 5 -76.748 62.442 -87.978 1 52.36 ? C4 SPH 300 A 1 HETATM 8 C C5 SPH . . . E 5 -77.673 61.538 -87.282 1 37.5 ? C5 SPH 300 A 1 HETATM 9 C C6 SPH . . . E 5 -78.427 62.006 -86.055 1 33.09 ? C6 SPH 300 A 1 HETATM 10 C C7 SPH . . . E 5 -77.706 61.768 -84.735 1 19.66 ? C7 SPH 300 A 1 HETATM 11 C C8 SPH . . . E 5 -78.296 60.606 -83.932 1 30.08 ? C8 SPH 300 A 1 HETATM 12 C C9 SPH . . . E 5 -79.793 60.743 -83.687 1 15.81 ? C9 SPH 300 A 1 HETATM 13 C C10 SPH . . . E 5 -80.491 59.388 -83.64 1 24.79 ? C10 SPH 300 A 1 HETATM 14 C C11 SPH . . . E 5 -82.015 59.508 -83.715 1 26.98 ? C11 SPH 300 A 1 HETATM 15 C C12 SPH . . . E 5 -82.698 59.417 -82.353 1 23.32 ? C12 SPH 300 A 1 HETATM 16 C C13 SPH . . . E 5 -84.144 59.898 -82.386 1 23.03 ? C13 SPH 300 A 1 HETATM 17 C C14 SPH . . . E 5 -84.924 59.507 -81.136 1 28.6 ? C14 SPH 300 A 1 HETATM 18 C C15 SPH . . . E 5 -86.189 60.342 -80.926 1 20.33 ? C15 SPH 300 A 1 HETATM 19 C C16 SPH . . . E 5 -86.907 59.842 -79.673 1 23.17 ? C16 SPH 300 A 1 HETATM 20 C C17 SPH . . . E 5 -88.395 60.165 -79.645 1 21.3 ? C17 SPH 300 A 1 HETATM 21 C C18 SPH . . . E 5 -89.067 59.503 -78.444 1 3.28 ? C18 SPH 300 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 367 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #