data_6LHK # _model_server_result.job_id IOdfLI83PHuHUIRRXIHrcg _model_server_result.datetime_utc '2024-10-19 02:17:50' _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 6lhk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6LHK # _exptl.entry_id 6LHK _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 6LHK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LHK _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 -422.30057 -161.1502 1.05739 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 422.55019 -160.90057 261.15038 3 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 683.29668 261.8039 422.30057 4 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 421.89668 683.95019 260.74649 5 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 -0.40389 522.14649 -0.24962 6 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 522.14648 521.74261 521.89687 7 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 -0.00001 521.49299 521.49298 8 'point symmetry operation' ? ? 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 -160.90058 260.34261 98.94279 9 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 261.80388 99.19242 -161.8037 10 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 683.95018 260.7465 99.5963 11 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 683.95018 262.0535 420.58968 12 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 522.14648 1.05739 -1.71089 13 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 1.30701 -1.307 14 'point symmetry operation' ? ? 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 -160.90058 262.45739 421.24319 15 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 261.80388 423.60758 681.98968 16 'point symmetry operation' ? ? 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 -160.4967 261.80389 97.88541 17 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 100.9033 683.95019 259.4395 18 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 523.20387 522.14649 520.4356 19 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 522.79998 0 520.18598 20 'point symmetry operation' ? ? -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 100.24979 -160.90057 259.0356 21 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 523.20387 0.65351 -0.24962 22 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 522.79998 522.8 0 23 'point symmetry operation' ? ? -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 100.24979 683.70057 261.15038 24 'point symmetry operation' ? ? 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 -160.4967 260.99611 422.30057 25 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 100.9033 -161.15019 260.74649 26 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 1.307 522.79999 521.49299 27 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 262.45738 100.2498 682.39356 28 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 423.60757 -160.49669 259.6891 29 'point symmetry operation' ? ? -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 262.05349 100.90331 -162.4572 30 'point symmetry operation' ? ? -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 1.05738 523.20388 -0.6535 31 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 99.19241 683.29669 259.6891 32 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 260.74649 421.89669 -162.4572 33 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 521.7426 -0.40388 -0.6535 34 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 521.49298 0.00001 521.49299 35 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 260.3426 422.5502 682.39356 36 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 421.89668 -161.15019 259.43949 37 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 -0.40389 0.65351 520.4356 38 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 522.8 520.18598 39 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 422.55019 683.70057 259.0356 40 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 683.29668 260.99611 97.88541 41 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 260.9961 423.60758 -161.8037 42 'point symmetry operation' ? ? 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 -161.1502 262.0535 99.5963 43 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.6535 1.05739 521.89687 44 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 522.79999 1.30701 521.49298 45 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 683.70056 262.45739 98.94279 46 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 260.74649 100.90331 682.64318 47 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 521.7426 523.20389 520.83948 48 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 521.49298 522.79999 -1.30701 49 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0.809017 0.309017 0.5 260.3426 100.2498 -162.20758 50 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 99.19241 -160.49669 260.49688 51 'point symmetry operation' ? ? -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 1.05738 -0.40388 520.83948 52 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 1.307 0 -1.30701 53 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 262.45738 422.5502 -162.20758 54 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 423.60757 683.29669 260.49688 55 'point symmetry operation' ? ? -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 262.05349 421.89669 682.64318 56 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 522.79999 521.49299 -1.307 57 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 683.70056 260.34261 421.24319 58 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 260.9961 99.19242 681.98968 59 'point symmetry operation' ? ? 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 -161.1502 260.7465 420.58968 60 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.6535 521.74261 -1.71089 # _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 6LHK _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 5 224.507 255.248 390.959 1 36.93 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 225.417 254.181 391.12 1 36.93 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 224.286 255.517 389.476 1 36.93 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 225.131 254.612 388.727 1 36.93 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 222.82 255.317 389.112 1 36.93 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 222.044 255.789 390.188 1 36.93 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 222.43 256.056 387.861 1 36.93 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 223.392 256.737 386.982 1 36.93 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 222.905 257.671 385.901 1 36.93 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 221.741 257.067 385.125 1 36.93 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 221.033 258.125 384.281 1 36.93 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 220.545 259.28 385.145 1 36.93 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 219.36 260.016 384.532 1 36.93 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 218.78 261.021 385.523 1 36.93 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 217.932 262.082 384.834 1 36.93 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 216.449 261.734 384.877 1 36.93 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 215.578 262.986 384.924 1 36.93 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 214.134 262.669 384.554 1 36.93 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 213.197 263.831 384.868 1 36.93 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 212.773 264.585 383.613 1 36.93 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 211.651 265.575 383.913 1 36.93 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #