data_9F5P # _model_server_result.job_id SruMfvzVjoFH6cGB_C47CA _model_server_result.datetime_utc '2025-02-05 03:33:47' _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 9f5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 9F5P # _exptl.entry_id 9F5P _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 4 _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 9F5P _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9F5P _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 180-meric _pdbx_struct_assembly.oligomeric_count 180 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60 # 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 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 420.81218 421.33152 421.6525 3 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 -0.4608 421.5476 421.0868 4 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 210.70012 551.62007 80.55265 5 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 210.52022 551.73125 340.62888 6 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 551.27045 340.70388 210.90602 7 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 340.24308 210.98102 551.65625 8 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 551.05438 341.26957 210.9162 9 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 210.1706 551.51518 80.27803 10 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 340.80877 210.6314 -129.96758 11 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 421.0868 421.1618 -0.075 12 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 551.15927 80.62765 211.08592 13 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 420.87072 421.7275 421.19798 14 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 551.27045 80.91872 210.56658 15 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 340.24308 210.64158 -130.18365 16 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 210.52022 -130.10865 80.84372 17 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 420.87072 -0.1049 0.27462 18 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 421.0868 0.4608 421.5476 19 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 551.15927 340.99495 210.38668 20 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 421.1618 0.075 421.0868 21 'point symmetry operation' ? ? -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 210.00088 -129.99747 80.55265 22 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 -0.11118 0.29108 421.6525 23 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 210.1706 -129.89258 341.19457 24 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 340.80877 210.9912 551.44018 25 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 551.05438 80.35303 210.5564 26 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 340.53415 210.46168 551.54507 27 'point symmetry operation' ? ? -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 -0.5657 0.34962 421.25652 28 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 421.6226 421.4726 29 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 80.16685 211.16092 551.54507 30 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 421.2667 421.27298 421.25652 31 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 420.701 0 421.4726 32 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 -0.11118 421.33152 -0.1799 33 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 421.1618 421.5476 0.3858 34 'point symmetry operation' ? ? -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 210.00088 551.62007 340.91995 35 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 210.18078 551.73125 80.84372 36 'point symmetry operation' ? ? 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 -130.56945 340.70388 210.56658 37 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 80.45792 210.98102 -130.18365 38 'point symmetry operation' ? ? 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 -130.35338 341.26957 210.5564 39 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 210.5304 551.51518 341.19457 40 'point symmetry operation' ? ? -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 79.89223 210.6314 551.44018 41 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 -0.3858 421.1618 421.5476 42 'point symmetry operation' ? ? 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 -130.45827 80.62765 210.38668 43 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 -0.16972 421.7275 0.27462 44 'point symmetry operation' ? ? 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 -130.56945 80.91872 210.90602 45 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 80.45792 210.64158 551.65625 46 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 210.18078 -130.10865 340.62888 47 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 -0.16972 -0.1049 421.19798 48 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 -0.3858 0.4608 -0.075 49 'point symmetry operation' ? ? 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 -130.45827 340.99495 211.08592 50 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 -0.4608 0.075 0.3858 51 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 210.70012 -129.99747 340.91995 52 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 420.81218 0.29108 -0.1799 53 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 210.5304 -129.89258 80.27803 54 'point symmetry operation' ? ? -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 79.89223 210.9912 -129.96758 55 'point symmetry operation' ? ? 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 -130.35338 80.35303 210.9162 56 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 0.5 0.309017 0.809017 80.16685 210.46168 -130.07247 57 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 421.2667 0.34962 0.21608 58 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 420.701 421.6226 0 59 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 340.53415 211.16092 -130.07247 60 'point symmetry operation' ? ? -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 -0.5657 421.27298 0.21608 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 9F5P _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 D _pdbx_nonpoly_scheme.entity_id 4 _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 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _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 . . . D 4 205.293 248.862 334.33 1 27.83 ? C1 SPH 401 A 1 HETATM 2 O O1 SPH . . . D 4 203.942 248.718 333.955 1 33.54 ? O1 SPH 401 A 1 HETATM 3 C C2 SPH . . . D 4 205.811 250.287 334.156 1 31.06 ? C2 SPH 401 A 1 HETATM 4 N N2 SPH . . . D 4 204.825 251.267 334.571 1 28.92 ? N2 SPH 401 A 1 HETATM 5 C C3 SPH . . . D 4 207.062 250.431 335.009 1 31.56 ? C3 SPH 401 A 1 HETATM 6 O O3 SPH . . . D 4 207.762 249.213 334.95 1 29.31 ? O3 SPH 401 A 1 HETATM 7 C C4 SPH . . . D 4 207.96 251.538 334.551 1 23.39 ? C4 SPH 401 A 1 HETATM 8 C C5 SPH . . . D 4 208.683 251.414 333.278 1 22.01 ? C5 SPH 401 A 1 HETATM 9 C C6 SPH . . . D 4 210.181 251.621 333.198 1 28.42 ? C6 SPH 401 A 1 HETATM 10 C C7 SPH . . . D 4 210.708 252.601 334.241 1 23.67 ? C7 SPH 401 A 1 HETATM 11 C C8 SPH . . . D 4 212.215 252.476 334.415 1 27.49 ? C8 SPH 401 A 1 HETATM 12 C C9 SPH . . . D 4 213.023 252.824 333.176 1 28.14 ? C9 SPH 401 A 1 HETATM 13 C C10 SPH . . . D 4 212.971 254.296 332.801 1 29.65 ? C10 SPH 401 A 1 HETATM 14 C C11 SPH . . . D 4 213.667 255.226 333.781 1 22.25 ? C11 SPH 401 A 1 HETATM 15 C C12 SPH . . . D 4 214.427 256.275 332.983 1 25.77 ? C12 SPH 401 A 1 HETATM 16 C C13 SPH . . . D 4 214.514 257.614 333.694 1 24.57 ? C13 SPH 401 A 1 HETATM 17 C C14 SPH . . . D 4 215.225 258.61 332.785 1 20.57 ? C14 SPH 401 A 1 HETATM 18 C C15 SPH . . . D 4 214.91 260.06 333.142 1 27.44 ? C15 SPH 401 A 1 HETATM 19 C C16 SPH . . . D 4 215.989 260.717 333.995 1 26.61 ? C16 SPH 401 A 1 HETATM 20 C C17 SPH . . . D 4 217.359 260.765 333.325 1 26.81 ? C17 SPH 401 A 1 HETATM 21 C C18 SPH . . . D 4 217.3 261.024 331.828 1 20.83 ? C18 SPH 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #