data_6ILP # _model_server_result.job_id jho_ewVaAku3zFsTXg9o8A _model_server_result.datetime_utc '2024-11-08 01:44:18' _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 6ilp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6ILP # _exptl.entry_id 6ILP _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 6ILP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ILP _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' ? ? 0.48856 -0.310832 0.815287 -0.290643 0.823055 0.487962 -0.8227 -0.475356 0.31177 -242.80208 -245.32616 239.60514 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.811348 -0.512907 -0.280431 0.479509 0.309572 0.821119 -0.334344 -0.800682 0.497114 237.52297 -150.77318 396.3493 3 'point symmetry operation' ? ? 0.506102 -0.350392 -0.788091 0.262955 -0.807564 0.527916 -0.821411 -0.474412 -0.316572 396.42068 241.89595 634.6872 4 'point symmetry operation' ? ? 0.506102 0.262955 -0.821411 -0.350392 -0.807564 -0.474412 -0.788091 0.527916 -0.316572 257.10188 635.352 385.63883 5 'point symmetry operation' ? ? 0.811348 0.479509 -0.334344 -0.512907 0.309572 -0.800682 -0.280431 0.821119 0.497114 12.10043 485.85208 -6.61943 6 'point symmetry operation' ? ? 0.353672 0.782151 -0.512987 0.782151 -0.548073 -0.296404 -0.512987 -0.296404 -0.805599 94.64173 252.89248 635.32624 7 'point symmetry operation' ? ? 0.833514 0.471471 0.288045 0.470891 -0.333514 -0.816719 -0.288992 0.816385 -0.5 -142.60248 403.82673 238.8713 8 'point symmetry operation' ? ? 0.806038 -0.512194 0.296582 0.495198 0.309162 -0.81191 0.324163 0.801297 0.502834 98.45763 242.2531 -151.03442 9 'point symmetry operation' ? ? 0.309215 -0.809451 -0.499175 0.821481 0.491799 -0.288622 0.479119 -0.320816 0.81702 484.68517 -8.53915 4.44553 10 'point symmetry operation' ? ? 0.029637 -0.009502 -0.999516 0.998828 -0.038002 0.029978 -0.038268 -0.999232 0.008364 482.32682 -1.96365 490.44315 11 'point symmetry operation' ? ? -0.831053 -0.478431 -0.283646 -0.478431 0.35484 0.803239 -0.283646 0.803239 -0.523787 631.49306 76.85404 246.50326 12 'point symmetry operation' ? ? -0.80885 0.505254 -0.3008 -0.486583 -0.2879 0.824834 0.33015 0.813531 0.478715 393.81074 228.07847 -149.5785 13 'point symmetry operation' ? ? -0.313414 0.812122 0.492168 -0.808617 -0.499984 0.31009 0.497907 -0.300789 0.813397 6.28974 482.83374 -4.08034 14 'point symmetry operation' ? ? -0.029421 0.018093 0.999403 -0.999493 0.011681 -0.029635 -0.01221 -0.999768 0.01774 4.47092 489.05672 481.92424 15 'point symmetry operation' ? ? -0.349339 -0.779513 0.519924 -0.795427 0.539991 0.275148 -0.495236 -0.317442 -0.808686 390.86782 238.14747 636.79342 16 'point symmetry operation' ? ? -0.522619 -0.30372 0.796632 -0.30372 -0.806767 -0.506835 0.796632 -0.506835 0.329386 251.64167 631.62946 90.01605 17 'point symmetry operation' ? ? -0.836012 -0.463818 0.293186 -0.463818 0.311841 -0.829233 0.293186 -0.829233 -0.47583 489.04522 480.24396 486.20346 18 'point symmetry operation' ? ? -0.998726 0.050463 -0.000659 0.050463 0.998385 -0.026096 -0.000659 -0.026096 -0.999659 476.60842 -5.60681 492.27311 19 'point symmetry operation' ? ? -0.785896 0.528403 0.321182 0.528403 0.304084 0.792668 0.321182 0.792668 -0.518188 231.51849 -154.4936 99.83696 20 'point symmetry operation' ? ? -0.491646 0.309506 0.813935 0.309506 -0.811561 0.495555 0.813935 0.495555 0.303207 92.48139 239.34008 -148.77158 21 'point symmetry operation' ? ? -0.304822 -0.819026 -0.486086 0.795992 -0.49932 0.342162 -0.522952 -0.282622 0.804143 633.90425 82.64473 243.34485 22 'point symmetry operation' ? ? -0.477528 0.291998 -0.828676 0.291998 -0.836809 -0.463128 -0.828676 -0.463128 0.314337 492.32941 482.61119 480.46483 23 'point symmetry operation' ? ? 0.029637 0.998828 -0.038268 -0.009502 -0.038002 -0.999232 -0.999516 0.029978 0.008364 6.43486 494.57512 478.04973 24 'point symmetry operation' ? ? 0.515788 0.324649 0.792821 0.308156 0.793177 -0.525272 -0.799376 0.515242 0.309069 -152.28965 102.00277 239.43714 25 'point symmetry operation' ? ? 0.309081 -0.798847 0.516055 0.805979 0.508066 0.303755 -0.504844 0.322044 0.800887 235.50775 -152.58421 94.38155 26 'point symmetry operation' ? ? -0.499054 0.354547 0.790722 -0.284549 0.794832 -0.535979 -0.818521 -0.492481 -0.295778 89.10676 249.08921 633.27181 27 'point symmetry operation' ? ? -0.499271 -0.267391 0.824155 0.329463 0.821154 0.466005 -0.801363 0.504191 -0.321883 230.51605 -150.77192 395.87557 28 'point symmetry operation' ? ? -0.80885 -0.486583 0.33015 0.505254 -0.2879 0.813531 -0.3008 0.824834 0.478715 478.89618 -11.62396 1.93695 29 'point symmetry operation' ? ? -0.999963 -0.000113 -0.008593 -0.000113 -0.999653 0.026329 -0.008593 0.026329 0.999616 490.99425 474.23534 -4.13428 30 'point symmetry operation' ? ? -0.808499 0.519734 0.276056 -0.488238 -0.330488 -0.807714 -0.328563 -0.787816 0.520953 250.09114 635.36494 386.05213 31 'point symmetry operation' ? ? 0.783047 -0.535229 -0.316807 -0.519674 -0.283168 -0.806073 0.341725 0.79583 -0.499879 258.64386 631.27781 89.60717 32 'point symmetry operation' ? ? 0.484598 -0.313661 -0.816567 -0.287913 0.824292 -0.487493 0.825997 0.471338 0.309144 399.76764 231.05073 -147.34188 33 'point symmetry operation' ? ? 0.515788 0.308156 -0.799376 0.324649 0.793177 0.515242 0.792821 -0.525272 0.309069 238.51687 -154.83357 100.3151 34 'point symmetry operation' ? ? 0.833514 0.470891 -0.288992 0.471471 -0.333514 0.816385 0.288045 -0.816719 -0.5 -2.26537 6.9039 490.32458 35 'point symmetry operation' ? ? 0.998689 -0.05035 0.009252 -0.05035 -0.998732 -0.000233 0.009252 -0.000233 -0.999957 10.1738 492.74745 483.70672 36 'point symmetry operation' ? ? 0.020829 0.999709 0.01217 0.008231 -0.012344 0.99989 0.999749 -0.020727 -0.008485 -3.8784 -1.63578 5.62172 37 'point symmetry operation' ? ? 0.4922 0.289054 0.821089 -0.333548 -0.808637 0.484616 0.804042 -0.512401 -0.301598 -144.83663 398.48598 242.84702 38 'point symmetry operation' ? ? 0.263424 -0.820401 0.507494 -0.820401 -0.467275 -0.32954 0.507494 -0.32954 -0.796149 253.92856 633.25839 391.54377 39 'point symmetry operation' ? ? -0.349339 -0.795427 -0.495236 -0.779513 0.539991 -0.317442 0.519924 0.275148 -0.808685 641.33724 378.23397 246.2181 40 'point symmetry operation' ? ? -0.499271 0.329463 -0.801363 -0.267391 0.821154 0.504191 0.824154 0.466005 -0.321883 482.00377 -14.15221 7.70516 41 'point symmetry operation' ? ? -0.304822 0.795992 -0.522953 -0.819026 -0.49932 -0.282622 -0.486086 0.342162 0.804143 254.70141 629.22499 84.16985 42 'point symmetry operation' ? ? 0.309215 0.821481 0.479119 -0.809451 0.491799 -0.320816 -0.499175 -0.288622 0.81702 -144.98708 397.95462 235.84585 43 'point symmetry operation' ? ? 0.484598 -0.287913 0.825997 -0.313661 0.824292 0.471338 -0.816567 -0.487493 0.309144 -5.50039 4.38602 484.62226 44 'point symmetry operation' ? ? -0.021046 -0.999044 0.038308 -0.016821 0.038665 0.999111 -0.999637 0.020383 -0.017619 480.39562 -7.58237 486.69855 45 'point symmetry operation' ? ? -0.508935 -0.329154 -0.795388 -0.329154 -0.779372 0.533138 -0.795388 0.533138 0.288307 641.20917 378.58935 239.20534 46 'point symmetry operation' ? ? 0.783047 -0.519674 0.341725 -0.535229 -0.283168 0.79583 -0.316807 -0.806073 -0.499879 94.90755 245.87951 635.58916 47 'point symmetry operation' ? ? 0.271881 -0.83612 -0.476429 -0.83612 -0.450345 0.313199 -0.476429 0.313199 -0.821537 494.69452 476.871 483.74782 48 'point symmetry operation' ? ? -0.021046 -0.016821 -0.999637 -0.999044 0.038665 0.020383 0.038308 0.999111 -0.017619 496.50479 470.30931 -2.25233 49 'point symmetry operation' ? ? 0.309081 0.805979 -0.504844 -0.798847 0.508066 0.322044 0.516055 0.303755 0.800887 97.83663 235.26247 -150.7756 50 'point symmetry operation' ? ? 0.806038 0.495198 0.324163 -0.512194 0.309162 0.801297 0.296582 -0.81191 0.502834 -150.36412 96.55723 243.43212 51 'point symmetry operation' ? ? 0.020829 0.008231 0.999749 0.999709 -0.012344 -0.020727 0.01217 0.99989 -0.008485 -5.52606 3.9736 1.7305 52 'point symmetry operation' ? ? -0.313414 -0.808617 0.497907 0.812122 -0.499984 -0.300789 0.492168 0.31009 0.813397 394.43028 235.07356 -149.49851 53 'point symmetry operation' ? ? -0.808499 -0.488238 -0.328563 0.519734 -0.330488 -0.787816 0.276056 -0.807714 0.520953 639.25 384.13798 243.03887 54 'point symmetry operation' ? ? -0.780235 0.526614 -0.337506 0.526614 0.261905 -0.808754 -0.337506 -0.808754 -0.48167 390.60055 245.1649 636.86931 55 'point symmetry operation' ? ? -0.267682 0.833448 0.483435 0.823255 0.458529 -0.334667 -0.500597 0.308406 -0.808881 -7.89297 10.21039 487.73254 56 'point symmetry operation' ? ? -0.499054 -0.284549 -0.818521 0.354547 0.794832 -0.492481 0.790722 -0.535979 -0.295778 633.69357 82.29787 250.35604 57 'point symmetry operation' ? ? -0.267682 0.823255 -0.500597 0.833448 0.458529 0.308406 0.483435 -0.334667 -0.808881 233.63874 -148.5232 401.75039 58 'point symmetry operation' ? ? 0.344947 0.792972 0.502203 0.792972 -0.532469 0.296096 0.502203 0.296096 -0.812478 -152.47793 102.54267 246.43675 59 'point symmetry operation' ? ? 0.4922 -0.333548 0.804042 0.289054 -0.808637 -0.512401 0.821089 0.484616 -0.301598 8.94367 488.53097 -0.9467 60 'point symmetry operation' ? ? -0.029421 -0.999493 -0.01221 0.018093 0.011681 -0.999768 0.999403 -0.029635 0.01774 494.82438 476.019 1.47555 # _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 6ILP _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 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 5 147.577 216.379 330.953 1 21.88 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 148.3 215.888 329.846 1 21.88 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 147.48 217.901 330.899 1 21.88 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 148.468 218.478 331.786 1 21.88 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 147.672 218.415 329.479 1 21.88 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 146.864 217.639 328.628 1 21.88 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 147.308 219.867 329.349 1 21.88 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 146.315 220.484 330.234 1 21.88 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 145.617 221.756 329.82 1 21.88 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 146.585 222.917 329.628 1 21.88 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 145.771 224.129 329.191 1 21.88 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 146.393 225.453 329.614 1 21.88 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 145.796 225.961 330.921 1 21.88 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 145.012 227.261 330.76 1 21.88 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 143.651 227.016 330.11 1 21.88 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 142.79 228.26 329.868 1 21.88 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 143.41 229.597 330.271 1 21.88 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 142.858 230.727 329.409 1 21.88 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 143.689 231.994 329.555 1 21.88 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 142.905 233.255 329.207 1 21.88 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 141.682 233.421 330.096 1 21.88 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 21 #