data_6IIJ # _model_server_result.job_id sEiimSJSMD5MuspAFOc5RQ _model_server_result.datetime_utc '2024-10-18 17:29:33' _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 6iij # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6IIJ # _exptl.entry_id 6IIJ _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 6IIJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IIJ _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' ? ? 0.587846 -0.808973 0.000031 0.688129 0.500054 0.52576 -0.425341 -0.309045 0.850633 47.9938 -372.07543 -25.22836 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.309017 -0.951057 -0.000027 0.951057 0.309017 0.000047 -0.000037 -0.000041 1 356.47492 -56.47394 0.01677 3 'point symmetry operation' ? ? -0.809017 -0.587785 -0.000081 0.587785 -0.809017 0.000036 -0.000087 -0.000018 1 520.34163 265.10245 0.02274 4 'point symmetry operation' ? ? -0.809017 0.587785 -0.000087 -0.587785 -0.809017 -0.000018 -0.000081 0.000036 1 265.14191 520.32153 0.00966 5 'point symmetry operation' ? ? 0.309017 0.951057 -0.000037 -0.951057 0.309017 -0.000041 -0.000027 0.000047 1 -56.4469 356.4792 -0.00439 6 'point symmetry operation' ? ? -0.638169 0.262899 -0.723619 0.262899 -0.808983 -0.525767 -0.723619 -0.525767 0.447152 455.64589 449.76725 391.24208 7 'point symmetry operation' ? ? 0.052853 0.688205 -0.723589 -0.688129 -0.5 -0.525813 -0.723661 0.525713 0.447147 213.29549 589.16181 162.98978 8 'point symmetry operation' ? ? 0.670881 0.16243 -0.723558 -0.688152 0.499962 -0.525818 0.276343 0.850679 0.447191 193.25862 372.08934 -124.65887 9 'point symmetry operation' ? ? 0.36182 -0.587822 -0.723568 0.262861 0.80899 -0.525775 0.894422 0.000038 0.447224 423.22555 98.53662 -74.1832 10 'point symmetry operation' ? ? -0.447217 -0.525729 -0.723606 0.850643 0.000018 -0.525744 0.276412 -0.850652 0.4472 585.3898 146.54421 244.66112 11 'point symmetry operation' ? ? -0.052957 0.688204 0.723582 0.688204 -0.499891 0.525818 0.723582 0.525818 -0.447152 -77.88727 62.05797 42.91714 12 'point symmetry operation' ? ? 0.63813 0.263002 0.723616 -0.262777 -0.809017 0.525775 0.723698 -0.525663 -0.447147 -135.6185 335.62504 271.15351 13 'point symmetry operation' ? ? 0.447296 -0.525655 0.723611 -0.850643 -0.000105 0.525744 -0.276284 -0.850698 -0.447191 77.01807 287.64866 558.81238 14 'point symmetry operation' ? ? -0.361732 -0.58787 0.723574 -0.262982 0.808956 0.525767 -0.894422 -0.000101 -0.447224 266.16594 -15.56943 508.35897 15 'point symmetry operation' ? ? -0.670905 0.162336 0.723556 0.688077 0.500071 0.525813 -0.276471 0.850633 -0.4472 170.42917 -154.99215 189.51818 16 'point symmetry operation' ? ? -0.308874 -0.951103 0.000037 -0.951103 0.308874 -0.000051 0.000037 -0.000051 -1 490.61048 356.52251 434.16522 17 'point symmetry operation' ? ? -1 -0.00015 0 -0.00015 1 -0.00001 0 -0.00001 -1 434.21719 0.03482 434.16439 18 'point symmetry operation' ? ? -0.30916 0.95101 0.000027 0.95101 0.30916 0.000037 0.000027 0.000037 -1 77.75077 -56.49273 434.14819 19 'point symmetry operation' ? ? 0.808929 0.587907 0.000081 0.587907 -0.808929 0.000026 0.000081 0.000026 -1 -86.1643 265.05901 434.139 20 'point symmetry operation' ? ? 0.809105 -0.587664 0.000087 -0.587664 -0.809105 -0.000028 0.000087 -0.000028 -1 168.99703 520.31647 434.14953 21 'point symmetry operation' ? ? -0.138211 -0.951042 0.276435 0.425382 -0.309061 -0.850607 0.894398 0.000027 0.447272 393.54693 376.48345 -74.18596 22 'point symmetry operation' ? ? -0.947215 -0.162453 0.276393 -0.162453 -0.500033 -0.850633 0.276394 -0.850633 0.447248 397.99184 545.5611 244.65047 23 'point symmetry operation' ? ? -0.447217 0.850643 0.276412 -0.525729 0.000018 -0.850652 -0.723606 -0.525744 0.4472 69.51253 515.87533 391.2239 24 'point symmetry operation' ? ? 0.670802 0.688181 0.276464 -0.162411 0.500038 -0.850638 -0.723635 0.525708 0.447195 -137.94376 328.45087 162.97484 25 'point symmetry operation' ? ? 0.861778 -0.425322 0.276478 0.425408 0.309017 -0.85061 0.276346 0.850653 0.447239 62.32052 242.30195 -124.66427 26 'point symmetry operation' ? ? -0.361859 0.587701 0.723647 0.262797 0.809078 -0.525671 -0.894425 -0.000046 -0.447219 10.97683 98.50853 508.3466 27 'point symmetry operation' ? ? 0.447089 0.525729 0.723685 0.850707 0.000105 -0.52564 -0.27642 0.850652 -0.447195 -151.19464 146.48854 189.5018 28 'point symmetry operation' ? ? 0.63813 -0.262777 0.723698 0.263002 -0.809017 -0.525663 0.723616 0.525775 -0.447147 -21.49633 449.72963 42.91781 29 'point symmetry operation' ? ? -0.05275 -0.688129 0.723668 -0.688129 -0.500109 -0.525708 0.723668 -0.525708 -0.447141 220.8331 589.16292 271.16872 30 'point symmetry operation' ? ? -0.670777 -0.162505 0.723637 -0.688256 0.499929 -0.525713 -0.276336 -0.850684 -0.447186 240.90262 372.09634 558.81954 31 'point symmetry operation' ? ? -0.447168 0.525655 -0.72369 -0.850707 -0.000018 0.52564 0.276292 0.850698 0.447186 357.15586 287.66632 -124.65087 32 'point symmetry operation' ? ? 0.361771 0.587748 -0.723653 -0.262919 0.809044 0.525663 0.894425 0.000093 0.447219 168.0536 -15.57972 -74.19443 33 'point symmetry operation' ? ? 0.670802 -0.162411 -0.723635 0.688181 0.500038 0.525708 0.276464 -0.850638 0.447195 263.81134 -154.98485 244.64776 34 'point symmetry operation' ? ? 0.052853 -0.688129 -0.723661 0.688205 -0.5 0.525713 -0.723589 -0.525813 0.447147 512.09513 62.10408 391.24663 35 'point symmetry operation' ? ? -0.63809 -0.262881 -0.723695 -0.262881 -0.809051 0.525671 -0.723695 0.525671 0.447141 569.78522 335.67755 163.00753 36 'point symmetry operation' ? ? 0.947239 -0.162313 -0.276392 0.162528 -0.5 0.850638 -0.276266 -0.850679 -0.447239 106.68947 105.68943 558.81466 37 'point symmetry operation' ? ? 0.138354 -0.951024 -0.276425 -0.425336 -0.309116 0.85061 -0.894398 -0.000112 -0.447272 453.51829 191.87781 508.3666 38 'point symmetry operation' ? ? -0.861714 -0.425454 -0.276474 -0.425454 0.308962 0.850607 -0.276474 0.850607 -0.447248 556.54156 57.72762 189.53497 39 'point symmetry operation' ? ? -0.670905 0.688077 -0.276471 0.162336 0.500071 0.850633 0.723556 0.525813 -0.4472 273.38462 -111.37013 42.93425 40 'point symmetry operation' ? ? 0.447089 0.850707 -0.27642 0.525729 0.000105 0.850652 0.723685 -0.52564 -0.447195 -4.63926 -81.7281 271.16165 41 'point symmetry operation' ? ? -0.138211 0.425382 0.894398 -0.951042 -0.309061 0.000027 0.276435 -0.850607 0.447272 -39.40493 490.63805 244.63052 42 'point symmetry operation' ? ? 0.36182 0.262861 0.894422 -0.587822 0.80899 0.000038 -0.723568 -0.525775 0.447224 -112.68177 169.0692 391.21721 43 'point symmetry operation' ? ? 0.361771 -0.262919 0.894425 0.587748 0.809044 0.000093 -0.723653 0.525663 0.447219 1.46818 -86.16162 162.98335 44 'point symmetry operation' ? ? -0.13829 -0.425347 0.894402 0.951071 -0.308973 0.000115 0.276297 0.850656 0.447263 145.29356 77.6659 -124.65961 45 'point symmetry operation' ? ? -0.447296 0.000046 0.894386 0.000046 -1 0.000074 0.894386 0.000074 0.447296 120.03259 434.1477 -74.19889 46 'point symmetry operation' ? ? -0.447168 -0.850707 0.276292 0.525655 -0.000018 0.850698 -0.72369 0.52564 0.447186 438.86875 -81.69529 163.00356 47 'point symmetry operation' ? ? -0.947264 0.162388 0.276264 0.162388 -0.499967 0.850684 0.276264 0.850684 0.447231 327.51183 105.70263 -124.65133 48 'point symmetry operation' ? ? -0.13829 0.951071 0.276297 -0.425347 -0.308973 0.850656 0.894402 0.000115 0.447263 -19.32995 191.83934 -74.20413 49 'point symmetry operation' ? ? 0.861778 0.425408 0.276346 -0.425322 0.309017 0.850653 0.276478 -0.85061 0.447239 -122.33304 57.67684 244.62884 50 'point symmetry operation' ? ? 0.670881 -0.688152 0.276343 0.16243 0.499962 0.850679 -0.723558 -0.525818 0.447191 160.84933 -111.37686 391.23125 51 'point symmetry operation' ? ? 0.947239 0.162528 -0.276266 -0.162313 -0.5 -0.850679 -0.276392 0.850638 -0.447239 36.14331 545.53362 189.50847 52 'point symmetry operation' ? ? 0.447296 -0.850643 -0.276284 -0.525655 -0.000105 -0.850698 0.723611 0.525744 -0.447191 364.62709 515.89579 42.93534 53 'point symmetry operation' ? ? -0.670777 -0.688256 -0.276336 -0.162505 0.499929 -0.850684 0.723637 -0.525713 -0.447186 572.11156 328.5048 271.18627 54 'point symmetry operation' ? ? -0.861842 0.425275 -0.276351 0.425275 0.309072 -0.850656 -0.276351 -0.850656 -0.447231 371.86024 242.32864 558.82624 55 'point symmetry operation' ? ? 0.138147 0.951089 -0.276307 0.425394 -0.308918 -0.850653 -0.894402 -0.000024 -0.447263 40.61365 376.45982 508.34659 56 'point symmetry operation' ? ? -0.361859 0.262797 -0.894425 0.587701 0.809078 -0.000046 0.723647 -0.525671 -0.447219 432.76197 -86.12865 271.18189 57 'point symmetry operation' ? ? 0.138147 0.425394 -0.894402 0.951089 -0.308918 -0.000024 -0.276307 -0.850653 -0.447263 288.91195 77.68012 558.82323 58 'point symmetry operation' ? ? 0.447296 0.000104 -0.894386 0.000104 -1 -0.000064 -0.894386 -0.000064 -0.447296 314.11931 434.16521 508.35895 59 'point symmetry operation' ? ? 0.138354 -0.425336 -0.894398 -0.951024 -0.309116 -0.000112 -0.276425 0.85061 -0.447272 473.54834 490.67635 189.52897 60 'point symmetry operation' ? ? -0.361732 -0.262982 -0.894422 -0.58787 0.808956 -0.000101 0.723574 0.525767 -0.447224 546.87353 169.11706 42.94549 # _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 6IIJ _atom_sites.fract_transf_matrix[1][1] 0.010051 _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] 0.009387 _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] 0.010365 _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 5 223.416 178.991 347.176 1 114.83 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 222.756 178.485 348.311 1 131.88 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 223.582 180.495 347.338 1 122.44 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 224.925 180.889 346.968 1 132.86 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 222.563 181.235 346.486 1 104.18 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 221.829 182.147 347.267 1 107.07 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 223.18 181.938 345.311 1 99.25 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 222.928 183.373 345.141 1 75.11 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 222.718 183.942 343.761 1 79.65 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 223.752 185.014 343.462 1 82.44 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 223.297 186.348 344.033 1 78.69 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 223.66 187.503 343.116 1 66.32 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 225.154 187.774 343.141 1 99.26 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 225.582 188.356 344.48 1 121.03 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 225.63 189.877 344.428 1 123.45 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 226.544 190.437 345.505 1 119 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 226.706 191.948 345.405 1 101.75 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 226.579 192.588 346.782 1 74.4 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 226.796 194.092 346.705 1 94.66 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 227.093 194.678 348.077 1 103.64 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 227.603 196.108 347.963 1 77.77 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 21 #