data_7C9X # _model_server_result.job_id WmZoa2xUvT6RmUV1XX872Q _model_server_result.datetime_utc '2025-07-12 13:18:11' _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 7c9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 7C9X # _exptl.entry_id 7C9X _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 ? # 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 ? 240-meric 240 'crystal asymmetric unit, crystal frame' 6 # 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,F 1 (1-60) A,B,C,D,E,F 2 1 A,B,C,D,E,F 3 (1-5) A,B,C,D,E,F 4 (1,2,6,10,23,24) A,B,C,D,E,F 5 P A,B,C,D,E,F 6 (X0)(1-60) # 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] P 'transform to point frame' ? ? -0.688198 -0.499999 -0.525724 -0.425312 -0.309023 0.850655 -0.587787 0.809016 0.000013 368.66907 -23.92915 -47.67943 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 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' ? ? 0.670815 -0.6882 0.276384 0.162477 0.499997 0.850649 -0.723608 -0.525722 0.447222 160.06577 -109.4462 387.63857 3 'point symmetry operation' ? ? 0.138183 -0.951054 -0.27641 -0.425306 -0.309025 0.850657 -0.894438 0.000013 -0.447191 449.89818 191.58259 502.71259 4 'point symmetry operation' ? ? 0.138183 -0.425306 -0.894438 -0.951054 -0.309025 0.000013 -0.27641 0.850657 -0.447191 468.95868 487.07482 186.19367 5 'point symmetry operation' ? ? 0.670815 0.162477 -0.723608 -0.6882 0.499997 -0.525722 0.276384 0.850649 0.447222 190.90632 368.67027 -124.49979 6 'point symmetry operation' ? ? -0.309012 -0.951058 -0.000016 -0.951058 0.309012 0.000022 -0.000016 0.000022 -1 487.07962 353.87882 428.34704 7 'point symmetry operation' ? ? -0.361804 -0.262855 -0.89443 -0.587792 0.809012 0.000014 0.723601 0.525744 -0.447208 541.70091 167.8352 40.70355 8 'point symmetry operation' ? ? 0.361805 0.587788 -0.723603 -0.262864 0.809015 0.525735 0.894427 -0.000004 0.447214 165.84148 -14.78818 -74.3685 9 'point symmetry operation' ? ? 0.861812 0.425312 0.276387 -0.425313 0.309017 0.850657 0.276387 -0.850657 0.447205 -121.07372 58.38798 242.15655 10 'point symmetry operation' ? ? 0.447224 -0.525747 0.723589 -0.85064 -0.000002 0.525748 -0.276409 -0.850641 -0.447222 77.46237 286.23672 552.85183 11 'point symmetry operation' ? ? -0.63822 0.262862 -0.723588 0.262862 -0.80901 -0.525744 -0.723588 -0.525744 0.447229 451.38359 445.81493 387.6374 12 'point symmetry operation' ? ? 0.138176 0.951059 -0.276394 0.425319 -0.309009 -0.850657 -0.894434 -0.000016 -0.447201 39.9667 372.63452 502.71977 13 'point symmetry operation' ? ? 0.447217 0.525741 0.723598 0.850646 0.000002 -0.525739 -0.276404 0.850645 -0.447218 -149.14706 144.78584 186.20097 14 'point symmetry operation' ? ? -0.13818 -0.425317 0.894434 0.951055 -0.309021 -0.000016 0.276405 0.850654 0.447201 145.3911 77.14802 -124.50079 15 'point symmetry operation' ? ? -0.809017 -0.587785 0.000024 0.587785 -0.809017 -0.000019 0.00003 -0.000002 1 516.53946 263.19423 -0.00623 16 'point symmetry operation' ? ? -0.052768 0.688196 0.723604 0.688196 -0.500003 0.525722 0.723604 0.525722 -0.447229 -76.40543 62.35748 40.7122 17 'point symmetry operation' ? ? -0.447187 -0.000004 0.894441 -0.000004 -1 -0.000006 0.894441 -0.000006 0.447187 120.3244 431.02771 -74.36526 18 'point symmetry operation' ? ? -0.947204 -0.162475 0.276415 -0.162475 -0.499991 -0.850653 0.276415 -0.850653 0.447196 395.46519 540.47097 242.15158 19 'point symmetry operation' ? ? -0.861814 0.425311 -0.276382 0.425311 0.309029 -0.850654 -0.276382 -0.850654 -0.447215 368.78171 239.4404 552.8472 20 'point symmetry operation' ? ? -0.309022 0.951055 -0.000005 0.951055 0.309022 -0.000007 -0.000005 -0.000007 -1 77.14963 -56.04999 428.35082 21 'point symmetry operation' ? ? 0.947205 -0.162467 -0.276417 0.162478 -0.5 0.850647 -0.276411 -0.850649 -0.447205 105.59323 106.0662 552.85038 22 'point symmetry operation' ? ? 0.80902 -0.587781 -0.00003 -0.587781 -0.80902 0.00001 -0.00003 0.00001 -1 167.83985 516.54018 428.35275 23 'point symmetry operation' ? ? 0.447224 -0.85064 -0.276409 -0.525747 -0.000002 -0.850641 0.723589 0.525748 -0.447222 361.65486 511.00454 40.70822 24 'point symmetry operation' ? ? 0.361807 -0.587782 -0.723608 0.262851 0.809019 -0.525735 0.89443 0.000013 0.447208 419.1925 97.10934 -74.37165 25 'point symmetry operation' ? ? 0.670812 -0.162468 -0.723612 0.688198 0.500003 0.525719 0.276396 -0.850647 0.447218 260.93771 -153.15631 242.14961 26 'point symmetry operation' ? ? -0.138178 -0.951058 0.276399 0.425308 -0.309013 -0.850661 0.894438 0.000012 0.447191 391.0614 372.63872 -74.36965 27 'point symmetry operation' ? ? -0.447221 -0.525741 -0.723595 0.85064 0.000009 -0.525748 0.276414 -0.850645 0.447212 580.17631 144.78737 242.14654 28 'point symmetry operation' ? ? 0.138176 0.425319 -0.894434 0.951059 -0.309009 -0.000016 -0.276394 -0.850657 -0.447201 285.63848 77.14449 552.84752 29 'point symmetry operation' ? ? 0.809014 0.587789 -0.000024 0.587789 -0.809014 -0.000008 -0.000024 -0.000008 -1 -85.51081 263.19025 428.35509 30 'point symmetry operation' ? ? 0.638218 -0.262858 0.72359 0.262857 -0.809017 -0.525735 0.723591 0.525735 -0.447235 -20.35587 445.81572 40.71357 31 'point symmetry operation' ? ? -0.447219 0.525747 -0.723592 -0.850646 -0.000009 0.525739 0.2764 0.850641 0.447228 353.56616 286.2413 -124.5027 32 'point symmetry operation' ? ? 0.309017 0.951057 0.000016 -0.951057 0.309017 0.00001 0.000005 -0.000018 1 -56.05142 353.8799 0.00287 33 'point symmetry operation' ? ? 0.361807 0.262851 0.89443 -0.587782 0.809019 0.000013 -0.723608 -0.525735 0.447208 -110.67178 167.83156 387.64422 34 'point symmetry operation' ? ? -0.361804 -0.587792 0.723601 -0.262856 0.809012 0.525744 -0.89443 0.000014 -0.447208 265.18858 -14.79124 502.71418 35 'point symmetry operation' ? ? -0.86181 -0.425314 -0.276392 -0.425314 0.309005 0.850661 -0.276392 0.850661 -0.447196 552.1034 58.39001 186.18997 36 'point symmetry operation' ? ? -0.361808 0.587778 0.72361 0.26286 0.809022 -0.525726 -0.894427 -0.000004 -0.447214 11.83699 97.105 502.71861 37 'point symmetry operation' ? ? -0.670816 0.162465 0.72361 0.688197 0.499994 0.525728 -0.276388 0.850653 -0.447212 170.09305 -153.15622 186.19448 38 'point symmetry operation' ? ? -0.947206 0.16247 0.276413 0.16247 -0.500009 0.850644 0.276413 0.850644 0.447215 325.43621 106.07065 -124.50332 39 'point symmetry operation' ? ? -0.809017 0.587785 0.00003 -0.587785 -0.809017 -0.000002 0.000024 -0.000019 1 263.18752 516.54288 -0.00098 40 'point symmetry operation' ? ? -0.447221 0.85064 0.276414 -0.525741 0.000009 -0.850645 -0.723595 -0.525748 0.447212 69.37254 511.00181 387.64349 41 'point symmetry operation' ? ? 0.947205 0.162478 -0.276411 -0.162467 -0.5 -0.850649 -0.276417 0.850647 -0.447205 35.56206 540.47038 186.20047 42 'point symmetry operation' ? ? 0.861812 -0.425313 0.276387 0.425312 0.309017 -0.850657 0.276387 0.850657 0.447205 62.24706 239.44351 -124.49861 43 'point symmetry operation' ? ? 0.309017 -0.951057 0.000005 0.951057 0.309017 -0.000018 0.000016 0.00001 1 353.88063 -56.04683 -0.00562 44 'point symmetry operation' ? ? 0.052765 -0.688193 -0.723606 0.688204 -0.5 0.525714 -0.723596 -0.525728 0.447235 507.43509 62.35697 387.63436 45 'point symmetry operation' ? ? 0.447187 0.000009 -0.894441 0.000009 -1 -0.000005 -0.894441 -0.000005 -0.447187 310.7034 431.02488 502.71605 46 'point symmetry operation' ? ? -0.447219 -0.850646 0.2764 0.525747 -0.000009 0.850641 -0.723592 0.525739 0.447228 436.02409 -79.97669 161.03032 47 'point symmetry operation' ? ? -0.638217 -0.262853 -0.723593 -0.262853 -0.809024 0.525726 -0.723593 0.525726 0.447241 564.68263 333.91963 161.03076 48 'point symmetry operation' ? ? 0.052765 0.688204 -0.723596 -0.688193 -0.5 -0.525728 -0.723606 0.525714 0.447235 210.80151 584.18217 161.0375 49 'point symmetry operation' ? ? 0.670812 0.688198 0.276396 -0.162468 0.500003 -0.850647 -0.723612 0.525719 0.447218 -136.56759 324.9566 161.04122 50 'point symmetry operation' ? ? 0.361805 -0.262864 0.894427 0.587788 0.809015 -0.000004 -0.723603 0.525735 0.447214 2.62761 -85.51615 161.03678 51 'point symmetry operation' ? ? -0.361808 0.26286 -0.894427 0.587778 0.809022 -0.000004 0.72361 -0.525726 -0.447214 428.4028 -85.51568 267.30809 52 'point symmetry operation' ? ? 0.447217 0.850646 -0.276404 0.525741 0.000002 0.850645 0.723598 -0.525739 -0.447218 -4.9937 -79.97842 267.31461 53 'point symmetry operation' ? ? 0.638218 0.262857 0.723591 -0.262858 -0.809017 0.525735 0.72359 -0.525735 -0.447235 -133.65434 333.91725 267.31891 54 'point symmetry operation' ? ? -0.052761 -0.688202 0.723598 -0.688202 -0.499997 -0.525719 0.723598 -0.525719 -0.447241 220.22552 584.18158 267.31505 55 'point symmetry operation' ? ? -0.670812 -0.6882 -0.276392 -0.16248 0.500006 -0.850644 0.723611 -0.525714 -0.447228 567.59593 324.95777 267.30836 56 'point symmetry operation' ? ? -0.138178 0.425308 0.894438 -0.951058 -0.309013 0.000012 0.276399 -0.850661 0.447191 -37.93116 487.07322 242.15776 57 'point symmetry operation' ? ? -0.670812 -0.16248 0.723611 -0.6882 0.500006 -0.525714 -0.276392 -0.850644 -0.447228 240.1218 368.66651 552.84987 58 'point symmetry operation' ? ? -1 -0.000005 0 -0.000005 1 0.000011 0 0.000011 -1 431.02998 -0.00137 428.34584 59 'point symmetry operation' ? ? -0.670816 0.688197 -0.276388 0.162465 0.499994 0.850653 0.72361 0.525728 -0.447212 270.96476 -109.44393 40.70601 60 'point symmetry operation' ? ? -0.13818 0.951055 0.276405 -0.425317 -0.309021 0.850654 0.894434 -0.000016 0.447201 -18.86916 191.58472 -74.36455 # _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 331 n n C1 C2 SPH sing 332 n n C1 H11 SPH sing 333 n n C1 H12 SPH sing 334 n n O1 HO1 SPH sing 335 n n C2 N2 SPH sing 336 n n C2 C3 SPH sing 337 n n C2 H2 SPH sing 338 n n N2 HN21 SPH sing 339 n n N2 HN22 SPH sing 340 n n C3 O3 SPH sing 341 n n C3 C4 SPH sing 342 n n C3 H3 SPH sing 343 n n O3 HO3 SPH sing 344 n n C4 C5 SPH doub 345 z n C4 H4 SPH sing 346 n n C5 C6 SPH sing 347 n n C5 H5 SPH sing 348 n n C6 C7 SPH sing 349 n n C6 H61 SPH sing 350 n n C6 H62 SPH sing 351 n n C7 C8 SPH sing 352 n n C7 H71 SPH sing 353 n n C7 H72 SPH sing 354 n n C8 C9 SPH sing 355 n n C8 H81 SPH sing 356 n n C8 H82 SPH sing 357 n n C9 C10 SPH sing 358 n n C9 H91 SPH sing 359 n n C9 H92 SPH sing 360 n n C10 C11 SPH sing 361 n n C10 H101 SPH sing 362 n n C10 H102 SPH sing 363 n n C11 C12 SPH sing 364 n n C11 H111 SPH sing 365 n n C11 H112 SPH sing 366 n n C12 C13 SPH sing 367 n n C12 H121 SPH sing 368 n n C12 H122 SPH sing 369 n n C13 C14 SPH sing 370 n n C13 H131 SPH sing 371 n n C13 H132 SPH sing 372 n n C14 C15 SPH sing 373 n n C14 H141 SPH sing 374 n n C14 H142 SPH sing 375 n n C15 C16 SPH sing 376 n n C15 H151 SPH sing 377 n n C15 H152 SPH sing 378 n n C16 C17 SPH sing 379 n n C16 H161 SPH sing 380 n n C16 H162 SPH sing 381 n n C17 C18 SPH sing 382 n n C17 H171 SPH sing 383 n n C17 H172 SPH sing 384 n n C18 H181 SPH sing 385 n n C18 H182 SPH sing 386 n n C18 H183 SPH sing 387 n n # _atom_sites.entry_id 7C9X _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 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 SPH A 1 301 499 SPH SPH . F 6 MYR D 1 101 1 MYR MYR . # 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 5 102.813 277.099 242.001 1 41.49 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 102.747 275.841 241.365 1 41.49 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 104.169 277.279 242.679 1 41.49 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 104.827 278.438 242.104 1 41.49 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 104.01 277.49 244.18 1 41.49 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 102.995 276.676 244.72 1 41.49 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 105.293 277.278 244.921 1 41.49 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 105.285 276.494 246.163 1 41.49 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 106.586 276.135 246.837 1 41.49 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 106.351 275.06 247.887 1 41.49 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 105.784 275.673 249.16 1 41.49 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 104.697 274.778 249.74 1 41.49 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 105.066 274.224 251.109 1 41.49 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 105.067 275.346 252.134 1 41.49 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 104.845 274.841 253.554 1 41.49 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 106.111 274.305 254.213 1 41.49 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 106.413 275.089 255.483 1 41.49 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 106.404 274.202 256.72 1 41.49 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 105.656 274.906 257.845 1 41.49 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 105.862 274.23 259.192 1 41.49 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 104.872 274.772 260.219 1 41.49 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #