data_7BZN # _model_server_result.job_id qERgAt2Tj6wg-pDxdNatIA _model_server_result.datetime_utc '2024-10-12 04:29:08' _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 7bzn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 7BZN # _exptl.entry_id 7BZN _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 7BZN _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BZN _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' ? ? -0.499134 -0.300082 0.812906 0.320038 0.807953 0.494761 -0.805258 0.507112 -0.307239 -3.76283 -437.60863 164.11267 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.493523 -0.304511 0.814682 -0.306874 0.815493 0.490714 -0.813795 -0.492184 0.309018 -1.06522 0.13919 539.05292 3 'point symmetry operation' ? ? -0.325973 -0.799584 0.504389 -0.801044 0.516953 0.301808 -0.502066 -0.305656 -0.809014 437.52365 265.10043 706.42837 4 'point symmetry operation' ? ? -0.325973 -0.801044 -0.502066 -0.799584 0.516953 -0.305656 0.504389 0.301808 -0.809014 709.65171 428.71629 270.81917 5 'point symmetry operation' ? ? 0.493523 -0.306874 -0.813795 -0.304511 0.815493 -0.492184 0.814682 0.490714 0.309018 439.24722 264.87521 -165.77757 6 'point symmetry operation' ? ? 0.296882 -0.816713 0.494814 -0.816713 -0.485674 -0.31161 0.494814 -0.31161 -0.811208 276.34617 704.87595 439.14072 7 'point symmetry operation' ? ? -0.005531 -0.999967 -0.006001 -0.00044 0.006004 -0.999982 0.999985 -0.005528 -0.000473 542.64712 537.70426 1.28614 8 'point symmetry operation' ? ? 0.309018 -0.810827 -0.497058 0.811721 0.497205 -0.306425 0.495597 -0.308782 0.811811 539.27876 -1.33758 -0.03479 9 'point symmetry operation' ? ? 0.805833 -0.510679 -0.299733 0.497391 0.309106 0.81059 -0.321302 -0.802284 0.503095 270.89606 -167.31207 437.00341 10 'point symmetry operation' ? ? 0.798333 -0.514317 0.313278 -0.509037 -0.298347 0.807385 -0.321786 -0.804032 -0.499986 108.39478 269.15189 708.4288 11 'point symmetry operation' ? ? -0.795152 0.517151 0.316684 0.517151 0.305576 0.799487 0.316684 0.799487 -0.510424 260.5499 -168.70545 106.96134 12 'point symmetry operation' ? ? -0.808842 0.507998 -0.296162 -0.489166 -0.301778 0.81832 0.32633 0.806764 0.492586 432.17838 261.75176 -168.41014 13 'point symmetry operation' ? ? -0.314059 0.806337 -0.501187 -0.814752 -0.499905 -0.293726 -0.487388 0.316096 0.813964 273.46368 703.3484 96.88451 14 'point symmetry operation' ? ? 0.005425 0.999872 -0.015053 -0.009658 -0.015 -0.999841 -0.999939 0.005569 0.009576 3.74412 545.81292 536.21711 15 'point symmetry operation' ? ? -0.291907 0.821145 0.490419 0.813502 0.482814 -0.324198 -0.502995 0.304321 -0.808941 -4.23704 6.854 542.44493 16 'point symmetry operation' ? ? -0.50173 0.299562 -0.811498 0.299562 -0.819902 -0.487877 -0.811498 -0.487877 0.321632 544.4087 540.68713 533.86676 17 'point symmetry operation' ? ? 0.32085 0.79648 -0.512519 0.79648 -0.519719 -0.309052 -0.512519 -0.309052 -0.801131 107.54449 277.26241 708.03991 18 'point symmetry operation' ? ? 0.331014 0.804074 0.493857 0.804074 -0.514253 0.298342 0.493857 0.298342 -0.81676 -168.96132 109.74638 276.69073 19 'point symmetry operation' ? ? -0.485285 0.311851 0.816852 0.311851 -0.811059 0.494907 0.816852 0.494907 0.296343 97.01289 269.6405 -164.07088 20 'point symmetry operation' ? ? -0.999949 0.000045 0.010099 0.000045 -0.99996 0.008997 0.010099 0.008997 0.999909 537.89981 535.97653 -5.12735 21 'point symmetry operation' ? ? -0.015523 -0.999765 0.015104 0.000662 0.015095 0.999886 -0.999879 0.015531 0.000427 539.59576 -4.9898 535.98918 22 'point symmetry operation' ? ? 0.28685 -0.818008 -0.498578 -0.818008 -0.480019 0.31693 -0.498578 0.31693 -0.806831 547.61491 534.00297 537.28685 23 'point symmetry operation' ? ? 0.798333 -0.509037 -0.321786 -0.514317 -0.298347 -0.804032 0.313278 0.807385 -0.499986 278.4357 705.64931 102.93758 24 'point symmetry operation' ? ? 0.812074 -0.499839 0.301159 0.492045 0.309047 -0.813868 0.313731 0.809105 0.496913 104.05464 272.73982 -166.80269 25 'point symmetry operation' ? ? 0.309084 -0.803126 0.509368 0.810319 0.502765 0.301014 -0.497845 0.319712 0.806185 265.46044 -166.45931 100.83792 26 'point symmetry operation' ? ? 0.819387 0.493531 0.291603 0.482625 -0.319446 -0.815492 -0.309319 0.808938 -0.499941 -162.77181 444.92408 270.81153 27 'point symmetry operation' ? ? 0.015629 0.009436 0.999833 0.99986 -0.006099 -0.015572 0.005951 0.999937 -0.00953 -6.38637 4.77223 1.75923 28 'point symmetry operation' ? ? -0.808842 -0.489166 0.32633 0.507998 -0.301778 0.806764 -0.296162 0.81832 0.492586 532.56137 -4.68783 -3.24527 29 'point symmetry operation' ? ? -0.514636 -0.313224 -0.798148 -0.313224 -0.797865 0.515075 -0.798148 0.515075 0.312501 709.26395 429.61739 262.71408 30 'point symmetry operation' ? ? 0.491665 0.294116 -0.81961 -0.328905 -0.808784 -0.487534 -0.80628 0.509277 -0.300914 279.52441 707.49283 432.0905 31 'point symmetry operation' ? ? -0.499903 -0.301456 -0.811924 0.323928 0.80435 -0.498087 0.803223 -0.512001 -0.304447 705.83269 99.58511 272.89628 32 'point symmetry operation' ? ? 0.506535 0.306007 -0.80609 0.318373 0.802452 0.504687 0.801287 -0.512279 0.309046 268.65312 -169.14341 107.85627 33 'point symmetry operation' ? ? 0.812074 0.492045 0.313731 -0.499839 0.309047 0.809105 0.301159 -0.813868 0.496913 -166.36926 102.68198 273.52366 34 'point symmetry operation' ? ? -0.005531 -0.00044 0.999985 -0.999967 0.006004 -0.005528 -0.006001 -0.999982 -0.000473 1.95169 539.40783 540.95176 35 'point symmetry operation' ? ? -0.816378 -0.490851 0.304292 -0.490851 0.312118 -0.813417 0.304292 -0.813417 -0.495741 541.00214 537.49386 540.56401 36 'point symmetry operation' ? ? -0.303961 0.80769 0.505217 -0.807215 -0.5 0.313693 0.505976 -0.312469 0.80396 -1.35187 537.33824 0.27183 37 'point symmetry operation' ? ? -0.809014 0.502565 0.304835 -0.500225 -0.316335 -0.806044 -0.30866 -0.804587 0.507315 271.42311 707.22584 433.06648 38 'point symmetry operation' ? ? -0.801565 0.506157 -0.318274 0.506157 0.291077 -0.811837 -0.318274 -0.811837 -0.489513 436.67697 273.21416 706.75285 39 'point symmetry operation' ? ? -0.291907 0.813502 -0.502995 0.821145 0.482814 0.304321 0.490419 -0.324198 -0.808941 266.03449 -164.9074 443.10567 40 'point symmetry operation' ? ? 0.015629 0.99986 0.005951 0.009436 -0.006099 0.999937 0.999833 -0.015572 -0.00953 -4.68222 -1.66975 6.47639 41 'point symmetry operation' ? ? -0.015523 0.000662 -0.999879 -0.999765 0.015095 0.015531 0.015104 0.999886 0.000427 544.30384 531.22003 -3.38984 42 'point symmetry operation' ? ? 0.805833 0.497391 -0.321302 -0.510679 0.309106 -0.802284 -0.299733 0.81059 0.503095 5.33262 540.65916 -3.03635 43 'point symmetry operation' ? ? 0.506535 0.318373 0.801287 0.306007 0.802452 -0.512279 -0.80609 0.504687 0.309046 -168.65539 108.77238 268.59057 44 'point symmetry operation' ? ? -0.499797 -0.288995 0.816508 0.32166 0.813347 0.48477 -0.8042 0.504924 -0.31355 262.78533 -167.58746 436.11174 45 'point symmetry operation' ? ? -0.822447 -0.485351 -0.296674 -0.485351 0.326734 0.810974 -0.296674 0.810974 -0.504287 703.41837 93.49954 268.0186 46 'point symmetry operation' ? ? -0.499903 0.323928 0.803223 -0.301456 0.80435 -0.512001 -0.811924 -0.498087 -0.304447 101.39301 272.39938 705.76724 47 'point symmetry operation' ? ? -0.999778 0.021054 -0.000096 0.021054 0.999737 -0.009102 -0.000096 -0.009102 -0.999959 534.95035 -3.16297 542.44966 48 'point symmetry operation' ? ? -0.499797 0.32166 -0.8042 -0.288995 0.813347 0.504924 0.816508 0.48477 -0.31355 535.96661 -7.95297 3.41791 49 'point symmetry operation' ? ? 0.309084 0.810319 -0.497845 -0.803126 0.502765 0.319712 0.509368 0.301014 0.806185 103.03736 264.649 -166.40445 50 'point symmetry operation' ? ? 0.309018 0.811721 0.495597 -0.810827 0.497205 -0.308782 -0.497058 -0.306425 0.811811 -165.5439 437.91628 267.6713 51 'point symmetry operation' ? ? -0.303961 -0.807215 0.505976 0.80769 -0.5 -0.312469 0.505217 0.313693 0.80396 433.19927 269.84579 -168.095 52 'point symmetry operation' ? ? -0.314059 -0.814752 -0.487388 0.806337 -0.499905 0.316096 -0.501187 -0.293726 0.813964 706.15828 100.47868 264.78762 53 'point symmetry operation' ? ? 0.491665 -0.328905 -0.80628 0.294116 -0.808784 0.509277 -0.81961 -0.487534 -0.300914 443.65164 269.94254 704.05003 54 'point symmetry operation' ? ? 0.999727 -0.021099 -0.010003 -0.021099 -0.999777 0.000106 -0.010003 0.000106 -0.99995 8.45461 544.04407 542.64651 55 'point symmetry operation' ? ? 0.508004 -0.316711 0.801016 0.296307 -0.808938 -0.507761 0.808786 0.495291 -0.3171 1.99469 543.98427 3.63124 56 'point symmetry operation' ? ? 0.819387 0.482625 -0.309319 0.493531 -0.319446 0.808938 0.291603 -0.815492 -0.499941 2.40865 3.39243 545.68643 57 'point symmetry operation' ? ? 0.508004 0.296307 0.808786 -0.316711 -0.808938 0.495291 0.801016 -0.507761 -0.3171 -165.13648 438.88275 275.76789 58 'point symmetry operation' ? ? -0.498403 -0.311128 0.809193 -0.311128 -0.807015 -0.501922 0.809193 -0.501922 0.305418 270.34191 706.09568 103.91031 59 'point symmetry operation' ? ? -0.809014 -0.500225 -0.30866 0.502565 -0.316335 -0.804587 0.304835 -0.806044 0.507315 707.02747 435.75203 267.61502 60 'point symmetry operation' ? ? 0.005425 -0.009658 -0.999939 0.999872 -0.015 0.005569 -0.015053 -0.999841 0.009576 541.43561 1.45754 540.64767 # _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 7BZN _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 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 . . . E 5 174.463 363.43 285.92 1 24.89 ? C1 SPH 401 A 1 HETATM 2 O O1 SPH . . . E 5 173.33 363.858 286.641 1 24.89 ? O1 SPH 401 A 1 HETATM 3 C C2 SPH . . . E 5 175.729 363.876 286.643 1 24.89 ? C2 SPH 401 A 1 HETATM 4 N N2 SPH . . . E 5 175.368 364.41 287.942 1 24.89 ? N2 SPH 401 A 1 HETATM 5 C C3 SPH . . . E 5 176.681 362.703 286.838 1 24.89 ? C3 SPH 401 A 1 HETATM 6 O O3 SPH . . . E 5 176.381 361.695 285.903 1 24.89 ? O3 SPH 401 A 1 HETATM 7 C C4 SPH . . . E 5 178.099 363.133 286.624 1 24.89 ? C4 SPH 401 A 1 HETATM 8 C C5 SPH . . . E 5 178.514 363.667 285.321 1 24.89 ? C5 SPH 401 A 1 HETATM 9 C C6 SPH . . . E 5 179.946 363.498 284.878 1 24.89 ? C6 SPH 401 A 1 HETATM 10 C C7 SPH . . . E 5 180.896 363.818 286.025 1 24.89 ? C7 SPH 401 A 1 HETATM 11 C C8 SPH . . . E 5 181.04 365.323 286.206 1 24.89 ? C8 SPH 401 A 1 HETATM 12 C C9 SPH . . . E 5 182.083 365.643 287.269 1 24.89 ? C9 SPH 401 A 1 HETATM 13 C C10 SPH . . . E 5 181.853 367.026 287.866 1 24.89 ? C10 SPH 401 A 1 HETATM 14 C C11 SPH . . . E 5 183.165 367.79 287.984 1 24.89 ? C11 SPH 401 A 1 HETATM 15 C C12 SPH . . . E 5 183.575 368.384 286.642 1 24.89 ? C12 SPH 401 A 1 HETATM 16 C C13 SPH . . . E 5 183.674 369.904 286.707 1 24.89 ? C13 SPH 401 A 1 HETATM 17 C C14 SPH . . . E 5 185.086 370.322 287.097 1 24.89 ? C14 SPH 401 A 1 HETATM 18 C C15 SPH . . . E 5 185.47 371.655 286.467 1 24.89 ? C15 SPH 401 A 1 HETATM 19 C C16 SPH . . . E 5 186.972 371.881 286.592 1 24.89 ? C16 SPH 401 A 1 HETATM 20 C C17 SPH . . . E 5 187.384 373.264 286.104 1 24.89 ? C17 SPH 401 A 1 HETATM 21 C C18 SPH . . . E 5 186.653 374.357 286.869 1 24.89 ? C18 SPH 401 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #