data_6LHA # _model_server_result.job_id pxNO9qjigHQrufFufCgk8Q _model_server_result.datetime_utc '2024-10-19 08:39:00' _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 6lha # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6LHA # _exptl.entry_id 6LHA _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 6LHA _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LHA _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' ? ? 0.808 0.308878 0.501727 -0.500452 0.809212 0.307773 -0.310939 -0.499771 0.808422 -365.36046 -138.92545 0.54625 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.501363 -0.808022 -0.309412 0.807805 0.309017 0.501956 -0.309978 -0.501606 0.807654 364.67693 -139.85442 226.54343 3 'point symmetry operation' ? ? -0.305449 -0.499602 -0.810616 0.499034 -0.809017 0.310575 -0.810966 -0.309661 0.496432 590.42267 225.2308 366.6223 4 'point symmetry operation' ? ? -0.305449 0.499034 -0.810966 -0.499602 -0.809017 -0.309661 -0.810616 0.310575 0.496432 365.26428 590.72028 226.65238 5 'point symmetry operation' ? ? 0.501363 0.807805 -0.309978 -0.808022 0.309017 -0.501606 -0.309412 0.501956 0.807654 0.363 451.52 0.06734 6 'point symmetry operation' ? ? -0.806634 0.310796 -0.50274 0.310796 -0.500459 -0.808051 -0.50274 -0.808051 0.307093 451.37173 450.54384 452.13714 7 'point symmetry operation' ? ? 0.002485 0.999997 -0.000452 0.002027 -0.000457 -0.999998 -0.999995 0.002484 -0.002028 -0.1477 450.81673 451.37885 8 'point symmetry operation' ? ? 0.809188 0.307235 0.50082 0.310624 0.499827 -0.808509 -0.498726 0.809802 0.309019 -139.19796 225.07674 85.89708 9 'point symmetry operation' ? ? 0.49864 -0.810116 0.308335 0.810117 0.309017 -0.498215 0.308331 0.498218 0.810377 226.38368 85.28886 -139.22479 10 'point symmetry operation' ? ? -0.499993 -0.807915 -0.311899 0.810224 -0.309193 -0.497933 0.30585 -0.501671 0.809186 591.37582 224.63519 87.12401 11 'point symmetry operation' ? ? -0.499095 -0.809943 -0.308051 -0.809943 0.309647 0.498107 -0.308051 0.498107 -0.810552 590.7625 226.24963 365.73902 12 'point symmetry operation' ? ? -0.809015 0.307514 -0.500928 -0.310343 0.500285 0.808333 0.499181 0.809413 -0.309304 452.24118 0.41916 0.11232 13 'point symmetry operation' ? ? -0.001922 0.999998 0.000101 -0.002027 -0.000104 0.999998 0.999996 0.001922 0.002027 0.72271 0.39974 -1.11875 14 'point symmetry operation' ? ? 0.806809 0.310519 0.502631 -0.311078 -0.5 0.808227 0.502285 -0.808442 -0.306809 -139.80973 226.21821 363.74711 15 'point symmetry operation' ? ? 0.499539 -0.808086 0.312183 -0.810398 -0.308563 0.498041 -0.306132 -0.501783 -0.80901 224.85492 365.80111 590.47768 16 'point symmetry operation' ? ? 0.305729 0.499147 0.810791 0.499147 -0.809189 0.309945 0.810791 0.309945 -0.496541 -138.71137 225.38621 84.63172 17 'point symmetry operation' ? ? 0.305168 -0.499489 0.810792 -0.499489 -0.808845 -0.310291 0.810792 -0.310291 -0.496323 86.65245 590.79821 224.47328 18 'point symmetry operation' ? ? -0.501817 -0.807631 0.309696 -0.807631 0.309295 -0.502064 0.309696 -0.502064 -0.807478 451.47544 451.47241 451.10724 19 'point symmetry operation' ? ? -1 0.000562 0 0.000562 1 -0.000351 0 -0.000351 -1 451.58463 -0.04767 451.33316 20 'point symmetry operation' ? ? -0.500909 0.808196 0.309694 0.808196 0.308739 0.501498 0.309694 0.501498 -0.80783 86.82912 -139.77662 224.83884 21 'point symmetry operation' ? ? -0.499994 -0.810009 0.306417 0.807913 -0.308841 0.501891 -0.311902 0.498501 0.808835 452.33983 -0.50947 1.14266 22 'point symmetry operation' ? ? -0.99999 -0.000001 -0.004406 -0.000001 -1 0.000352 -0.004406 0.000352 0.99999 452.70348 451.01048 0.91778 23 'point symmetry operation' ? ? -0.499993 0.810224 0.30585 -0.807915 -0.309193 -0.501671 -0.311899 -0.497933 0.809186 87.0321 590.94445 225.80301 24 'point symmetry operation' ? ? 0.309018 0.500962 0.808421 -0.49932 0.808908 -0.310399 -0.809437 -0.307742 0.500108 -139.32889 225.90846 365.01461 25 'point symmetry operation' ? ? 0.309018 -0.500397 0.808771 0.499316 0.809126 0.309836 -0.809439 0.308088 0.499891 86.44371 -139.63017 226.16688 26 'point symmetry operation' ? ? -0.002483 0.002379 0.999994 -0.999997 0.000104 -0.002484 -0.00011 -0.999997 0.002379 0.25434 451.93676 450.65941 27 'point symmetry operation' ? ? -0.309299 -0.498862 0.809612 -0.500507 0.809298 0.307457 -0.808596 -0.31012 -0.499999 225.55807 86.68372 591.01214 28 'point symmetry operation' ? ? -0.809015 -0.310343 0.499181 0.307514 0.500285 0.809413 -0.500928 0.808333 -0.309304 365.94412 -139.37111 226.2363 29 'point symmetry operation' ? ? -0.811042 0.307409 0.497706 0.307409 -0.499888 0.809698 0.497706 0.809698 0.31093 227.40375 86.17237 -139.5603 30 'point symmetry operation' ? ? -0.312577 0.500682 0.807226 -0.500677 -0.809017 0.307918 0.807228 -0.307911 0.50356 1.39504 451.62073 -0.85919 31 'point symmetry operation' ? ? 0.811214 0.306778 -0.497814 -0.30769 -0.5 -0.809523 -0.497251 0.809869 -0.311215 85.76627 590.46104 225.49047 32 'point symmetry operation' ? ? 0.808841 -0.310973 -0.499072 -0.307233 0.500173 -0.809589 0.501383 0.80816 0.30902 225.91673 364.78875 -139.61268 33 'point symmetry operation' ? ? 0.309018 -0.49932 -0.809437 0.500962 0.808908 -0.307742 0.808421 -0.310399 0.500108 451.31189 -0.61053 0.21164 34 'point symmetry operation' ? ? 0.002485 0.002027 -0.999995 0.999997 -0.000457 0.002484 -0.000452 -0.999998 -0.002028 450.46328 -0.76741 451.73096 35 'point symmetry operation' ? ? 0.312859 0.500222 -0.807401 0.500222 -0.809406 -0.307634 -0.807401 -0.307634 -0.503452 224.54366 364.53491 590.96094 36 'point symmetry operation' ? ? -0.308737 0.500852 -0.808597 0.499774 0.808736 0.310115 0.809263 -0.308372 -0.499999 365.06242 -139.70865 225.21533 37 'point symmetry operation' ? ? 0.500448 0.809835 -0.306135 0.807741 -0.309471 0.501779 0.311619 -0.498392 -0.809011 -0.75542 -0.30326 450.19063 38 'point symmetry operation' ? ? 0.99999 -0.000561 0.004406 -0.000561 -1 -0.000001 0.004406 -0.000001 -0.99999 -0.86525 451.21687 450.25693 39 'point symmetry operation' ? ? 0.499539 -0.810398 -0.306132 -0.808086 -0.308563 -0.501783 0.312183 0.498041 -0.80901 364.88472 590.86627 225.3226 40 'point symmetry operation' ? ? -0.309299 -0.500507 -0.808596 -0.498862 0.809298 -0.31012 0.809612 0.307457 -0.499999 591.04045 225.65422 86.23924 41 'point symmetry operation' ? ? -0.499994 0.807913 -0.311902 -0.810009 -0.308841 0.498501 0.306417 0.501891 0.808835 226.93532 365.67237 -139.27299 42 'point symmetry operation' ? ? 0.49864 0.810117 0.308331 -0.810116 0.309017 0.498218 0.308335 -0.498215 0.810377 -139.05063 226.40555 85.51464 43 'point symmetry operation' ? ? 0.808841 -0.307233 0.501383 -0.310973 0.500173 0.80816 -0.499072 -0.809589 0.30902 -0.65624 0.62568 451.22066 44 'point symmetry operation' ? ? 0.001921 -0.999998 0.000462 -0.002379 0.000457 0.999997 -0.999995 -0.001922 -0.002378 450.86215 0.35287 452.45177 45 'point symmetry operation' ? ? -0.806983 -0.3108 -0.502176 -0.3108 -0.499541 0.808617 -0.502176 0.808617 0.306525 591.52146 225.96414 87.50663 46 'point symmetry operation' ? ? 0.811214 -0.30769 -0.497251 0.306778 -0.5 0.809869 -0.497814 -0.809523 -0.311215 224.22937 86.30153 590.86316 47 'point symmetry operation' ? ? 0.312296 -0.501136 -0.807052 -0.501136 -0.808627 0.308195 -0.807052 0.308195 -0.503669 450.44346 451.57405 452.03373 48 'point symmetry operation' ? ? 0.001921 -0.002379 -0.999995 -0.999998 0.000457 -0.001922 0.000462 0.999997 -0.002378 451.5843 451.73085 0.51505 49 'point symmetry operation' ? ? 0.309018 0.499316 -0.809439 -0.500397 0.809126 0.308088 0.808771 0.309836 0.499891 226.07527 86.55524 -139.70941 50 'point symmetry operation' ? ? 0.809188 0.310624 -0.498726 0.307235 0.499827 0.809802 0.50082 -0.808509 0.309019 85.5622 -139.2925 225.1458 51 'point symmetry operation' ? ? -0.308737 0.499774 0.809263 0.500852 0.808736 -0.308372 -0.808597 0.310115 -0.499999 0.27247 -0.40457 451.1217 52 'point symmetry operation' ? ? -0.001922 -0.002027 0.999996 0.999998 -0.000104 0.001922 0.000101 0.999998 0.002027 1.12094 -0.72052 -0.39754 53 'point symmetry operation' ? ? -0.312577 -0.500677 0.807228 0.500682 -0.809017 -0.307911 0.807226 0.307918 0.50356 227.24586 364.40582 -139.75579 54 'point symmetry operation' ? ? -0.811387 -0.307059 0.497359 -0.307059 -0.500112 -0.809693 0.497359 -0.809693 0.311499 366.15028 590.38226 225.63531 55 'point symmetry operation' ? ? -0.809013 0.311254 0.498616 -0.306954 0.499715 -0.809978 -0.501275 -0.808335 -0.308735 225.87301 364.91704 590.81768 56 'point symmetry operation' ? ? -0.002483 -0.999997 -0.00011 0.002379 0.000104 -0.999997 0.999994 -0.002484 0.002379 451.9857 450.61034 -0.204 57 'point symmetry operation' ? ? -0.809013 -0.306954 -0.501275 0.311254 0.499715 -0.808335 0.498616 -0.809978 -0.308735 590.90908 224.9206 365.35704 58 'point symmetry operation' ? ? -0.498185 0.810289 -0.308616 0.810289 0.308387 -0.498326 -0.308616 -0.498326 -0.810202 225.24894 85.41734 590.52796 59 'point symmetry operation' ? ? 0.500448 0.807741 0.311619 0.809835 -0.309471 -0.498392 -0.306135 0.501779 -0.809011 -139.66483 224.88932 364.1302 60 'point symmetry operation' ? ? 0.806809 -0.311078 0.502285 0.310519 -0.5 -0.808442 0.502631 0.808227 -0.306809 0.46619 450.59101 -0.96224 # _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 6LHA _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 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 5 188.068 219.272 358.565 1 105.89 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 189.159 218.394 358.729 1 105.89 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 188.022 219.749 357.12 1 105.89 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 189.029 219.03 356.365 1 105.89 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 186.639 219.558 356.508 1 105.89 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 185.677 220.185 357.328 1 105.89 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 186.56 220.11 355.112 1 105.89 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 187.372 221.253 354.678 1 105.89 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 186.911 222.15 353.55 1 105.89 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 185.8 221.503 352.734 1 105.89 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 185.025 222.551 351.94 1 105.89 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 184.347 223.557 352.861 1 105.89 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 183.225 224.29 352.143 1 105.89 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 182.728 225.478 352.956 1 105.89 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 181.834 226.384 352.121 1 105.89 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 180.372 225.981 352.257 1 105.89 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 179.468 227.206 352.28 1 105.89 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 178.003 226.812 352.147 1 105.89 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 177.102 228.04 352.072 1 105.89 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 176.735 228.41 350.64 1 105.89 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 175.67 229.499 350.608 1 105.89 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 21 #