data_7EAI # _model_server_result.job_id rEA62u6MY2i0e7TuMfwxyg _model_server_result.datetime_utc '2025-08-31 15:16:38' _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 7eai # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 7EAI # _exptl.entry_id 7EAI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 4 _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 ? 180-meric 180 'complete icosahedral assembly' 1 ? trimeric 3 'icosahedral asymmetric unit' 2 ? pentadecameric 15 'icosahedral pentamer' 3 ? octadecameric 18 'icosahedral 23 hexamer' 4 ? trimeric 3 '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 1 (1-60) A,B,C,D 2 1 A,B,C,D 3 (1-5) A,B,C,D 4 (1,2,6,10,23,24) A,B,C,D 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' ? ? -0.688191 -0.5 -0.525731 -0.425325 -0.309017 0.850651 -0.587785 0.809017 0 369.35021 -25.06446 -47.67544 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.67082 -0.688191 0.276393 0.16246 0.5 0.850651 -0.723607 -0.525731 0.447214 159.68063 -110.57535 388.35779 3 'point symmetry operation' ? ? 0.138197 -0.951057 -0.276393 -0.425325 -0.309017 0.850651 -0.894427 0 -0.447214 450.23405 190.43554 504.62359 4 'point symmetry operation' ? ? 0.138197 -0.425325 -0.894427 -0.951057 -0.309017 0 -0.276393 0.850651 -0.447214 470.12532 487.04585 188.12201 5 'point symmetry operation' ? ? 0.67082 0.16246 -0.723607 -0.688191 0.5 -0.525731 0.276393 0.850651 0.447214 191.86537 369.35021 -123.75252 6 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 0 0 0 -1 487.04585 353.85952 431 7 'point symmetry operation' ? ? -0.361803 -0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 -0.447214 542.86523 167.82456 42.6422 8 'point symmetry operation' ? ? 0.361803 0.587785 -0.723607 -0.262866 0.809017 0.525731 0.894427 0 0.447214 166.80091 -15.49069 -73.62359 9 'point symmetry operation' ? ? 0.861803 0.425325 0.276393 -0.425325 0.309017 0.850651 0.276393 -0.850651 0.447214 -121.43899 57.24922 242.87799 10 'point symmetry operation' ? ? 0.447214 -0.525731 0.723607 -0.850651 0 0.525731 -0.276393 -0.850651 -0.447214 76.48326 285.5202 554.75252 11 'point symmetry operation' ? ? -0.638197 0.262866 -0.723607 0.262866 -0.809017 -0.525731 -0.723607 -0.525731 0.447214 452.32111 446.49069 388.35779 12 'point symmetry operation' ? ? 0.138197 0.951057 -0.276393 0.425325 -0.309017 -0.850651 -0.894427 0 -0.447214 40.32869 373.75079 504.62359 13 'point symmetry operation' ? ? 0.447214 0.525731 0.723607 0.850651 0 -0.525731 -0.276393 0.850651 -0.447214 -150.10685 145.47981 188.12201 14 'point symmetry operation' ? ? -0.138197 -0.425325 0.894427 0.951057 -0.309017 0 0.276393 0.850651 0.447214 144.18994 77.14048 -123.75252 15 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 516.51089 263.17544 0 16 'point symmetry operation' ? ? -0.052786 0.688191 0.723607 0.688191 -0.5 0.525731 0.723607 0.525731 -0.447214 -77.36694 61.64979 42.64221 17 'point symmetry operation' ? ? -0.447214 0 0.894427 0 -1 0 0.894427 0 0.447214 119.12548 431.00001 -73.62359 18 'point symmetry operation' ? ? -0.947214 -0.16246 0.276393 -0.16246 -0.5 -0.850651 0.276393 -0.850651 0.447214 395.0719 541.57535 242.87798 19 'point symmetry operation' ? ? -0.861803 0.425325 -0.276393 0.425325 0.309017 -0.850651 -0.276393 -0.850651 -0.447214 369.12375 240.56446 554.75251 20 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0 0 0 -1 77.14049 -56.04584 431 21 'point symmetry operation' ? ? 0.947214 -0.16246 -0.276393 0.16246 -0.5 0.850651 -0.276393 -0.850651 -0.447214 105.9483 104.92466 554.75252 22 'point symmetry operation' ? ? 0.809017 -0.587785 0 -0.587785 -0.809017 0 0 0 -1 167.82456 516.51089 431 23 'point symmetry operation' ? ? 0.447214 -0.850651 -0.276393 -0.525731 0 -0.850651 0.723607 0.525731 -0.447214 362.00346 512.11031 42.6422 24 'point symmetry operation' ? ? 0.361803 -0.587785 -0.723607 0.262866 0.809017 -0.525731 0.894427 0 0.447214 420.13636 97.80436 -73.62359 25 'point symmetry operation' ? ? 0.67082 -0.16246 -0.723607 0.688191 0.5 0.525731 0.276393 -0.850651 0.447214 261.88557 -153.85021 242.87798 26 'point symmetry operation' ? ? -0.138197 -0.951057 0.276393 0.425325 -0.309017 -0.850651 0.894427 0 0.447214 390.67132 373.75079 -73.6236 27 'point symmetry operation' ? ? -0.447214 -0.525731 -0.723607 0.850651 0 -0.525731 0.276393 -0.850651 0.447214 581.10686 145.47981 242.87798 28 'point symmetry operation' ? ? 0.138197 0.425325 -0.894427 0.951057 -0.309017 0 -0.276393 -0.850651 -0.447214 286.81007 77.14048 554.75252 29 'point symmetry operation' ? ? 0.809017 0.587785 0 0.587785 -0.809017 0 0 0 -1 -85.51088 263.17544 431 30 'point symmetry operation' ? ? 0.638197 -0.262866 0.723607 0.262866 -0.809017 -0.525731 0.723607 0.525731 -0.447214 -21.3211 446.49069 42.6422 31 'point symmetry operation' ? ? -0.447214 0.525731 -0.723607 -0.850651 0 0.525731 0.276393 0.850651 0.447214 354.51674 285.5202 -123.75252 32 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 -56.04584 353.85952 0 33 'point symmetry operation' ? ? 0.361803 0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 0.447214 -111.86522 167.82456 388.35779 34 'point symmetry operation' ? ? -0.361803 -0.587785 0.723607 -0.262866 0.809017 0.525731 -0.894427 0 -0.447214 264.1991 -15.49069 504.62359 35 'point symmetry operation' ? ? -0.861803 -0.425325 -0.276393 -0.425325 0.309017 0.850651 -0.276393 0.850651 -0.447214 552.439 57.24922 188.12201 36 'point symmetry operation' ? ? -0.361803 0.587785 0.723607 0.262866 0.809017 -0.525731 -0.894427 0 -0.447214 10.86365 97.80437 504.62359 37 'point symmetry operation' ? ? -0.67082 0.16246 0.723607 0.688191 0.5 0.525731 -0.276393 0.850651 -0.447214 169.11444 -153.85021 188.12201 38 'point symmetry operation' ? ? -0.947214 0.16246 0.276393 0.16246 -0.5 0.850651 0.276393 0.850651 0.447214 325.0517 104.92466 -123.75252 39 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 263.17545 516.51089 0 40 'point symmetry operation' ? ? -0.447214 0.850651 0.276393 -0.525731 0 -0.850651 -0.723607 -0.525731 0.447214 68.99655 512.11031 388.35779 41 'point symmetry operation' ? ? 0.947214 0.16246 -0.276393 -0.16246 -0.5 -0.850651 -0.276393 0.850651 -0.447214 35.92811 541.57535 188.12201 42 'point symmetry operation' ? ? 0.861803 -0.425325 0.276393 0.425325 0.309017 -0.850651 0.276393 0.850651 0.447214 61.87626 240.56446 -123.75252 43 'point symmetry operation' ? ? 0.309017 -0.951057 0 0.951057 0.309017 0 0 0 1 353.85952 -56.04584 0 44 'point symmetry operation' ? ? 0.052786 -0.688191 -0.723607 0.688191 -0.5 0.525731 -0.723607 -0.525731 0.447214 508.36695 61.64979 388.35779 45 'point symmetry operation' ? ? 0.447214 0 -0.894427 0 -1 0 -0.894427 0 -0.447214 311.87453 431.00001 504.62359 46 'point symmetry operation' ? ? -0.447214 -0.850651 0.276393 0.525731 0 0.850651 -0.723607 0.525731 0.447214 435.62705 -81.1103 161.76768 47 'point symmetry operation' ? ? -0.638197 -0.262866 -0.723607 -0.262866 -0.809017 0.525731 -0.723607 0.525731 0.447214 565.61617 333.19564 161.76768 48 'point symmetry operation' ? ? 0.052786 0.688191 -0.723607 -0.688191 -0.5 -0.525731 -0.723607 0.525731 0.447214 211.75665 584.85022 161.76768 49 'point symmetry operation' ? ? 0.67082 0.688191 0.276393 -0.16246 0.5 -0.850651 -0.723607 0.525731 0.447214 -136.92968 326.07535 161.76768 50 'point symmetry operation' ? ? 0.361803 -0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 0.447214 1.42984 -85.51089 161.76768 51 'point symmetry operation' ? ? -0.361803 0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 -0.447214 429.57017 -85.51089 269.23232 52 'point symmetry operation' ? ? 0.447214 0.850651 -0.276393 0.525731 0 0.850651 0.723607 -0.525731 -0.447214 -4.62704 -81.1103 269.23232 53 'point symmetry operation' ? ? 0.638197 0.262866 0.723607 -0.262866 -0.809017 0.525731 0.723607 -0.525731 -0.447214 -134.61616 333.19564 269.23232 54 'point symmetry operation' ? ? -0.052786 -0.688191 0.723607 -0.688191 -0.5 -0.525731 0.723607 -0.525731 -0.447214 219.24336 584.85022 269.23231 55 'point symmetry operation' ? ? -0.67082 -0.688191 -0.276393 -0.16246 0.5 -0.850651 0.723607 -0.525731 -0.447214 567.92969 326.07535 269.23231 56 'point symmetry operation' ? ? -0.138197 0.425325 0.894427 -0.951057 -0.309017 0 0.276393 -0.850651 0.447214 -39.12531 487.04585 242.87798 57 'point symmetry operation' ? ? -0.67082 -0.16246 0.723607 -0.688191 0.5 -0.525731 -0.276393 -0.850651 -0.447214 239.13464 369.35021 554.75251 58 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 431.00001 0 431 59 'point symmetry operation' ? ? -0.67082 0.688191 -0.276393 0.16246 0.5 0.850651 0.723607 0.525731 -0.447214 271.31938 -110.57535 42.64221 60 'point symmetry operation' ? ? -0.138197 0.951057 0.276393 -0.425325 -0.309017 0.850651 0.894427 0 0.447214 -19.23405 190.43554 -73.62359 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id CE _struct_conn.ptnr1_label_comp_id MET _struct_conn.ptnr1_label_seq_id 181 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id MET _struct_conn.ptnr1_auth_seq_id 181 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id C18 _struct_conn.ptnr2_label_comp_id SPH _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id SPH _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.492 _struct_conn.pdbx_value_order ? # _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 7EAI _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 D _pdbx_nonpoly_scheme.entity_id 4 _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 499 _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 . . . D 4 100.556 278.862 241.445 1 124.78 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . D 4 99.366 279.587 241.664 1 124.78 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . D 4 101.25 278.602 242.776 1 124.78 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . D 4 100.402 279.048 243.863 1 124.78 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . D 4 101.542 277.116 242.94 1 124.78 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . D 4 102.063 276.621 241.727 1 124.78 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . D 4 102.528 276.882 244.047 1 124.78 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . D 4 103.537 277.894 244.394 1 124.78 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . D 4 104.79 277.499 245.136 1 124.78 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . D 4 104.511 276.303 246.037 1 124.78 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . D 4 104.063 276.73 247.427 1 124.78 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . D 4 104.647 275.791 248.474 1 124.78 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . D 4 103.684 275.595 249.633 1 124.78 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . D 4 104.323 275.976 250.959 1 124.78 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . D 4 104.932 274.761 251.644 1 124.78 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . D 4 104.057 274.263 252.79 1 124.78 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . D 4 103.903 275.301 253.893 1 124.78 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . D 4 104.573 274.849 255.186 1 124.78 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . D 4 104.151 275.749 256.343 1 124.78 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . D 4 104.775 275.31 257.666 1 124.78 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . D 4 106.282 275.542 257.71 1 124.78 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 403 _model_server_stats.encode_time_ms 51 _model_server_stats.element_count 21 #