data_7C9W # _model_server_result.job_id 03CZNA5Z2xFxyEIXkPO3EQ _model_server_result.datetime_utc '2025-07-09 23:11:41' _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 7c9w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":500}' # _entry.id 7C9W # _exptl.entry_id 7C9W _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 6 _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 ? 300-meric 300 'complete icosahedral assembly' 1 ? pentameric 5 'icosahedral asymmetric unit' 2 ? 25-meric 25 'icosahedral pentamer' 3 ? 30-meric 30 'icosahedral 23 hexamer' 4 ? pentameric 5 'icosahedral asymmetric unit, std point frame' 5 ? 300-meric 300 '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,G 1 (1-60) A,B,C,D,E,F,G 2 1 A,B,C,D,E,F,G 3 (1-5) A,B,C,D,E,F,G 4 (1,2,6,10,23,24) A,B,C,D,E,F,G 5 P A,B,C,D,E,F,G 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' ? ? -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 121.8145 0 -318.9145 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' ? ? 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 75.2855 197.1 -121.8145 3 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0 394.2 0 4 'point symmetry operation' ? ? 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 -121.8145 318.9145 197.1 5 'point symmetry operation' ? ? 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 -121.8145 75.2855 197.1 6 'point symmetry operation' ? ? -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 75.2855 197.1 -121.8145 7 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 8 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 197.1 -121.8145 75.2855 9 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 394.2 0 0 10 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 318.9145 197.1 -121.8145 11 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 394.2 394.20001 394.2 12 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 318.9145 197.1 516.0145 13 'point symmetry operation' ? ? -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 75.2855 197.1 516.0145 14 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 394.2 394.2 15 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 197.1 516.01451 318.9145 16 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 318.9145 197.1 516.0145 17 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 394.2 394.20001 394.2 18 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 516.0145 318.9145 197.1 19 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 516.0145 75.2855 197.1 20 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 394.2 0 394.2 21 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 394.2 394.2 0 22 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 197.1 516.0145 75.2855 23 'point symmetry operation' ? ? -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 0 394.2 0 24 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 0.5 0.309017 0.809017 75.2855 197.1 -121.8145 25 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 318.9145 197.1 -121.8145 26 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 197.1 516.0145 75.2855 27 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 394.2 394.2 0 28 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 516.0145 318.9145 197.1 29 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 394.2 394.20001 394.2 30 'point symmetry operation' ? ? -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 197.1 516.0145 318.9145 31 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0 0 394.2 32 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 197.1 -121.8145 318.9145 33 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 197.1 -121.8145 75.2855 34 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 35 'point symmetry operation' ? ? 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 -121.8145 75.2855 197.1 36 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 197.1 -121.8145 318.9145 37 'point symmetry operation' ? ? -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 0 0 394.2 38 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 75.2855 197.1 516.0145 39 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 318.9145 197.1 516.0145 40 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 394.2 0 394.2 41 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 0 394.2 394.2 42 'point symmetry operation' ? ? 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 -121.8145 318.9145 197.1 43 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0 394.2 0 44 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 197.1 516.0145 75.2855 45 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 197.1 516.01451 318.9145 46 'point symmetry operation' ? ? 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 -121.8145 318.9145 197.1 47 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 394.20001 394.2 48 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 75.2855 197.1 516.0145 49 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0 0 394.2 50 'point symmetry operation' ? ? 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 -121.8145 75.2855 197.1 51 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 394.2 0 0 52 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 516.0145 75.2855 197.1 53 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 516.0145 318.9145 197.1 54 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 394.2 394.2 0 55 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 318.9145 197.1 -121.8145 56 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 516.0145 75.2855 197.1 57 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 394.2 0 0 58 'point symmetry operation' ? ? -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 197.1 -121.8145 75.2855 59 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 197.1 -121.8145 318.9145 60 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 394.2 0 394.2 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order disulf ? disulf1 E SG CYS 5 E CYS 66 1_555 E SG CYS 52 E CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 E SG CYS 36 E CYS 97 1_555 E SG CYS 65 E CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 E SG CYS 70 E CYS 131 1_555 E SG CYS 111 E CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 E SG CYS 97 E CYS 158 1_555 E SG CYS 127 E CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 E SG CYS 132 E CYS 193 1_555 E SG CYS 174 E CYS 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 E SG CYS 160 E CYS 221 1_555 E SG CYS 190 E CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _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 7C9W _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 F 6 SPH A 1 500 500 SPH SPH . G 7 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 . . . F 6 287.421 181.376 293.366 1 36.96 ? C1 SPH 500 A 1 HETATM 2 O O1 SPH . . . F 6 288.606 181.514 294.115 1 36.96 ? O1 SPH 500 A 1 HETATM 3 C C2 SPH . . . F 6 287.477 182.265 292.129 1 36.96 ? C2 SPH 500 A 1 HETATM 4 N N2 SPH . . . F 6 288.526 183.248 292.286 1 36.96 ? N2 SPH 500 A 1 HETATM 5 C C3 SPH . . . F 6 287.738 181.389 290.914 1 36.96 ? C3 SPH 500 A 1 HETATM 6 O O3 SPH . . . F 6 286.522 180.92 290.394 1 36.96 ? O3 SPH 500 A 1 HETATM 7 C C4 SPH . . . F 6 288.546 182.062 289.846 1 36.96 ? C4 SPH 500 A 1 HETATM 8 C C5 SPH . . . F 6 289.609 181.269 289.214 1 36.96 ? C5 SPH 500 A 1 HETATM 9 C C6 SPH . . . F 6 290.299 181.716 287.951 1 36.96 ? C6 SPH 500 A 1 HETATM 10 C C7 SPH . . . F 6 289.468 181.332 286.739 1 36.96 ? C7 SPH 500 A 1 HETATM 11 C C8 SPH . . . F 6 290.338 181.31 285.491 1 36.96 ? C8 SPH 500 A 1 HETATM 12 C C9 SPH . . . F 6 291.418 180.241 285.595 1 36.96 ? C9 SPH 500 A 1 HETATM 13 C C10 SPH . . . F 6 292.669 180.659 284.835 1 36.96 ? C10 SPH 500 A 1 HETATM 14 C C11 SPH . . . F 6 293.225 179.507 284.013 1 36.96 ? C11 SPH 500 A 1 HETATM 15 C C12 SPH . . . F 6 293.853 180.016 282.722 1 36.96 ? C12 SPH 500 A 1 HETATM 16 C C13 SPH . . . F 6 295.375 179.998 282.758 1 36.96 ? C13 SPH 500 A 1 HETATM 17 C C14 SPH . . . F 6 295.954 179.79 281.361 1 36.96 ? C14 SPH 500 A 1 HETATM 18 C C15 SPH . . . F 6 297.347 180.394 281.241 1 36.96 ? C15 SPH 500 A 1 HETATM 19 C C16 SPH . . . F 6 297.832 180.375 279.798 1 36.96 ? C16 SPH 500 A 1 HETATM 20 C C17 SPH . . . F 6 299.347 180.511 279.734 1 36.96 ? C17 SPH 500 A 1 HETATM 21 C C18 SPH . . . F 6 299.845 180.277 278.317 1 36.96 ? C18 SPH 500 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #