data_7THX # _model_server_result.job_id eoCjg4kkqGk_4Cil1oKrQw _model_server_result.datetime_utc '2024-10-20 19:49:00' _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 7thx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 7THX # _exptl.entry_id 7THX _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 7THX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7THX _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,F,G,H 1 (1-60) A,B,C,D,E,F,G,H 2 1 A,B,C,D,E,F,G,H 3 (1-5) A,B,C,D,E,F,G,H 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H 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 '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' ? ? 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 0 0 0 3 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 0 0 0 4 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 0 0 0 5 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0 0 0 6 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 0 0 0 7 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 0 0 0 8 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0 0 0 9 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 0 0 0 10 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 0 0 0 11 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 12 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 0 0 0 13 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0 0 0 14 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 0 0 0 15 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 0 0 0 16 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 0 0 17 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 0 0 0 18 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 0 0 0 19 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 0 0 0 20 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 0 0 0 21 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 22 'point symmetry operation' ? ? -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 0 0 0 23 'point symmetry operation' ? ? -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 0 0 0 24 'point symmetry operation' ? ? 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 0 0 0 25 'point symmetry operation' ? ? 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 0 0 0 26 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 0 0 0 27 'point symmetry operation' ? ? -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 0 0 0 28 'point symmetry operation' ? ? -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 0 0 0 29 'point symmetry operation' ? ? 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 0 0 0 30 'point symmetry operation' ? ? 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0 0 0 31 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 0 0 0 32 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 0 0 0 33 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 0 0 0 34 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 0 0 0 35 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 0 0 0 36 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 0 0 0 37 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 0 0 0 38 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 0 0 0 39 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 0 0 0 40 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 0 0 0 41 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 42 'point symmetry operation' ? ? 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 0 0 0 43 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0 0 0 44 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 0 0 0 45 'point symmetry operation' ? ? -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 0 0 0 46 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 0 0 0 47 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 0 0 0 48 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 0 0 0 49 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 0 0 0 50 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 0 0 0 51 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 0 0 52 'point symmetry operation' ? ? 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 0 0 0 53 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0 0 0 54 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 0 0 0 55 'point symmetry operation' ? ? -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 0 0 0 56 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 0 0 0 57 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 0 0 0 58 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 0 0 0 59 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 0 0 0 60 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 0 0 0 # _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 # 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 metalc ? metalc1 A OG1 THR 14 1 THR 14 1_555 F K K . 1 K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc2 A O VAL 15 1 VAL 15 1_555 F K K . 1 K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc3 A OD1 ASN 17 1 ASN 17 1_555 F K K . 1 K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.063 ? metalc ? metalc4 A O ASN 57 1 ASN 57 1_555 F K K . 1 K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? # _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 290 n n C1 C2 SPH sing 291 n n C1 H11 SPH sing 292 n n C1 H12 SPH sing 293 n n O1 HO1 SPH sing 294 n n C2 N2 SPH sing 295 n n C2 C3 SPH sing 296 n n C2 H2 SPH sing 297 n n N2 HN21 SPH sing 298 n n N2 HN22 SPH sing 299 n n C3 O3 SPH sing 300 n n C3 C4 SPH sing 301 n n C3 H3 SPH sing 302 n n O3 HO3 SPH sing 303 n n C4 C5 SPH doub 304 z n C4 H4 SPH sing 305 n n C5 C6 SPH sing 306 n n C5 H5 SPH sing 307 n n C6 C7 SPH sing 308 n n C6 H61 SPH sing 309 n n C6 H62 SPH sing 310 n n C7 C8 SPH sing 311 n n C7 H71 SPH sing 312 n n C7 H72 SPH sing 313 n n C8 C9 SPH sing 314 n n C8 H81 SPH sing 315 n n C8 H82 SPH sing 316 n n C9 C10 SPH sing 317 n n C9 H91 SPH sing 318 n n C9 H92 SPH sing 319 n n C10 C11 SPH sing 320 n n C10 H101 SPH sing 321 n n C10 H102 SPH sing 322 n n C11 C12 SPH sing 323 n n C11 H111 SPH sing 324 n n C11 H112 SPH sing 325 n n C12 C13 SPH sing 326 n n C12 H121 SPH sing 327 n n C12 H122 SPH sing 328 n n C13 C14 SPH sing 329 n n C13 H131 SPH sing 330 n n C13 H132 SPH sing 331 n n C14 C15 SPH sing 332 n n C14 H141 SPH sing 333 n n C14 H142 SPH sing 334 n n C15 C16 SPH sing 335 n n C15 H151 SPH sing 336 n n C15 H152 SPH sing 337 n n C16 C17 SPH sing 338 n n C16 H161 SPH sing 339 n n C16 H162 SPH sing 340 n n C17 C18 SPH sing 341 n n C17 H171 SPH sing 342 n n C17 H172 SPH sing 343 n n C18 H181 SPH sing 344 n n C18 H182 SPH sing 345 n n C18 H183 SPH sing 346 n n # _atom_sites.entry_id 7THX _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 1 1 301 301 SPH SPH . F 6 K 1 1 302 302 K K . G 7 HOH 3 1 301 107 HOH HOH . G 7 HOH 3 2 302 114 HOH HOH . H 7 HOH 4 1 101 102 HOH HOH . H 7 HOH 4 2 102 101 HOH HOH . H 7 HOH 4 3 103 110 HOH HOH . H 7 HOH 4 4 104 111 HOH HOH . H 7 HOH 4 5 105 108 HOH HOH . H 7 HOH 4 6 106 121 HOH HOH . H 7 HOH 4 7 107 106 HOH HOH . H 7 HOH 4 8 108 104 HOH HOH . H 7 HOH 4 9 109 105 HOH HOH . H 7 HOH 4 10 110 103 HOH HOH . H 7 HOH 4 11 111 112 HOH HOH . H 7 HOH 4 12 112 117 HOH HOH . H 7 HOH 4 13 113 113 HOH HOH . H 7 HOH 4 14 114 109 HOH HOH . H 7 HOH 4 15 115 116 HOH HOH . H 7 HOH 4 16 116 115 HOH HOH . H 7 HOH 4 17 117 119 HOH HOH . H 7 HOH 4 18 118 118 HOH HOH . H 7 HOH 4 19 119 120 HOH HOH . # 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 33.686 53.548 121.246 1 128.43 ? C1 SPH 301 1 1 HETATM 2 O O1 SPH . . . E 5 34.381 52.834 122.255 1 134.77 ? O1 SPH 301 1 1 HETATM 3 C C2 SPH . . . E 5 32.268 53.007 121.067 1 119.73 ? C2 SPH 301 1 1 HETATM 4 N N2 SPH . . . E 5 31.633 52.829 122.398 1 125.75 ? N2 SPH 301 1 1 HETATM 5 C C3 SPH . . . E 5 31.437 53.852 120.033 1 99.07 ? C3 SPH 301 1 1 HETATM 6 O O3 SPH . . . E 5 31.405 55.203 120.44 1 100.43 ? O3 SPH 301 1 1 HETATM 7 C C4 SPH . . . E 5 31.964 53.805 118.62 1 79.4 ? C4 SPH 301 1 1 HETATM 8 C C5 SPH . . . E 5 31.438 54.391 117.575 1 61.33 ? C5 SPH 301 1 1 HETATM 9 C C6 SPH . . . E 5 30.097 55.06 117.473 1 56.7 ? C6 SPH 301 1 1 HETATM 10 C C7 SPH . . . E 5 30.131 56.39 116.739 1 52.22 ? C7 SPH 301 1 1 HETATM 11 C C8 SPH . . . E 5 28.789 56.905 116.269 1 47.86 ? C8 SPH 301 1 1 HETATM 12 C C9 SPH . . . E 5 28.883 57.98 115.22 1 46.53 ? C9 SPH 301 1 1 HETATM 13 C C10 SPH . . . E 5 28.695 59.379 115.718 1 46.46 ? C10 SPH 301 1 1 HETATM 14 C C11 SPH . . . E 5 28.986 60.47 114.692 1 47.08 ? C11 SPH 301 1 1 HETATM 15 C C12 SPH . . . E 5 28.672 61.899 115.131 1 48.67 ? C12 SPH 301 1 1 HETATM 16 C C13 SPH . . . E 5 27.279 62.328 114.808 1 53.48 ? C13 SPH 301 1 1 HETATM 17 C C14 SPH . . . E 5 26.744 63.59 115.457 1 56.6 ? C14 SPH 301 1 1 HETATM 18 C C15 SPH . . . E 5 25.255 63.762 115.169 1 56.02 ? C15 SPH 301 1 1 HETATM 19 C C16 SPH . . . E 5 24.6 64.943 115.853 1 57.21 ? C16 SPH 301 1 1 HETATM 20 C C17 SPH . . . E 5 23.352 65.546 115.223 1 57.35 ? C17 SPH 301 1 1 HETATM 21 C C18 SPH . . . E 5 23.366 67.068 114.92 1 57.95 ? C18 SPH 301 1 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 21 #