data_5YTH # _model_server_result.job_id czGQfjoeJJ6FfUnNBoTs2A _model_server_result.datetime_utc '2024-11-26 14:51:24' _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 5yth # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":904}' # _entry.id 5YTH # _exptl.entry_id 5YTH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 120 _cell.entry_id 5YTH _cell.length_a 109.273 _cell.length_b 109.273 _cell.length_c 91.119 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YTH _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _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 covale ? covale1 B O3' DC 11 B DC 111 1_555 B P DOC 12 B DOC 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.536 ? covale ? covale2 C O3' DG 11 C DG 211 1_555 C P 92F 12 C 92F 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? covale ? covale3 C O3' 92F 12 C 92F 212 1_555 C P DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.589 ? metalc ? metalc1 A OD1 ASP 317 A ASP 610 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc2 A OD2 ASP 317 A ASP 610 1_555 F MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc3 A O TYR 318 A TYR 611 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc4 A OD2 ASP 492 A ASP 785 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc5 A OD1 ASP 492 A ASP 785 1_555 F MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc6 D O3G DGT . A DGT 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc7 D O2B DGT . A DGT 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc8 D O2A DGT . A DGT 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc9 D O2A DGT . A DGT 901 1_555 F MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc10 F MG MG . A MG 903 1_555 H O HOH . A HOH 1022 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc11 F MG MG . A MG 903 1_555 I O HOH . B HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 B DG 101 1_555 C N3 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 B DG 101 1_555 C O2 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 B DG 101 1_555 C N4 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 B DA 102 1_555 C N3 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 B DA 102 1_555 C O4 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 B DC 103 1_555 C N1 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 B DC 103 1_555 C O6 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 B DC 103 1_555 C N2 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 4 B DC 104 1_555 C N1 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 4 B DC 104 1_555 C O6 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 4 B DC 104 1_555 C N2 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-92F MISPAIR' hydrog12 B N2 DG 5 B DG 105 1_555 C O2 92F 12 C 92F 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DC 6 B DC 106 1_555 C N1 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 DC 6 B DC 106 1_555 C O6 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 DC 6 B DC 106 1_555 C N2 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 7 B DG 107 1_555 C N3 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 7 B DG 107 1_555 C O2 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 7 B DG 107 1_555 C N4 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 8 B DG 108 1_555 C N3 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 8 B DG 108 1_555 C O2 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 8 B DG 108 1_555 C N4 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DC 9 B DC 109 1_555 C N1 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N4 DC 9 B DC 109 1_555 C O6 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O2 DC 9 B DC 109 1_555 C N2 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 DG 10 B DG 110 1_555 C N3 DC 7 C DC 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N2 DG 10 B DG 110 1_555 C O2 DC 7 C DC 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O6 DG 10 B DG 110 1_555 C N4 DC 7 C DC 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N3 DC 11 B DC 111 1_555 C N1 DG 6 C DG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N4 DC 11 B DC 111 1_555 C O6 DG 6 C DG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B O2 DC 11 B DC 111 1_555 C N2 DG 6 C DG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N3 DOC 12 B DOC 112 1_555 C N1 DG 5 C DG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N4 DOC 12 B DOC 112 1_555 C O6 DG 5 C DG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B O2 DOC 12 B DOC 112 1_555 C N2 DG 5 C DG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 390 n n C1 C2 GOL sing 391 n n C1 H11 GOL sing 392 n n C1 H12 GOL sing 393 n n O1 HO1 GOL sing 394 n n C2 O2 GOL sing 395 n n C2 C3 GOL sing 396 n n C2 H2 GOL sing 397 n n O2 HO2 GOL sing 398 n n C3 O3 GOL sing 399 n n C3 H31 GOL sing 400 n n C3 H32 GOL sing 401 n n O3 HO3 GOL sing 402 n n # _atom_sites.entry_id 5YTH _atom_sites.fract_transf_matrix[1][1] 0.009151 _atom_sites.fract_transf_matrix[1][2] 0.005284 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010567 _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] 0.010975 _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 D 4 DGT A 1 901 1 DGT DGT . E 5 MG A 1 902 1 MG MG . F 5 MG A 1 903 2 MG MG . G 6 GOL A 1 904 1 GOL GOL . H 7 HOH A 1 1001 41 HOH HOH . H 7 HOH A 2 1002 51 HOH HOH . H 7 HOH A 3 1003 40 HOH HOH . H 7 HOH A 4 1004 54 HOH HOH . H 7 HOH A 5 1005 17 HOH HOH . H 7 HOH A 6 1006 39 HOH HOH . H 7 HOH A 7 1007 55 HOH HOH . H 7 HOH A 8 1008 21 HOH HOH . H 7 HOH A 9 1009 64 HOH HOH . H 7 HOH A 10 1010 53 HOH HOH . H 7 HOH A 11 1011 58 HOH HOH . H 7 HOH A 12 1012 71 HOH HOH . H 7 HOH A 13 1013 50 HOH HOH . H 7 HOH A 14 1014 3 HOH HOH . H 7 HOH A 15 1015 68 HOH HOH . H 7 HOH A 16 1016 61 HOH HOH . H 7 HOH A 17 1017 30 HOH HOH . H 7 HOH A 18 1018 67 HOH HOH . H 7 HOH A 19 1019 34 HOH HOH . H 7 HOH A 20 1020 74 HOH HOH . H 7 HOH A 21 1021 14 HOH HOH . H 7 HOH A 22 1022 72 HOH HOH . H 7 HOH A 23 1023 52 HOH HOH . H 7 HOH A 24 1024 25 HOH HOH . H 7 HOH A 25 1025 1 HOH HOH . H 7 HOH A 26 1026 75 HOH HOH . H 7 HOH A 27 1027 15 HOH HOH . H 7 HOH A 28 1028 49 HOH HOH . H 7 HOH A 29 1029 6 HOH HOH . H 7 HOH A 30 1030 29 HOH HOH . H 7 HOH A 31 1031 63 HOH HOH . H 7 HOH A 32 1032 56 HOH HOH . H 7 HOH A 33 1033 47 HOH HOH . H 7 HOH A 34 1034 37 HOH HOH . H 7 HOH A 35 1035 32 HOH HOH . H 7 HOH A 36 1036 33 HOH HOH . H 7 HOH A 37 1037 27 HOH HOH . H 7 HOH A 38 1038 36 HOH HOH . H 7 HOH A 39 1039 35 HOH HOH . H 7 HOH A 40 1040 44 HOH HOH . H 7 HOH A 41 1041 7 HOH HOH . H 7 HOH A 42 1042 69 HOH HOH . H 7 HOH A 43 1043 42 HOH HOH . H 7 HOH A 44 1044 77 HOH HOH . H 7 HOH A 45 1045 5 HOH HOH . H 7 HOH A 46 1046 60 HOH HOH . H 7 HOH A 47 1047 18 HOH HOH . H 7 HOH A 48 1048 16 HOH HOH . H 7 HOH A 49 1049 45 HOH HOH . H 7 HOH A 50 1050 24 HOH HOH . H 7 HOH A 51 1051 38 HOH HOH . H 7 HOH A 52 1052 26 HOH HOH . H 7 HOH A 53 1053 78 HOH HOH . H 7 HOH A 54 1054 2 HOH HOH . H 7 HOH A 55 1055 19 HOH HOH . H 7 HOH A 56 1056 12 HOH HOH . H 7 HOH A 57 1057 59 HOH HOH . H 7 HOH A 58 1058 22 HOH HOH . H 7 HOH A 59 1059 28 HOH HOH . H 7 HOH A 60 1060 62 HOH HOH . H 7 HOH A 61 1061 13 HOH HOH . I 7 HOH B 1 201 73 HOH HOH . I 7 HOH B 2 202 70 HOH HOH . I 7 HOH B 3 203 43 HOH HOH . J 7 HOH C 1 301 76 HOH HOH . J 7 HOH C 2 302 10 HOH HOH . J 7 HOH C 3 303 65 HOH HOH . J 7 HOH C 4 304 46 HOH HOH . J 7 HOH C 5 305 20 HOH HOH . J 7 HOH C 6 306 9 HOH HOH . J 7 HOH C 7 307 66 HOH HOH . J 7 HOH C 8 308 11 HOH HOH . J 7 HOH C 9 309 8 HOH HOH . J 7 HOH C 10 310 79 HOH HOH . J 7 HOH C 11 311 31 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 GOL . . . G 6 -19.315 119.792 8.946 1 66.37 ? C1 GOL 904 A 1 HETATM 2 O O1 GOL . . . G 6 -19.474 118.601 8.166 1 72.8 ? O1 GOL 904 A 1 HETATM 3 C C2 GOL . . . G 6 -17.916 120.402 8.808 1 62.6 ? C2 GOL 904 A 1 HETATM 4 O O2 GOL . . . G 6 -17.777 121.517 9.699 1 87.12 ? O2 GOL 904 A 1 HETATM 5 C C3 GOL . . . G 6 -16.818 119.394 9.139 1 76.55 ? C3 GOL 904 A 1 HETATM 6 O O3 GOL . . . G 6 -15.483 119.915 9.002 1 91.97 ? O3 GOL 904 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #