data_2F13 # _model_server_result.job_id UdOUI5ABT_A5q7SwRYXuow _model_server_result.datetime_utc '2024-12-30 17:01:22' _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 2f13 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 2F13 # _exptl.entry_id 2F13 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.255 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid' _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 2F13 _cell.length_a 87.5 _cell.length_b 88.06 _cell.length_c 92.59 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F13 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H17 N O8' _chem_comp.formula_weight 291.255 _chem_comp.id DYM _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid' _chem_comp.type l-saccharide _chem_comp.pdbx_synonyms '6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID;2,3-DIHYDROXYPROPYL ETHER MIMETIC;(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enosiduronic acid;(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-L-threo-hex-4-enosiduronic acid;(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-threo-hex-4-enosiduronic acid' # 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 C2 DYM sing 83 n n C1 O1A DYM doub 84 n n C1 O1B DYM sing 85 n n C2 C3 DYM doub 86 n n C2 O6 DYM sing 87 n n C3 C4 DYM sing 88 n n C3 H3 DYM sing 89 n n C4 C5 DYM sing 90 n n C4 O4 DYM sing 91 n n C4 H4 DYM sing 92 n n C5 C6 DYM sing 93 n n C5 N5 DYM sing 94 n n C5 H5 DYM sing 95 n n C6 O6 DYM sing 96 n n C6 O7 DYM sing 97 n n C6 H6 DYM sing 98 n n C7 C8 DYM sing 99 n n C7 O7 DYM sing 100 n n C7 H71 DYM sing 101 n n C7 H72 DYM sing 102 n n C8 C9 DYM sing 103 n n C8 O8 DYM sing 104 n n C8 H8 DYM sing 105 n n C9 O9 DYM sing 106 n n C9 H91 DYM sing 107 n n C9 H92 DYM sing 108 n n C10 C11 DYM sing 109 n n C10 N5 DYM sing 110 n n C10 O10 DYM doub 111 n n C11 H111 DYM sing 112 n n C11 H112 DYM sing 113 n n C11 H113 DYM sing 114 n n N5 HN5 DYM sing 115 n n O4 HO4 DYM sing 116 n n O8 HO8 DYM sing 117 n n O9 HO9 DYM sing 118 n n O1B HO1B DYM sing 119 n n # _atom_sites.entry_id 2F13 _atom_sites.fract_transf_matrix[1][1] 0.011429 _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] 0.011356 _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] 0.0108 _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 B 2 PO4 A 1 1002 2 PO4 PO4 . C 3 DYM A 1 1001 1 DYM DEM . D 4 HOH A 1 1003 1 HOH HOH . D 4 HOH A 2 1004 2 HOH HOH . D 4 HOH A 3 1005 3 HOH HOH . D 4 HOH A 4 1006 4 HOH HOH . D 4 HOH A 5 1007 5 HOH HOH . D 4 HOH A 6 1008 6 HOH HOH . D 4 HOH A 7 1009 7 HOH HOH . D 4 HOH A 8 1010 8 HOH HOH . D 4 HOH A 9 1011 9 HOH HOH . D 4 HOH A 10 1012 10 HOH HOH . D 4 HOH A 11 1013 11 HOH HOH . D 4 HOH A 12 1014 12 HOH HOH . D 4 HOH A 13 1015 13 HOH HOH . D 4 HOH A 14 1016 14 HOH HOH . D 4 HOH A 15 1017 15 HOH HOH . D 4 HOH A 16 1018 16 HOH HOH . D 4 HOH A 17 1019 17 HOH HOH . D 4 HOH A 18 1020 18 HOH HOH . D 4 HOH A 19 1021 19 HOH HOH . D 4 HOH A 20 1022 20 HOH HOH . D 4 HOH A 21 1023 21 HOH HOH . D 4 HOH A 22 1024 22 HOH HOH . D 4 HOH A 23 1025 23 HOH HOH . D 4 HOH A 24 1026 24 HOH HOH . D 4 HOH A 25 1027 25 HOH HOH . D 4 HOH A 26 1028 26 HOH HOH . D 4 HOH A 27 1029 27 HOH HOH . D 4 HOH A 28 1030 28 HOH HOH . D 4 HOH A 29 1031 29 HOH HOH . D 4 HOH A 30 1032 30 HOH HOH . D 4 HOH A 31 1033 31 HOH HOH . D 4 HOH A 32 1034 32 HOH HOH . D 4 HOH A 33 1035 33 HOH HOH . D 4 HOH A 34 1036 34 HOH HOH . D 4 HOH A 35 1037 35 HOH HOH . D 4 HOH A 36 1038 36 HOH HOH . D 4 HOH A 37 1039 37 HOH HOH . D 4 HOH A 38 1040 38 HOH HOH . D 4 HOH A 39 1041 39 HOH HOH . D 4 HOH A 40 1042 40 HOH HOH . D 4 HOH A 41 1043 41 HOH HOH . D 4 HOH A 42 1044 42 HOH HOH . D 4 HOH A 43 1045 43 HOH HOH . D 4 HOH A 44 1046 44 HOH HOH . D 4 HOH A 45 1047 45 HOH HOH . D 4 HOH A 46 1048 46 HOH HOH . D 4 HOH A 47 1049 47 HOH HOH . D 4 HOH A 48 1050 48 HOH HOH . D 4 HOH A 49 1051 49 HOH HOH . D 4 HOH A 50 1052 50 HOH HOH . D 4 HOH A 51 1053 51 HOH HOH . D 4 HOH A 52 1054 52 HOH HOH . D 4 HOH A 53 1055 53 HOH HOH . D 4 HOH A 54 1056 54 HOH HOH . D 4 HOH A 55 1057 55 HOH HOH . D 4 HOH A 56 1058 56 HOH HOH . D 4 HOH A 57 1059 57 HOH HOH . D 4 HOH A 58 1060 58 HOH HOH . D 4 HOH A 59 1061 59 HOH HOH . D 4 HOH A 60 1062 60 HOH HOH . D 4 HOH A 61 1063 61 HOH HOH . D 4 HOH A 62 1064 62 HOH HOH . D 4 HOH A 63 1065 63 HOH HOH . D 4 HOH A 64 1066 64 HOH HOH . D 4 HOH A 65 1067 65 HOH HOH . D 4 HOH A 66 1068 66 HOH HOH . D 4 HOH A 67 1069 67 HOH HOH . D 4 HOH A 68 1070 68 HOH HOH . D 4 HOH A 69 1071 69 HOH HOH . D 4 HOH A 70 1072 70 HOH HOH . D 4 HOH A 71 1073 71 HOH HOH . D 4 HOH A 72 1074 72 HOH HOH . D 4 HOH A 73 1075 73 HOH HOH . D 4 HOH A 74 1076 74 HOH HOH . D 4 HOH A 75 1077 75 HOH HOH . D 4 HOH A 76 1078 76 HOH HOH . D 4 HOH A 77 1079 77 HOH HOH . D 4 HOH A 78 1080 78 HOH HOH . D 4 HOH A 79 1081 79 HOH HOH . D 4 HOH A 80 1082 80 HOH HOH . D 4 HOH A 81 1083 81 HOH HOH . D 4 HOH A 82 1084 82 HOH HOH . D 4 HOH A 83 1085 83 HOH HOH . D 4 HOH A 84 1086 84 HOH HOH . D 4 HOH A 85 1087 85 HOH HOH . D 4 HOH A 86 1088 86 HOH HOH . D 4 HOH A 87 1089 87 HOH HOH . D 4 HOH A 88 1090 88 HOH HOH . D 4 HOH A 89 1091 89 HOH HOH . D 4 HOH A 90 1092 90 HOH HOH . D 4 HOH A 91 1093 91 HOH HOH . D 4 HOH A 92 1094 92 HOH HOH . D 4 HOH A 93 1095 93 HOH HOH . D 4 HOH A 94 1096 94 HOH HOH . D 4 HOH A 95 1097 95 HOH HOH . D 4 HOH A 96 1098 96 HOH HOH . D 4 HOH A 97 1099 97 HOH HOH . D 4 HOH A 98 1100 98 HOH HOH . D 4 HOH A 99 1101 99 HOH HOH . D 4 HOH A 100 1102 100 HOH HOH . D 4 HOH A 101 1103 101 HOH HOH . D 4 HOH A 102 1104 102 HOH HOH . D 4 HOH A 103 1105 103 HOH HOH . D 4 HOH A 104 1106 104 HOH HOH . D 4 HOH A 105 1107 105 HOH HOH . D 4 HOH A 106 1108 106 HOH HOH . D 4 HOH A 107 1109 107 HOH HOH . D 4 HOH A 108 1110 108 HOH HOH . D 4 HOH A 109 1111 109 HOH HOH . D 4 HOH A 110 1112 110 HOH HOH . D 4 HOH A 111 1113 111 HOH HOH . D 4 HOH A 112 1114 112 HOH HOH . D 4 HOH A 113 1115 113 HOH HOH . D 4 HOH A 114 1116 114 HOH HOH . D 4 HOH A 115 1117 115 HOH HOH . D 4 HOH A 116 1118 116 HOH HOH . D 4 HOH A 117 1119 117 HOH HOH . D 4 HOH A 118 1120 118 HOH HOH . D 4 HOH A 119 1121 119 HOH HOH . D 4 HOH A 120 1122 120 HOH HOH . D 4 HOH A 121 1123 121 HOH HOH . D 4 HOH A 122 1124 122 HOH HOH . D 4 HOH A 123 1125 123 HOH HOH . D 4 HOH A 124 1126 124 HOH HOH . D 4 HOH A 125 1127 125 HOH HOH . D 4 HOH A 126 1128 126 HOH HOH . D 4 HOH A 127 1129 127 HOH HOH . D 4 HOH A 128 1130 128 HOH HOH . D 4 HOH A 129 1131 129 HOH HOH . D 4 HOH A 130 1132 130 HOH HOH . D 4 HOH A 131 1133 131 HOH HOH . D 4 HOH A 132 1134 132 HOH HOH . D 4 HOH A 133 1135 133 HOH HOH . D 4 HOH A 134 1136 134 HOH HOH . D 4 HOH A 135 1137 135 HOH HOH . D 4 HOH A 136 1138 136 HOH HOH . D 4 HOH A 137 1139 137 HOH HOH . D 4 HOH A 138 1140 138 HOH HOH . D 4 HOH A 139 1141 139 HOH HOH . D 4 HOH A 140 1142 140 HOH HOH . D 4 HOH A 141 1143 141 HOH HOH . D 4 HOH A 142 1144 142 HOH HOH . D 4 HOH A 143 1145 143 HOH HOH . D 4 HOH A 144 1146 144 HOH HOH . D 4 HOH A 145 1147 145 HOH HOH . D 4 HOH A 146 1148 146 HOH HOH . D 4 HOH A 147 1149 147 HOH HOH . D 4 HOH A 148 1150 148 HOH HOH . D 4 HOH A 149 1151 149 HOH HOH . D 4 HOH A 150 1152 150 HOH HOH . D 4 HOH A 151 1153 151 HOH HOH . D 4 HOH A 152 1154 152 HOH HOH . D 4 HOH A 153 1155 153 HOH HOH . D 4 HOH A 154 1156 154 HOH HOH . D 4 HOH A 155 1157 155 HOH HOH . D 4 HOH A 156 1158 156 HOH HOH . D 4 HOH A 157 1159 157 HOH HOH . D 4 HOH A 158 1160 158 HOH HOH . D 4 HOH A 159 1161 159 HOH HOH . D 4 HOH A 160 1162 160 HOH HOH . D 4 HOH A 161 1163 161 HOH HOH . D 4 HOH A 162 1164 162 HOH HOH . D 4 HOH A 163 1165 163 HOH HOH . D 4 HOH A 164 1166 164 HOH HOH . D 4 HOH A 165 1167 165 HOH HOH . D 4 HOH A 166 1168 166 HOH HOH . D 4 HOH A 167 1169 167 HOH HOH . D 4 HOH A 168 1170 168 HOH HOH . D 4 HOH A 169 1171 169 HOH HOH . D 4 HOH A 170 1172 170 HOH HOH . D 4 HOH A 171 1173 171 HOH HOH . D 4 HOH A 172 1174 172 HOH HOH . D 4 HOH A 173 1175 173 HOH HOH . D 4 HOH A 174 1176 174 HOH HOH . D 4 HOH A 175 1177 175 HOH HOH . D 4 HOH A 176 1178 176 HOH HOH . D 4 HOH A 177 1179 177 HOH HOH . D 4 HOH A 178 1180 178 HOH HOH . D 4 HOH A 179 1181 179 HOH HOH . D 4 HOH A 180 1182 180 HOH HOH . D 4 HOH A 181 1183 181 HOH HOH . D 4 HOH A 182 1184 182 HOH HOH . D 4 HOH A 183 1185 183 HOH HOH . D 4 HOH A 184 1186 184 HOH HOH . D 4 HOH A 185 1187 185 HOH HOH . D 4 HOH A 186 1188 186 HOH HOH . D 4 HOH A 187 1189 187 HOH HOH . D 4 HOH A 188 1190 188 HOH HOH . D 4 HOH A 189 1191 189 HOH HOH . D 4 HOH A 190 1192 190 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 DYM . . . C 3 77.991 30.365 24.64 1 34.41 ? C1 DYM 1001 A 1 HETATM 2 C C2 DYM . . . C 3 77.516 30.208 25.973 1 38.56 ? C2 DYM 1001 A 1 HETATM 3 C C3 DYM . . . C 3 76.68 31.309 26.69 1 40.43 ? C3 DYM 1001 A 1 HETATM 4 C C4 DYM . . . C 3 76.274 30.879 28.168 1 42.47 ? C4 DYM 1001 A 1 HETATM 5 C C5 DYM . . . C 3 77.318 29.943 28.807 1 43.57 ? C5 DYM 1001 A 1 HETATM 6 C C6 DYM . . . C 3 77.429 28.672 27.911 1 43.32 ? C6 DYM 1001 A 1 HETATM 7 C C7 DYM . . . C 3 78.638 26.398 27.603 1 48.9 ? C7 DYM 1001 A 1 HETATM 8 C C8 DYM . . . C 3 79.711 25.471 28.185 1 51.15 ? C8 DYM 1001 A 1 HETATM 9 C C9 DYM . . . C 3 81.047 25.908 28.038 1 52.49 ? C9 DYM 1001 A 1 HETATM 10 C C10 DYM . . . C 3 77.454 29.804 31.356 1 45.02 ? C10 DYM 1001 A 1 HETATM 11 C C11 DYM . . . C 3 76.732 29.336 32.597 1 45.94 ? C11 DYM 1001 A 1 HETATM 12 N N5 DYM . . . C 3 76.859 29.598 30.177 1 44.48 ? N5 DYM 1001 A 1 HETATM 13 O O1A DYM . . . C 3 78.715 29.382 24.031 1 31.56 ? O1A DYM 1001 A 1 HETATM 14 O O1B DYM . . . C 3 77.749 31.429 23.968 1 31.81 ? O1B DYM 1001 A 1 HETATM 15 O O4 DYM . . . C 3 76.137 32.092 28.952 1 41.55 ? O4 DYM 1001 A 1 HETATM 16 O O6 DYM . . . C 3 77.843 29.04 26.543 1 42.23 ? O6 DYM 1001 A 1 HETATM 17 O O7 DYM . . . C 3 78.471 27.683 28.439 1 44.94 ? O7 DYM 1001 A 1 HETATM 18 O O8 DYM . . . C 3 79.655 25.321 29.539 1 51.78 ? O8 DYM 1001 A 1 HETATM 19 O O9 DYM . . . C 3 82.115 25.186 28.504 1 54.99 ? O9 DYM 1001 A 1 HETATM 20 O O10 DYM . . . C 3 78.687 30.419 31.51 1 45.79 ? O10 DYM 1001 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 20 #