data_1YZ3 # _model_server_result.job_id XNTKDPg5q011L_l6eDPa-Q _model_server_result.datetime_utc '2024-11-04 23:00:23' _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 1yz3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2001}' # _entry.id 1YZ3 # _exptl.entry_id 1YZ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 2 _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 1YZ3 _cell.length_a 93.9 _cell.length_b 93.9 _cell.length_c 188.3 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YZ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 1YZ3 _atom_sites.fract_transf_matrix[1][1] 0.01065 _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] 0.01065 _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] 0.005311 _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 C 2 SKA A 1 3001 3001 SKA SKA . D 3 SAH A 1 2002 2002 SAH SAH . E 2 SKA B 1 3002 3002 SKA SKA . F 3 SAH B 1 2001 2001 SAH SAH . G 4 HOH A 1 1003 1003 HOH HOH . G 4 HOH A 2 1004 1004 HOH HOH . G 4 HOH A 3 1005 1005 HOH HOH . G 4 HOH A 4 1006 1006 HOH HOH . G 4 HOH A 5 1007 1007 HOH HOH . G 4 HOH A 6 1015 1015 HOH HOH . G 4 HOH A 7 1016 1016 HOH HOH . G 4 HOH A 8 1019 1019 HOH HOH . G 4 HOH A 9 1023 1023 HOH HOH . G 4 HOH A 10 1025 1025 HOH HOH . G 4 HOH A 11 1026 1026 HOH HOH . G 4 HOH A 12 1032 1032 HOH HOH . G 4 HOH A 13 1033 1033 HOH HOH . G 4 HOH A 14 1034 1034 HOH HOH . G 4 HOH A 15 1037 1037 HOH HOH . G 4 HOH A 16 1038 1038 HOH HOH . G 4 HOH A 17 1039 1039 HOH HOH . G 4 HOH A 18 1040 1040 HOH HOH . G 4 HOH A 19 1041 1041 HOH HOH . G 4 HOH A 20 1043 1043 HOH HOH . G 4 HOH A 21 1047 1047 HOH HOH . G 4 HOH A 22 1053 1053 HOH HOH . G 4 HOH A 23 1054 1054 HOH HOH . G 4 HOH A 24 1067 1067 HOH HOH . G 4 HOH A 25 1071 1071 HOH HOH . G 4 HOH A 26 1075 1075 HOH HOH . G 4 HOH A 27 1076 1076 HOH HOH . G 4 HOH A 28 1078 1078 HOH HOH . G 4 HOH A 29 1079 1079 HOH HOH . G 4 HOH A 30 1081 1081 HOH HOH . G 4 HOH A 31 1082 1082 HOH HOH . G 4 HOH A 32 1084 1084 HOH HOH . G 4 HOH A 33 1086 1086 HOH HOH . G 4 HOH A 34 1087 1087 HOH HOH . G 4 HOH A 35 1088 1088 HOH HOH . G 4 HOH A 36 1090 1090 HOH HOH . G 4 HOH A 37 1092 1092 HOH HOH . G 4 HOH A 38 1095 1095 HOH HOH . G 4 HOH A 39 1096 1096 HOH HOH . G 4 HOH A 40 1098 1098 HOH HOH . G 4 HOH A 41 1100 1100 HOH HOH . G 4 HOH A 42 1101 1101 HOH HOH . G 4 HOH A 43 1102 1102 HOH HOH . G 4 HOH A 44 1103 1103 HOH HOH . G 4 HOH A 45 1104 1104 HOH HOH . G 4 HOH A 46 1105 1105 HOH HOH . G 4 HOH A 47 1108 1108 HOH HOH . G 4 HOH A 48 1113 1113 HOH HOH . G 4 HOH A 49 1118 1118 HOH HOH . G 4 HOH A 50 1119 1119 HOH HOH . G 4 HOH A 51 1120 1120 HOH HOH . G 4 HOH A 52 1121 1121 HOH HOH . G 4 HOH A 53 1126 1126 HOH HOH . G 4 HOH A 54 1128 1128 HOH HOH . G 4 HOH A 55 1129 1129 HOH HOH . G 4 HOH A 56 1133 1133 HOH HOH . G 4 HOH A 57 1134 1134 HOH HOH . G 4 HOH A 58 1135 1135 HOH HOH . G 4 HOH A 59 1137 1137 HOH HOH . G 4 HOH A 60 1139 1139 HOH HOH . G 4 HOH A 61 1141 1141 HOH HOH . G 4 HOH A 62 1143 1143 HOH HOH . G 4 HOH A 63 1145 1145 HOH HOH . G 4 HOH A 64 1146 1146 HOH HOH . G 4 HOH A 65 1148 1148 HOH HOH . G 4 HOH A 66 1151 1151 HOH HOH . G 4 HOH A 67 1152 1152 HOH HOH . G 4 HOH A 68 1153 1153 HOH HOH . G 4 HOH A 69 1157 1157 HOH HOH . G 4 HOH A 70 1160 1160 HOH HOH . G 4 HOH A 71 1163 1163 HOH HOH . G 4 HOH A 72 1170 1170 HOH HOH . G 4 HOH A 73 1175 1175 HOH HOH . G 4 HOH A 74 1180 1180 HOH HOH . G 4 HOH A 75 1182 1182 HOH HOH . G 4 HOH A 76 1183 1183 HOH HOH . G 4 HOH A 77 1186 1186 HOH HOH . G 4 HOH A 78 1187 1187 HOH HOH . G 4 HOH A 79 1189 1189 HOH HOH . G 4 HOH A 80 1190 1190 HOH HOH . G 4 HOH A 81 1191 1191 HOH HOH . G 4 HOH A 82 1192 1192 HOH HOH . G 4 HOH A 83 1193 1193 HOH HOH . G 4 HOH A 84 1194 1194 HOH HOH . H 4 HOH B 1 1001 1001 HOH HOH . H 4 HOH B 2 1002 1002 HOH HOH . H 4 HOH B 3 1008 1008 HOH HOH . H 4 HOH B 4 1009 1009 HOH HOH . H 4 HOH B 5 1010 1010 HOH HOH . H 4 HOH B 6 1011 1011 HOH HOH . H 4 HOH B 7 1012 1012 HOH HOH . H 4 HOH B 8 1013 1013 HOH HOH . H 4 HOH B 9 1014 1014 HOH HOH . H 4 HOH B 10 1017 1017 HOH HOH . H 4 HOH B 11 1018 1018 HOH HOH . H 4 HOH B 12 1020 1020 HOH HOH . H 4 HOH B 13 1021 1021 HOH HOH . H 4 HOH B 14 1022 1022 HOH HOH . H 4 HOH B 15 1024 1024 HOH HOH . H 4 HOH B 16 1027 1027 HOH HOH . H 4 HOH B 17 1028 1028 HOH HOH . H 4 HOH B 18 1029 1029 HOH HOH . H 4 HOH B 19 1030 1030 HOH HOH . H 4 HOH B 20 1031 1031 HOH HOH . H 4 HOH B 21 1035 1035 HOH HOH . H 4 HOH B 22 1036 1036 HOH HOH . H 4 HOH B 23 1042 1042 HOH HOH . H 4 HOH B 24 1044 1044 HOH HOH . H 4 HOH B 25 1045 1045 HOH HOH . H 4 HOH B 26 1046 1046 HOH HOH . H 4 HOH B 27 1048 1048 HOH HOH . H 4 HOH B 28 1049 1049 HOH HOH . H 4 HOH B 29 1050 1050 HOH HOH . H 4 HOH B 30 1051 1051 HOH HOH . H 4 HOH B 31 1052 1052 HOH HOH . H 4 HOH B 32 1055 1055 HOH HOH . H 4 HOH B 33 1056 1056 HOH HOH . H 4 HOH B 34 1057 1057 HOH HOH . H 4 HOH B 35 1058 1058 HOH HOH . H 4 HOH B 36 1059 1059 HOH HOH . H 4 HOH B 37 1060 1060 HOH HOH . H 4 HOH B 38 1061 1061 HOH HOH . H 4 HOH B 39 1062 1062 HOH HOH . H 4 HOH B 40 1063 1063 HOH HOH . H 4 HOH B 41 1064 1064 HOH HOH . H 4 HOH B 42 1065 1065 HOH HOH . H 4 HOH B 43 1066 1066 HOH HOH . H 4 HOH B 44 1068 1068 HOH HOH . H 4 HOH B 45 1069 1069 HOH HOH . H 4 HOH B 46 1070 1070 HOH HOH . H 4 HOH B 47 1072 1072 HOH HOH . H 4 HOH B 48 1073 1073 HOH HOH . H 4 HOH B 49 1074 1074 HOH HOH . H 4 HOH B 50 1077 1077 HOH HOH . H 4 HOH B 51 1080 1080 HOH HOH . H 4 HOH B 52 1083 1083 HOH HOH . H 4 HOH B 53 1085 1085 HOH HOH . H 4 HOH B 54 1089 1089 HOH HOH . H 4 HOH B 55 1091 1091 HOH HOH . H 4 HOH B 56 1093 1093 HOH HOH . H 4 HOH B 57 1094 1094 HOH HOH . H 4 HOH B 58 1097 1097 HOH HOH . H 4 HOH B 59 1099 1099 HOH HOH . H 4 HOH B 60 1106 1106 HOH HOH . H 4 HOH B 61 1107 1107 HOH HOH . H 4 HOH B 62 1109 1109 HOH HOH . H 4 HOH B 63 1110 1110 HOH HOH . H 4 HOH B 64 1111 1111 HOH HOH . H 4 HOH B 65 1112 1112 HOH HOH . H 4 HOH B 66 1114 1114 HOH HOH . H 4 HOH B 67 1115 1115 HOH HOH . H 4 HOH B 68 1116 1116 HOH HOH . H 4 HOH B 69 1117 1117 HOH HOH . H 4 HOH B 70 1122 1122 HOH HOH . H 4 HOH B 71 1123 1123 HOH HOH . H 4 HOH B 72 1124 1124 HOH HOH . H 4 HOH B 73 1125 1125 HOH HOH . H 4 HOH B 74 1127 1127 HOH HOH . H 4 HOH B 75 1130 1130 HOH HOH . H 4 HOH B 76 1131 1131 HOH HOH . H 4 HOH B 77 1132 1132 HOH HOH . H 4 HOH B 78 1136 1136 HOH HOH . H 4 HOH B 79 1138 1138 HOH HOH . H 4 HOH B 80 1140 1140 HOH HOH . H 4 HOH B 81 1142 1142 HOH HOH . H 4 HOH B 82 1144 1144 HOH HOH . H 4 HOH B 83 1147 1147 HOH HOH . H 4 HOH B 84 1149 1149 HOH HOH . H 4 HOH B 85 1150 1150 HOH HOH . H 4 HOH B 86 1154 1154 HOH HOH . H 4 HOH B 87 1155 1155 HOH HOH . H 4 HOH B 88 1156 1156 HOH HOH . H 4 HOH B 89 1158 1158 HOH HOH . H 4 HOH B 90 1159 1159 HOH HOH . H 4 HOH B 91 1161 1161 HOH HOH . H 4 HOH B 92 1162 1162 HOH HOH . H 4 HOH B 93 1164 1164 HOH HOH . H 4 HOH B 94 1165 1165 HOH HOH . H 4 HOH B 95 1166 1166 HOH HOH . H 4 HOH B 96 1167 1167 HOH HOH . H 4 HOH B 97 1168 1168 HOH HOH . H 4 HOH B 98 1169 1169 HOH HOH . H 4 HOH B 99 1171 1171 HOH HOH . H 4 HOH B 100 1172 1172 HOH HOH . H 4 HOH B 101 1173 1173 HOH HOH . H 4 HOH B 102 1174 1174 HOH HOH . H 4 HOH B 103 1176 1176 HOH HOH . H 4 HOH B 104 1177 1177 HOH HOH . H 4 HOH B 105 1178 1178 HOH HOH . H 4 HOH B 106 1179 1179 HOH HOH . H 4 HOH B 107 1181 1181 HOH HOH . H 4 HOH B 108 1184 1184 HOH HOH . H 4 HOH B 109 1185 1185 HOH HOH . H 4 HOH B 110 1188 1188 HOH HOH . H 4 HOH B 111 1195 1195 HOH HOH . H 4 HOH B 112 1196 1196 HOH HOH . H 4 HOH B 113 1197 1197 HOH HOH . H 4 HOH B 114 1198 1198 HOH HOH . H 4 HOH B 115 1199 1199 HOH HOH . H 4 HOH B 116 1200 1200 HOH HOH . H 4 HOH B 117 1201 1201 HOH HOH . H 4 HOH B 118 1202 1202 HOH HOH . H 4 HOH B 119 1203 1203 HOH HOH . H 4 HOH B 120 1204 1204 HOH HOH . H 4 HOH B 121 1205 1205 HOH HOH . H 4 HOH B 122 1206 1206 HOH HOH . H 4 HOH B 123 1207 1207 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 N N SAH . . . F 3 3.575 18.886 19.284 1 35.99 ? N SAH 2001 B 1 HETATM 2 C CA SAH . . . F 3 4.538 18.029 19.972 1 36.06 ? CA SAH 2001 B 1 HETATM 3 C CB SAH . . . F 3 5.224 17.073 18.964 1 37.31 ? CB SAH 2001 B 1 HETATM 4 C CG SAH . . . F 3 6.021 17.719 17.809 1 39.59 ? CG SAH 2001 B 1 HETATM 5 S SD SAH . . . F 3 6.955 16.462 16.838 1 39.57 ? SD SAH 2001 B 1 HETATM 6 C C SAH . . . F 3 5.564 18.806 20.795 1 36.03 ? C SAH 2001 B 1 HETATM 7 O O SAH . . . F 3 5.379 20.026 20.994 1 34.74 ? O SAH 2001 B 1 HETATM 8 O OXT SAH . . . F 3 6.538 18.18 21.267 1 42.18 ? OXT SAH 2001 B 1 HETATM 9 C C5' SAH . . . F 3 6.161 16.509 15.192 1 33.83 ? C5' SAH 2001 B 1 HETATM 10 C C4' SAH . . . F 3 4.859 15.743 15.104 1 41.29 ? C4' SAH 2001 B 1 HETATM 11 O O4' SAH . . . F 3 4.221 15.901 13.802 1 38.7 ? O4' SAH 2001 B 1 HETATM 12 C C3' SAH . . . F 3 4.896 14.242 15.391 1 42.86 ? C3' SAH 2001 B 1 HETATM 13 O O3' SAH . . . F 3 3.963 13.918 16.419 1 41.11 ? O3' SAH 2001 B 1 HETATM 14 C C2' SAH . . . F 3 4.534 13.614 14.042 1 38.49 ? C2' SAH 2001 B 1 HETATM 15 O O2' SAH . . . F 3 3.854 12.38 14.132 1 44.5 ? O2' SAH 2001 B 1 HETATM 16 C C1' SAH . . . F 3 3.617 14.677 13.444 1 39.57 ? C1' SAH 2001 B 1 HETATM 17 N N9 SAH . . . F 3 3.468 14.617 11.988 1 42.66 ? N9 SAH 2001 B 1 HETATM 18 C C8 SAH . . . F 3 4.304 13.971 11.035 1 42.18 ? C8 SAH 2001 B 1 HETATM 19 N N7 SAH . . . F 3 3.859 14.067 9.806 1 42.97 ? N7 SAH 2001 B 1 HETATM 20 C C5 SAH . . . F 3 2.695 14.81 9.94 1 40.5 ? C5 SAH 2001 B 1 HETATM 21 C C6 SAH . . . F 3 1.775 15.219 8.941 1 42.44 ? C6 SAH 2001 B 1 HETATM 22 N N6 SAH . . . F 3 1.903 14.932 7.638 1 42.35 ? N6 SAH 2001 B 1 HETATM 23 N N1 SAH . . . F 3 0.694 15.947 9.348 1 42.21 ? N1 SAH 2001 B 1 HETATM 24 C C2 SAH . . . F 3 0.569 16.235 10.672 1 37.25 ? C2 SAH 2001 B 1 HETATM 25 N N3 SAH . . . F 3 1.385 15.891 11.696 1 41.61 ? N3 SAH 2001 B 1 HETATM 26 C C4 SAH . . . F 3 2.441 15.167 11.254 1 42.29 ? C4 SAH 2001 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #