data_1S59 # _model_server_result.job_id Qaa2BkItU5dru48cVBNhrA _model_server_result.datetime_utc '2024-10-31 07:26:34' _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 1s59 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1101}' # _entry.id 1S59 # _exptl.entry_id 1S59 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-DIPHOSPHATE" _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 1S59 _cell.length_a 69.035 _cell.length_b 108.52 _cell.length_c 118.316 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S59 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,K,L,M,N _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 2 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id DGI _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXYGUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'dna 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 O1B PB DGI doub 83 n n PB O2B DGI sing 84 n n PB O3B DGI sing 85 n n PB O3A DGI sing 86 n n O2B HOB2 DGI sing 87 n n O3B HOB3 DGI sing 88 n n O3A PA DGI sing 89 n n PA O1A DGI doub 90 n n PA O2A DGI sing 91 n n PA O5' DGI sing 92 n n O2A HOA2 DGI sing 93 n n O5' C5' DGI sing 94 n n C5' C4' DGI sing 95 n n C5' H5' DGI sing 96 n n C5' "H5''" DGI sing 97 n n C4' O4' DGI sing 98 n n C4' C3' DGI sing 99 n n C4' H4' DGI sing 100 n n O4' C1' DGI sing 101 n n C3' O3' DGI sing 102 n n C3' C2' DGI sing 103 n n C3' H3' DGI sing 104 n n O3' HO3' DGI sing 105 n n C2' C1' DGI sing 106 n n C2' H2' DGI sing 107 n n C2' "H2''" DGI sing 108 n n C1' N9 DGI sing 109 n n C1' H1' DGI sing 110 n n N9 C8 DGI sing 111 n y N9 C4 DGI sing 112 n y C8 N7 DGI doub 113 n y C8 H8 DGI sing 114 n n N7 C5 DGI sing 115 n y C5 C4 DGI doub 116 n y C5 C6 DGI sing 117 n n C4 N3 DGI sing 118 n n N3 C2 DGI doub 119 n n C2 N2 DGI sing 120 n n C2 N1 DGI sing 121 n n N2 HN21 DGI sing 122 n n N2 HN22 DGI sing 123 n n N1 C6 DGI sing 124 n n N1 HN1 DGI sing 125 n n C6 O6 DGI doub 126 n n # _atom_sites.entry_id 1S59 _atom_sites.fract_transf_matrix[1][1] 0.014485 _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] 0.009215 _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] 0.008452 _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 G 2 DGI A 1 1101 101 DGI DGD . H 3 DGT C 1 1102 102 DGT DGT . I 4 HOH A 1 1102 5 HOH TIP . I 4 HOH A 2 1103 8 HOH TIP . I 4 HOH A 3 1104 10 HOH TIP . I 4 HOH A 4 1105 20 HOH TIP . I 4 HOH A 5 1106 31 HOH TIP . I 4 HOH A 6 1107 47 HOH TIP . I 4 HOH A 7 1108 52 HOH TIP . I 4 HOH A 8 1109 60 HOH TIP . I 4 HOH A 9 1110 62 HOH TIP . I 4 HOH A 10 1111 67 HOH TIP . I 4 HOH A 11 1112 70 HOH TIP . I 4 HOH A 12 1113 72 HOH TIP . I 4 HOH A 13 1114 75 HOH TIP . I 4 HOH A 14 1115 79 HOH TIP . I 4 HOH A 15 1116 80 HOH TIP . I 4 HOH A 16 1117 100 HOH TIP . I 4 HOH A 17 1118 101 HOH TIP . I 4 HOH A 18 1119 108 HOH TIP . I 4 HOH A 19 1120 109 HOH TIP . I 4 HOH A 20 1121 114 HOH TIP . I 4 HOH A 21 1122 118 HOH TIP . I 4 HOH A 22 1123 119 HOH TIP . I 4 HOH A 23 1124 122 HOH TIP . I 4 HOH A 24 1125 124 HOH TIP . I 4 HOH A 25 1126 128 HOH TIP . I 4 HOH A 26 1127 129 HOH TIP . I 4 HOH A 27 1128 132 HOH TIP . I 4 HOH A 28 1129 134 HOH TIP . I 4 HOH A 29 1130 142 HOH TIP . I 4 HOH A 30 1131 149 HOH TIP . I 4 HOH A 31 1132 156 HOH TIP . I 4 HOH A 32 1133 158 HOH TIP . I 4 HOH A 33 1134 159 HOH TIP . I 4 HOH A 34 1135 160 HOH TIP . I 4 HOH A 35 1136 166 HOH TIP . I 4 HOH A 36 1137 170 HOH TIP . I 4 HOH A 37 1138 179 HOH TIP . I 4 HOH A 38 1139 180 HOH TIP . I 4 HOH A 39 1140 183 HOH TIP . I 4 HOH A 40 1141 204 HOH TIP . I 4 HOH A 41 1142 208 HOH TIP . I 4 HOH A 42 1143 214 HOH TIP . I 4 HOH A 43 1144 217 HOH TIP . I 4 HOH A 44 1145 224 HOH TIP . I 4 HOH A 45 1146 225 HOH TIP . I 4 HOH A 46 1147 234 HOH TIP . I 4 HOH A 47 1148 238 HOH TIP . J 4 HOH B 1 232 7 HOH TIP . J 4 HOH B 2 233 18 HOH TIP . J 4 HOH B 3 234 24 HOH TIP . J 4 HOH B 4 235 25 HOH TIP . J 4 HOH B 5 236 27 HOH TIP . J 4 HOH B 6 237 28 HOH TIP . J 4 HOH B 7 238 33 HOH TIP . J 4 HOH B 8 239 39 HOH TIP . J 4 HOH B 9 240 41 HOH TIP . J 4 HOH B 10 241 43 HOH TIP . J 4 HOH B 11 242 71 HOH TIP . J 4 HOH B 12 243 76 HOH TIP . J 4 HOH B 13 244 77 HOH TIP . J 4 HOH B 14 245 78 HOH TIP . J 4 HOH B 15 246 81 HOH TIP . J 4 HOH B 16 247 83 HOH TIP . J 4 HOH B 17 248 87 HOH TIP . J 4 HOH B 18 249 90 HOH TIP . J 4 HOH B 19 250 92 HOH TIP . J 4 HOH B 20 251 94 HOH TIP . J 4 HOH B 21 252 95 HOH TIP . J 4 HOH B 22 253 98 HOH TIP . J 4 HOH B 23 254 107 HOH TIP . J 4 HOH B 24 255 110 HOH TIP . J 4 HOH B 25 256 112 HOH TIP . J 4 HOH B 26 257 116 HOH TIP . J 4 HOH B 27 258 123 HOH TIP . J 4 HOH B 28 259 138 HOH TIP . J 4 HOH B 29 260 146 HOH TIP . J 4 HOH B 30 261 148 HOH TIP . J 4 HOH B 31 262 163 HOH TIP . J 4 HOH B 32 263 164 HOH TIP . J 4 HOH B 33 264 168 HOH TIP . J 4 HOH B 34 265 172 HOH TIP . J 4 HOH B 35 266 173 HOH TIP . J 4 HOH B 36 267 174 HOH TIP . J 4 HOH B 37 268 182 HOH TIP . J 4 HOH B 38 269 185 HOH TIP . J 4 HOH B 39 270 201 HOH TIP . J 4 HOH B 40 271 206 HOH TIP . J 4 HOH B 41 272 215 HOH TIP . J 4 HOH B 42 273 218 HOH TIP . J 4 HOH B 43 274 227 HOH TIP . J 4 HOH B 44 275 233 HOH TIP . J 4 HOH B 45 276 237 HOH TIP . J 4 HOH B 46 277 239 HOH TIP . K 4 HOH C 1 1103 1 HOH TIP . K 4 HOH C 2 1104 36 HOH TIP . K 4 HOH C 3 1105 37 HOH TIP . K 4 HOH C 4 1106 46 HOH TIP . K 4 HOH C 5 1107 48 HOH TIP . K 4 HOH C 6 1108 49 HOH TIP . K 4 HOH C 7 1109 53 HOH TIP . K 4 HOH C 8 1110 56 HOH TIP . K 4 HOH C 9 1111 57 HOH TIP . K 4 HOH C 10 1112 58 HOH TIP . K 4 HOH C 11 1113 59 HOH TIP . K 4 HOH C 12 1114 68 HOH TIP . K 4 HOH C 13 1115 86 HOH TIP . K 4 HOH C 14 1116 96 HOH TIP . K 4 HOH C 15 1117 111 HOH TIP . K 4 HOH C 16 1118 136 HOH TIP . K 4 HOH C 17 1119 144 HOH TIP . K 4 HOH C 18 1120 150 HOH TIP . K 4 HOH C 19 1121 153 HOH TIP . K 4 HOH C 20 1122 167 HOH TIP . K 4 HOH C 21 1123 176 HOH TIP . K 4 HOH C 22 1124 177 HOH TIP . K 4 HOH C 23 1125 181 HOH TIP . K 4 HOH C 24 1126 184 HOH TIP . K 4 HOH C 25 1127 189 HOH TIP . K 4 HOH C 26 1128 193 HOH TIP . K 4 HOH C 27 1129 205 HOH TIP . K 4 HOH C 28 1130 209 HOH TIP . K 4 HOH C 29 1131 219 HOH TIP . K 4 HOH C 30 1132 220 HOH TIP . K 4 HOH C 31 1133 221 HOH TIP . K 4 HOH C 32 1134 232 HOH TIP . L 4 HOH D 1 232 6 HOH TIP . L 4 HOH D 2 233 14 HOH TIP . L 4 HOH D 3 234 16 HOH TIP . L 4 HOH D 4 235 23 HOH TIP . L 4 HOH D 5 236 34 HOH TIP . L 4 HOH D 6 237 35 HOH TIP . L 4 HOH D 7 238 44 HOH TIP . L 4 HOH D 8 239 55 HOH TIP . L 4 HOH D 9 240 64 HOH TIP . L 4 HOH D 10 241 74 HOH TIP . L 4 HOH D 11 242 82 HOH TIP . L 4 HOH D 12 243 89 HOH TIP . L 4 HOH D 13 244 93 HOH TIP . L 4 HOH D 14 245 99 HOH TIP . L 4 HOH D 15 246 102 HOH TIP . L 4 HOH D 16 247 103 HOH TIP . L 4 HOH D 17 248 104 HOH TIP . L 4 HOH D 18 249 105 HOH TIP . L 4 HOH D 19 250 117 HOH TIP . L 4 HOH D 20 251 121 HOH TIP . L 4 HOH D 21 252 126 HOH TIP . L 4 HOH D 22 253 127 HOH TIP . L 4 HOH D 23 254 137 HOH TIP . L 4 HOH D 24 255 140 HOH TIP . L 4 HOH D 25 256 143 HOH TIP . L 4 HOH D 26 257 147 HOH TIP . L 4 HOH D 27 258 155 HOH TIP . L 4 HOH D 28 259 165 HOH TIP . L 4 HOH D 29 260 171 HOH TIP . L 4 HOH D 30 261 186 HOH TIP . L 4 HOH D 31 262 187 HOH TIP . L 4 HOH D 32 263 195 HOH TIP . L 4 HOH D 33 264 197 HOH TIP . L 4 HOH D 34 265 202 HOH TIP . L 4 HOH D 35 266 207 HOH TIP . L 4 HOH D 36 267 210 HOH TIP . L 4 HOH D 37 268 216 HOH TIP . L 4 HOH D 38 269 222 HOH TIP . L 4 HOH D 39 270 230 HOH TIP . L 4 HOH D 40 271 236 HOH TIP . L 4 HOH D 41 272 240 HOH TIP . M 4 HOH E 1 232 2 HOH TIP . M 4 HOH E 2 233 9 HOH TIP . M 4 HOH E 3 234 15 HOH TIP . M 4 HOH E 4 235 17 HOH TIP . M 4 HOH E 5 236 29 HOH TIP . M 4 HOH E 6 237 40 HOH TIP . M 4 HOH E 7 238 51 HOH TIP . M 4 HOH E 8 239 54 HOH TIP . M 4 HOH E 9 240 69 HOH TIP . M 4 HOH E 10 241 84 HOH TIP . M 4 HOH E 11 242 85 HOH TIP . M 4 HOH E 12 243 106 HOH TIP . M 4 HOH E 13 244 113 HOH TIP . M 4 HOH E 14 245 130 HOH TIP . M 4 HOH E 15 246 131 HOH TIP . M 4 HOH E 16 247 133 HOH TIP . M 4 HOH E 17 248 152 HOH TIP . M 4 HOH E 18 249 162 HOH TIP . M 4 HOH E 19 250 169 HOH TIP . M 4 HOH E 20 251 190 HOH TIP . M 4 HOH E 21 252 191 HOH TIP . M 4 HOH E 22 253 192 HOH TIP . M 4 HOH E 23 254 194 HOH TIP . M 4 HOH E 24 255 198 HOH TIP . M 4 HOH E 25 256 200 HOH TIP . M 4 HOH E 26 257 203 HOH TIP . M 4 HOH E 27 258 212 HOH TIP . M 4 HOH E 28 259 226 HOH TIP . M 4 HOH E 29 260 231 HOH TIP . N 4 HOH F 1 232 3 HOH TIP . N 4 HOH F 2 233 4 HOH TIP . N 4 HOH F 3 234 11 HOH TIP . N 4 HOH F 4 235 12 HOH TIP . N 4 HOH F 5 236 13 HOH TIP . N 4 HOH F 6 237 19 HOH TIP . N 4 HOH F 7 238 21 HOH TIP . N 4 HOH F 8 239 22 HOH TIP . N 4 HOH F 9 240 26 HOH TIP . N 4 HOH F 10 241 30 HOH TIP . N 4 HOH F 11 242 32 HOH TIP . N 4 HOH F 12 243 38 HOH TIP . N 4 HOH F 13 244 42 HOH TIP . N 4 HOH F 14 245 45 HOH TIP . N 4 HOH F 15 246 50 HOH TIP . N 4 HOH F 16 247 61 HOH TIP . N 4 HOH F 17 248 63 HOH TIP . N 4 HOH F 18 249 66 HOH TIP . N 4 HOH F 19 250 73 HOH TIP . N 4 HOH F 20 251 88 HOH TIP . N 4 HOH F 21 252 91 HOH TIP . N 4 HOH F 22 253 97 HOH TIP . N 4 HOH F 23 254 115 HOH TIP . N 4 HOH F 24 255 120 HOH TIP . N 4 HOH F 25 256 135 HOH TIP . N 4 HOH F 26 257 139 HOH TIP . N 4 HOH F 27 258 141 HOH TIP . N 4 HOH F 28 259 145 HOH TIP . N 4 HOH F 29 260 151 HOH TIP . N 4 HOH F 30 261 154 HOH TIP . N 4 HOH F 31 262 157 HOH TIP . N 4 HOH F 32 263 161 HOH TIP . N 4 HOH F 33 264 175 HOH TIP . N 4 HOH F 34 265 178 HOH TIP . N 4 HOH F 35 266 188 HOH TIP . N 4 HOH F 36 267 199 HOH TIP . N 4 HOH F 37 268 211 HOH TIP . N 4 HOH F 38 269 213 HOH TIP . N 4 HOH F 39 270 223 HOH TIP . N 4 HOH F 40 271 235 HOH TIP . # 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 O O1B DGI . . . G 2 26.618 47.524 18.372 1 83.33 ? O1B DGI 1101 A 1 HETATM 2 P PB DGI . . . G 2 27.44 47.745 17.001 1 83.82 ? PB DGI 1101 A 1 HETATM 3 O O2B DGI . . . G 2 28.965 48.032 17.441 1 83.62 ? O2B DGI 1101 A 1 HETATM 4 O O3B DGI . . . G 2 27.321 46.594 16.074 1 83.02 ? O3B DGI 1101 A 1 HETATM 5 O O3A DGI . . . G 2 26.907 49.144 16.393 1 84.41 ? O3A DGI 1101 A 1 HETATM 6 P PA DGI . . . G 2 26.045 49.233 15.031 1 84.61 ? PA DGI 1101 A 1 HETATM 7 O O1A DGI . . . G 2 24.792 49.954 15.364 1 84.74 ? O1A DGI 1101 A 1 HETATM 8 O O2A DGI . . . G 2 26.918 49.79 13.973 1 83.71 ? O2A DGI 1101 A 1 HETATM 9 O O5' DGI . . . G 2 25.686 47.697 14.69 1 83.59 ? O5' DGI 1101 A 1 HETATM 10 C C5' DGI . . . G 2 25.016 47.363 13.47 1 82.58 ? C5' DGI 1101 A 1 HETATM 11 C C4' DGI . . . G 2 24.897 45.846 13.29 1 82.06 ? C4' DGI 1101 A 1 HETATM 12 O O4' DGI . . . G 2 24.244 45.523 12.051 1 82.03 ? O4' DGI 1101 A 1 HETATM 13 C C3' DGI . . . G 2 26.267 45.175 13.191 1 82.26 ? C3' DGI 1101 A 1 HETATM 14 O O3' DGI . . . G 2 26.764 44.929 14.509 1 81.74 ? O3' DGI 1101 A 1 HETATM 15 C C2' DGI . . . G 2 25.838 43.84 12.585 1 81.81 ? C2' DGI 1101 A 1 HETATM 16 C C1' DGI . . . G 2 24.789 44.283 11.562 1 82.16 ? C1' DGI 1101 A 1 HETATM 17 N N9 DGI . . . G 2 25.358 44.524 10.214 1 82.2 ? N9 DGI 1101 A 1 HETATM 18 C C8 DGI . . . G 2 25.861 45.664 9.749 1 81.89 ? C8 DGI 1101 A 1 HETATM 19 N N7 DGI . . . G 2 26.192 45.511 8.467 1 81.85 ? N7 DGI 1101 A 1 HETATM 20 C C5 DGI . . . G 2 25.907 44.264 8.106 1 82.29 ? C5 DGI 1101 A 1 HETATM 21 C C4 DGI . . . G 2 25.382 43.635 9.228 1 82.29 ? C4 DGI 1101 A 1 HETATM 22 N N3 DGI . . . G 2 24.979 42.293 9.171 1 82.41 ? N3 DGI 1101 A 1 HETATM 23 C C2 DGI . . . G 2 25.102 41.577 7.977 1 82.77 ? C2 DGI 1101 A 1 HETATM 24 N N2 DGI . . . G 2 24.735 40.297 7.923 1 82.48 ? N2 DGI 1101 A 1 HETATM 25 N N1 DGI . . . G 2 25.63 42.216 6.849 1 82.72 ? N1 DGI 1101 A 1 HETATM 26 C C6 DGI . . . G 2 26.03 43.557 6.915 1 82.61 ? C6 DGI 1101 A 1 HETATM 27 O O6 DGI . . . G 2 26.482 44.103 5.909 1 82.88 ? O6 DGI 1101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #