data_3SK6 # _model_server_result.job_id W-4BvsyTkbmu8cHnOQECEg _model_server_result.datetime_utc '2024-10-11 10:26:16' _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 3sk6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":150}' # _entry.id 3SK6 # _exptl.entry_id 3SK6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',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 3SK6 _cell.length_a 31.012 _cell.length_b 60.472 _cell.length_c 79.157 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SK6 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',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 P2 O4P THP doub 298 n n P2 O5P THP sing 299 n n P2 O6P THP sing 300 n n P2 O5' THP sing 301 n n O5P HOP5 THP sing 302 n n O6P HOP6 THP sing 303 n n P1 O1P THP doub 304 n n P1 O2P THP sing 305 n n P1 O3P THP sing 306 n n P1 O3' THP sing 307 n n O2P HOP2 THP sing 308 n n O3P HOP3 THP sing 309 n n O5' C5' THP sing 310 n n C5' C4' THP sing 311 n n C5' "H5'1" THP sing 312 n n C5' "H5'2" THP sing 313 n n C4' O4' THP sing 314 n n C4' C3' THP sing 315 n n C4' H4' THP sing 316 n n O4' C1' THP sing 317 n n C3' O3' THP sing 318 n n C3' C2' THP sing 319 n n C3' H3' THP sing 320 n n C2' C1' THP sing 321 n n C2' "H2'1" THP sing 322 n n C2' "H2'2" THP sing 323 n n C1' N1 THP sing 324 n n C1' H1' THP sing 325 n n N1 C2 THP sing 326 n n N1 C6 THP sing 327 n n C2 O2 THP doub 328 n n C2 N3 THP sing 329 n n N3 C4 THP sing 330 n n N3 H3 THP sing 331 n n C4 O4 THP doub 332 n n C4 C5 THP sing 333 n n C5 C5M THP sing 334 n n C5 C6 THP doub 335 n n C5M H51 THP sing 336 n n C5M H52 THP sing 337 n n C5M H53 THP sing 338 n n C6 H6 THP sing 339 n n # _atom_sites.entry_id 3SK6 _atom_sites.fract_transf_matrix[1][1] 0.032246 _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] 0.016537 _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] 0.012633 _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 THP A 1 150 150 THP THP . C 3 MRD A 1 151 151 MRD MRD . D 4 HOH A 1 152 152 HOH HOH . D 4 HOH A 2 153 153 HOH HOH . D 4 HOH A 3 154 154 HOH HOH . D 4 HOH A 4 155 155 HOH HOH . D 4 HOH A 5 156 156 HOH HOH . D 4 HOH A 6 157 157 HOH HOH . D 4 HOH A 7 158 158 HOH HOH . D 4 HOH A 8 159 159 HOH HOH . D 4 HOH A 9 160 160 HOH HOH . D 4 HOH A 10 161 161 HOH HOH . D 4 HOH A 11 162 162 HOH HOH . D 4 HOH A 12 163 163 HOH HOH . D 4 HOH A 13 164 164 HOH HOH . D 4 HOH A 14 165 165 HOH HOH . D 4 HOH A 15 166 166 HOH HOH . D 4 HOH A 16 167 167 HOH HOH . D 4 HOH A 17 168 168 HOH HOH . D 4 HOH A 18 169 169 HOH HOH . D 4 HOH A 19 170 170 HOH HOH . D 4 HOH A 20 171 171 HOH HOH . D 4 HOH A 21 172 172 HOH HOH . D 4 HOH A 22 173 173 HOH HOH . D 4 HOH A 23 174 174 HOH HOH . D 4 HOH A 24 175 175 HOH HOH . D 4 HOH A 25 176 176 HOH HOH . D 4 HOH A 26 177 177 HOH HOH . D 4 HOH A 27 178 178 HOH HOH . D 4 HOH A 28 179 179 HOH HOH . D 4 HOH A 29 180 180 HOH HOH . D 4 HOH A 30 181 181 HOH HOH . D 4 HOH A 31 182 182 HOH HOH . D 4 HOH A 32 183 183 HOH HOH . D 4 HOH A 33 184 184 HOH HOH . D 4 HOH A 34 185 185 HOH HOH . D 4 HOH A 35 186 186 HOH HOH . D 4 HOH A 36 187 187 HOH HOH . D 4 HOH A 37 188 188 HOH HOH . D 4 HOH A 38 189 189 HOH HOH . D 4 HOH A 39 190 190 HOH HOH . D 4 HOH A 40 191 191 HOH HOH . D 4 HOH A 41 192 192 HOH HOH . D 4 HOH A 42 193 193 HOH HOH . D 4 HOH A 43 194 194 HOH HOH . D 4 HOH A 44 195 195 HOH HOH . D 4 HOH A 45 196 196 HOH HOH . D 4 HOH A 46 197 197 HOH HOH . D 4 HOH A 47 198 198 HOH HOH . D 4 HOH A 48 199 199 HOH HOH . D 4 HOH A 49 200 200 HOH HOH . D 4 HOH A 50 201 201 HOH HOH . D 4 HOH A 51 202 202 HOH HOH . D 4 HOH A 52 203 203 HOH HOH . D 4 HOH A 53 204 204 HOH HOH . D 4 HOH A 54 205 205 HOH HOH . D 4 HOH A 55 206 206 HOH HOH . D 4 HOH A 56 207 207 HOH HOH . D 4 HOH A 57 208 208 HOH HOH . D 4 HOH A 58 209 209 HOH HOH . D 4 HOH A 59 210 210 HOH HOH . D 4 HOH A 60 211 211 HOH HOH . D 4 HOH A 61 212 212 HOH HOH . D 4 HOH A 62 213 213 HOH HOH . D 4 HOH A 63 214 214 HOH HOH . D 4 HOH A 64 215 215 HOH HOH . D 4 HOH A 65 216 216 HOH HOH . D 4 HOH A 66 217 217 HOH HOH . D 4 HOH A 67 218 218 HOH HOH . D 4 HOH A 68 219 219 HOH HOH . D 4 HOH A 69 220 220 HOH HOH . D 4 HOH A 70 221 221 HOH HOH . D 4 HOH A 71 222 222 HOH HOH . D 4 HOH A 72 223 223 HOH HOH . D 4 HOH A 73 224 224 HOH HOH . D 4 HOH A 74 225 225 HOH HOH . D 4 HOH A 75 226 226 HOH HOH . D 4 HOH A 76 227 227 HOH HOH . D 4 HOH A 77 228 228 HOH HOH . D 4 HOH A 78 229 229 HOH HOH . D 4 HOH A 79 230 230 HOH HOH . D 4 HOH A 80 231 231 HOH HOH . D 4 HOH A 81 232 232 HOH HOH . D 4 HOH A 82 233 233 HOH HOH . D 4 HOH A 83 234 234 HOH HOH . D 4 HOH A 84 235 235 HOH HOH . D 4 HOH A 85 236 236 HOH HOH . D 4 HOH A 86 237 237 HOH HOH . D 4 HOH A 87 238 238 HOH HOH . D 4 HOH A 88 239 239 HOH HOH . D 4 HOH A 89 240 240 HOH HOH . D 4 HOH A 90 241 241 HOH HOH . D 4 HOH A 91 242 242 HOH HOH . D 4 HOH A 92 243 243 HOH HOH . D 4 HOH A 93 244 244 HOH HOH . D 4 HOH A 94 245 245 HOH HOH . D 4 HOH A 95 246 246 HOH HOH . D 4 HOH A 96 247 247 HOH HOH . D 4 HOH A 97 248 248 HOH HOH . D 4 HOH A 98 249 249 HOH HOH . D 4 HOH A 99 250 250 HOH HOH . D 4 HOH A 100 251 251 HOH HOH . D 4 HOH A 101 252 252 HOH HOH . D 4 HOH A 102 253 253 HOH HOH . D 4 HOH A 103 254 254 HOH HOH . D 4 HOH A 104 255 255 HOH HOH . D 4 HOH A 105 256 256 HOH HOH . D 4 HOH A 106 257 257 HOH HOH . D 4 HOH A 107 258 258 HOH HOH . D 4 HOH A 108 259 259 HOH HOH . D 4 HOH A 109 260 260 HOH HOH . D 4 HOH A 110 261 261 HOH HOH . D 4 HOH A 111 262 262 HOH HOH . D 4 HOH A 112 263 263 HOH HOH . D 4 HOH A 113 264 264 HOH HOH . D 4 HOH A 114 265 265 HOH HOH . D 4 HOH A 115 266 266 HOH HOH . D 4 HOH A 116 267 267 HOH HOH . D 4 HOH A 117 268 268 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 P P2 THP . . . B 2 17.731 -4.763 -14.909 1 7.19 ? P2 THP 150 A 1 HETATM 2 O O4P THP . . . B 2 17.677 -6.224 -14.594 1 5.9 ? O4P THP 150 A 1 HETATM 3 O O5P THP . . . B 2 16.471 -4.021 -14.338 1 7.33 ? O5P THP 150 A 1 HETATM 4 O O6P THP . . . B 2 18.956 -3.974 -14.329 1 7.75 ? O6P THP 150 A 1 HETATM 5 P P1 THP . . . B 2 20.948 -1.19 -18.804 1 8.35 ? P1 THP 150 A 1 HETATM 6 O O1P THP . . . B 2 21.948 -0.61 -19.744 1 8.76 ? O1P THP 150 A 1 HETATM 7 O O2P THP . . . B 2 21.715 -2.332 -18.013 1 7.99 ? O2P THP 150 A 1 HETATM 8 O O3P THP . . . B 2 20.334 -0.261 -17.731 1 7.81 ? O3P THP 150 A 1 HETATM 9 O O5' THP . . . B 2 17.792 -4.738 -16.535 1 8.57 ? O5' THP 150 A 1 HETATM 10 C C5' THP . . . B 2 17.697 -3.446 -17.144 1 4.1 ? C5' THP 150 A 1 HETATM 11 C C4' THP . . . B 2 18.632 -3.476 -18.344 1 3.55 ? C4' THP 150 A 1 HETATM 12 O O4' THP . . . B 2 18.305 -4.584 -19.18 1 6.73 ? O4' THP 150 A 1 HETATM 13 C C3' THP . . . B 2 18.629 -2.21 -19.217 1 5.69 ? C3' THP 150 A 1 HETATM 14 O O3' THP . . . B 2 19.927 -1.958 -19.777 1 6.72 ? O3' THP 150 A 1 HETATM 15 C C2' THP . . . B 2 17.625 -2.625 -20.334 1 5.86 ? C2' THP 150 A 1 HETATM 16 C C1' THP . . . B 2 17.884 -4.129 -20.475 1 5.22 ? C1' THP 150 A 1 HETATM 17 N N1 THP . . . B 2 16.604 -4.75 -20.894 1 7.75 ? N1 THP 150 A 1 HETATM 18 C C2 THP . . . B 2 16.426 -5.022 -22.224 1 6.46 ? C2 THP 150 A 1 HETATM 19 O O2 THP . . . B 2 17.326 -4.721 -23.06 1 8.43 ? O2 THP 150 A 1 HETATM 20 N N3 THP . . . B 2 15.273 -5.526 -22.696 1 7.58 ? N3 THP 150 A 1 HETATM 21 C C4 THP . . . B 2 14.266 -5.803 -21.789 1 7.92 ? C4 THP 150 A 1 HETATM 22 O O4 THP . . . B 2 13.182 -6.175 -22.212 1 6.12 ? O4 THP 150 A 1 HETATM 23 C C5 THP . . . B 2 14.445 -5.536 -20.403 1 4.31 ? C5 THP 150 A 1 HETATM 24 C C5M THP . . . B 2 13.346 -5.831 -19.394 1 3.58 ? C5M THP 150 A 1 HETATM 25 C C6 THP . . . B 2 15.617 -5.028 -19.923 1 3.05 ? C6 THP 150 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #