data_1SMC # _model_server_result.job_id 8CRs-86l0ajcpwOda33Etw _model_server_result.datetime_utc '2024-11-13 05:40:09' _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 1smc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2170}' # _entry.id 1SMC # _exptl.entry_id 1SMC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 1SMC _cell.length_a 58.595 _cell.length_b 77.697 _cell.length_c 94.781 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SMC _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 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,K,L,M _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 ? 2 D N N ? 2 H N N ? 2 I N N # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id DUT _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 N1 C2 DUT sing 70 n n N1 C6 DUT sing 71 n n N1 C1' DUT sing 72 n n C2 N3 DUT sing 73 n n C2 O2 DUT doub 74 n n N3 C4 DUT sing 75 n n N3 HN3 DUT sing 76 n n C4 C5 DUT sing 77 n n C4 O4 DUT doub 78 n n C5 C6 DUT doub 79 n n C5 H5 DUT sing 80 n n C6 H6 DUT sing 81 n n C1' C2' DUT sing 82 n n C1' O4' DUT sing 83 n n C1' H1' DUT sing 84 n n C2' C3' DUT sing 85 n n C2' "H2'1" DUT sing 86 n n C2' "H2'2" DUT sing 87 n n C3' C4' DUT sing 88 n n C3' O3' DUT sing 89 n n C3' H3' DUT sing 90 n n C4' O4' DUT sing 91 n n C4' C5' DUT sing 92 n n C4' H4' DUT sing 93 n n O3' HO3' DUT sing 94 n n C5' O5' DUT sing 95 n n C5' "H5'1" DUT sing 96 n n C5' "H5'2" DUT sing 97 n n O5' PA DUT sing 98 n n PA O1A DUT doub 99 n n PA O2A DUT sing 100 n n PA O3A DUT sing 101 n n O2A HOA2 DUT sing 102 n n O3A PB DUT sing 103 n n PB O1B DUT doub 104 n n PB O2B DUT sing 105 n n PB O3B DUT sing 106 n n O2B HOB2 DUT sing 107 n n O3B PG DUT sing 108 n n PG O1G DUT doub 109 n n PG O2G DUT sing 110 n n PG O3G DUT sing 111 n n O2G HOG2 DUT sing 112 n n O3G HOG3 DUT sing 113 n n # _atom_sites.entry_id 1SMC _atom_sites.fract_transf_matrix[1][1] 0.017066 _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] 0.012871 _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] 0.010551 _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 2 DUT A 1 2170 150 DUT DUT . E 3 TRS A 1 2171 152 TRS TRS . F 3 TRS B 1 155 153 TRS TRS . G 4 NO3 C 1 155 154 NO3 NO3 . H 2 DUT C 1 1170 150 DUT DUT . I 2 DUT C 1 3170 150 DUT DUT . J 3 TRS C 1 3171 151 TRS TRS . K 5 HOH A 1 155 155 HOH HOH . K 5 HOH A 2 159 159 HOH HOH . K 5 HOH A 3 161 161 HOH HOH . K 5 HOH A 4 162 162 HOH HOH . K 5 HOH A 5 164 164 HOH HOH . K 5 HOH A 6 166 166 HOH HOH . K 5 HOH A 7 175 175 HOH HOH . K 5 HOH A 8 177 177 HOH HOH . K 5 HOH A 9 180 180 HOH HOH . K 5 HOH A 10 182 182 HOH HOH . K 5 HOH A 11 187 187 HOH HOH . K 5 HOH A 12 193 193 HOH HOH . K 5 HOH A 13 194 194 HOH HOH . K 5 HOH A 14 196 196 HOH HOH . K 5 HOH A 15 199 199 HOH HOH . K 5 HOH A 16 202 202 HOH HOH . K 5 HOH A 17 203 203 HOH HOH . K 5 HOH A 18 207 207 HOH HOH . K 5 HOH A 19 208 208 HOH HOH . K 5 HOH A 20 209 209 HOH HOH . K 5 HOH A 21 214 214 HOH HOH . K 5 HOH A 22 215 215 HOH HOH . K 5 HOH A 23 216 216 HOH HOH . K 5 HOH A 24 218 218 HOH HOH . K 5 HOH A 25 222 222 HOH HOH . K 5 HOH A 26 225 225 HOH HOH . K 5 HOH A 27 226 226 HOH HOH . K 5 HOH A 28 235 235 HOH HOH . K 5 HOH A 29 240 240 HOH HOH . K 5 HOH A 30 243 243 HOH HOH . K 5 HOH A 31 244 244 HOH HOH . K 5 HOH A 32 245 245 HOH HOH . K 5 HOH A 33 258 258 HOH HOH . K 5 HOH A 34 264 264 HOH HOH . K 5 HOH A 35 266 266 HOH HOH . K 5 HOH A 36 268 268 HOH HOH . K 5 HOH A 37 269 269 HOH HOH . K 5 HOH A 38 270 270 HOH HOH . K 5 HOH A 39 271 271 HOH HOH . K 5 HOH A 40 274 274 HOH HOH . K 5 HOH A 41 279 279 HOH HOH . K 5 HOH A 42 280 280 HOH HOH . K 5 HOH A 43 286 286 HOH HOH . K 5 HOH A 44 287 287 HOH HOH . K 5 HOH A 45 288 288 HOH HOH . K 5 HOH A 46 293 293 HOH HOH . K 5 HOH A 47 295 295 HOH HOH . K 5 HOH A 48 303 303 HOH HOH . K 5 HOH A 49 309 309 HOH HOH . K 5 HOH A 50 314 314 HOH HOH . K 5 HOH A 51 317 317 HOH HOH . K 5 HOH A 52 321 321 HOH HOH . K 5 HOH A 53 324 324 HOH HOH . K 5 HOH A 54 328 328 HOH HOH . K 5 HOH A 55 331 331 HOH HOH . K 5 HOH A 56 334 334 HOH HOH . K 5 HOH A 57 335 335 HOH HOH . K 5 HOH A 58 341 341 HOH HOH . K 5 HOH A 59 343 343 HOH HOH . K 5 HOH A 60 356 356 HOH HOH . K 5 HOH A 61 357 357 HOH HOH . K 5 HOH A 62 359 359 HOH HOH . K 5 HOH A 63 360 360 HOH HOH . K 5 HOH A 64 364 364 HOH HOH . K 5 HOH A 65 365 365 HOH HOH . K 5 HOH A 66 370 370 HOH HOH . K 5 HOH A 67 372 372 HOH HOH . K 5 HOH A 68 375 375 HOH HOH . L 5 HOH B 1 157 157 HOH HOH . L 5 HOH B 2 160 160 HOH HOH . L 5 HOH B 3 170 170 HOH HOH . L 5 HOH B 4 172 172 HOH HOH . L 5 HOH B 5 173 173 HOH HOH . L 5 HOH B 6 176 176 HOH HOH . L 5 HOH B 7 184 184 HOH HOH . L 5 HOH B 8 186 186 HOH HOH . L 5 HOH B 9 188 188 HOH HOH . L 5 HOH B 10 189 189 HOH HOH . L 5 HOH B 11 205 205 HOH HOH . L 5 HOH B 12 206 206 HOH HOH . L 5 HOH B 13 217 217 HOH HOH . L 5 HOH B 14 219 219 HOH HOH . L 5 HOH B 15 221 221 HOH HOH . L 5 HOH B 16 227 227 HOH HOH . L 5 HOH B 17 233 233 HOH HOH . L 5 HOH B 18 234 234 HOH HOH . L 5 HOH B 19 236 236 HOH HOH . L 5 HOH B 20 247 247 HOH HOH . L 5 HOH B 21 249 249 HOH HOH . L 5 HOH B 22 251 251 HOH HOH . L 5 HOH B 23 252 252 HOH HOH . L 5 HOH B 24 253 253 HOH HOH . L 5 HOH B 25 254 254 HOH HOH . L 5 HOH B 26 257 257 HOH HOH . L 5 HOH B 27 259 259 HOH HOH . L 5 HOH B 28 260 260 HOH HOH . L 5 HOH B 29 262 262 HOH HOH . L 5 HOH B 30 265 265 HOH HOH . L 5 HOH B 31 273 273 HOH HOH . L 5 HOH B 32 276 276 HOH HOH . L 5 HOH B 33 277 277 HOH HOH . L 5 HOH B 34 283 283 HOH HOH . L 5 HOH B 35 289 289 HOH HOH . L 5 HOH B 36 290 290 HOH HOH . L 5 HOH B 37 294 294 HOH HOH . L 5 HOH B 38 296 296 HOH HOH . L 5 HOH B 39 299 299 HOH HOH . L 5 HOH B 40 300 300 HOH HOH . L 5 HOH B 41 301 301 HOH HOH . L 5 HOH B 42 304 304 HOH HOH . L 5 HOH B 43 306 306 HOH HOH . L 5 HOH B 44 308 308 HOH HOH . L 5 HOH B 45 315 315 HOH HOH . L 5 HOH B 46 316 316 HOH HOH . L 5 HOH B 47 319 319 HOH HOH . L 5 HOH B 48 325 325 HOH HOH . L 5 HOH B 49 326 326 HOH HOH . L 5 HOH B 50 327 327 HOH HOH . L 5 HOH B 51 330 330 HOH HOH . L 5 HOH B 52 332 332 HOH HOH . L 5 HOH B 53 333 333 HOH HOH . L 5 HOH B 54 336 336 HOH HOH . L 5 HOH B 55 338 338 HOH HOH . L 5 HOH B 56 344 344 HOH HOH . L 5 HOH B 57 345 345 HOH HOH . L 5 HOH B 58 347 347 HOH HOH . L 5 HOH B 59 349 349 HOH HOH . L 5 HOH B 60 351 351 HOH HOH . L 5 HOH B 61 352 352 HOH HOH . L 5 HOH B 62 358 358 HOH HOH . L 5 HOH B 63 361 361 HOH HOH . L 5 HOH B 64 363 363 HOH HOH . L 5 HOH B 65 367 367 HOH HOH . L 5 HOH B 66 374 374 HOH HOH . L 5 HOH B 67 376 376 HOH HOH . L 5 HOH B 68 377 377 HOH HOH . L 5 HOH B 69 378 378 HOH HOH . L 5 HOH B 70 379 379 HOH HOH . L 5 HOH B 71 381 381 HOH HOH . L 5 HOH B 72 382 382 HOH HOH . L 5 HOH B 73 383 383 HOH HOH . M 5 HOH C 1 156 156 HOH HOH . M 5 HOH C 2 158 158 HOH HOH . M 5 HOH C 3 163 163 HOH HOH . M 5 HOH C 4 165 165 HOH HOH . M 5 HOH C 5 167 167 HOH HOH . M 5 HOH C 6 168 168 HOH HOH . M 5 HOH C 7 169 169 HOH HOH . M 5 HOH C 8 171 171 HOH HOH . M 5 HOH C 9 174 174 HOH HOH . M 5 HOH C 10 178 178 HOH HOH . M 5 HOH C 11 179 179 HOH HOH . M 5 HOH C 12 181 181 HOH HOH . M 5 HOH C 13 183 183 HOH HOH . M 5 HOH C 14 185 185 HOH HOH . M 5 HOH C 15 191 191 HOH HOH . M 5 HOH C 16 192 192 HOH HOH . M 5 HOH C 17 195 195 HOH HOH . M 5 HOH C 18 197 197 HOH HOH . M 5 HOH C 19 198 198 HOH HOH . M 5 HOH C 20 201 201 HOH HOH . M 5 HOH C 21 204 204 HOH HOH . M 5 HOH C 22 210 210 HOH HOH . M 5 HOH C 23 212 212 HOH HOH . M 5 HOH C 24 213 213 HOH HOH . M 5 HOH C 25 220 220 HOH HOH . M 5 HOH C 26 223 223 HOH HOH . M 5 HOH C 27 224 224 HOH HOH . M 5 HOH C 28 228 228 HOH HOH . M 5 HOH C 29 229 229 HOH HOH . M 5 HOH C 30 230 230 HOH HOH . M 5 HOH C 31 231 231 HOH HOH . M 5 HOH C 32 232 232 HOH HOH . M 5 HOH C 33 237 237 HOH HOH . M 5 HOH C 34 238 238 HOH HOH . M 5 HOH C 35 239 239 HOH HOH . M 5 HOH C 36 241 241 HOH HOH . M 5 HOH C 37 242 242 HOH HOH . M 5 HOH C 38 246 246 HOH HOH . M 5 HOH C 39 248 248 HOH HOH . M 5 HOH C 40 255 255 HOH HOH . M 5 HOH C 41 256 256 HOH HOH . M 5 HOH C 42 261 261 HOH HOH . M 5 HOH C 43 267 267 HOH HOH . M 5 HOH C 44 275 275 HOH HOH . M 5 HOH C 45 278 278 HOH HOH . M 5 HOH C 46 281 281 HOH HOH . M 5 HOH C 47 282 282 HOH HOH . M 5 HOH C 48 284 284 HOH HOH . M 5 HOH C 49 285 285 HOH HOH . M 5 HOH C 50 291 291 HOH HOH . M 5 HOH C 51 292 292 HOH HOH . M 5 HOH C 52 297 297 HOH HOH . M 5 HOH C 53 298 298 HOH HOH . M 5 HOH C 54 302 302 HOH HOH . M 5 HOH C 55 305 305 HOH HOH . M 5 HOH C 56 307 307 HOH HOH . M 5 HOH C 57 310 310 HOH HOH . M 5 HOH C 58 311 311 HOH HOH . M 5 HOH C 59 312 312 HOH HOH . M 5 HOH C 60 313 313 HOH HOH . M 5 HOH C 61 318 318 HOH HOH . M 5 HOH C 62 320 320 HOH HOH . M 5 HOH C 63 322 322 HOH HOH . M 5 HOH C 64 323 323 HOH HOH . M 5 HOH C 65 329 329 HOH HOH . M 5 HOH C 66 337 337 HOH HOH . M 5 HOH C 67 339 339 HOH HOH . M 5 HOH C 68 340 340 HOH HOH . M 5 HOH C 69 342 342 HOH HOH . M 5 HOH C 70 346 346 HOH HOH . M 5 HOH C 71 348 348 HOH HOH . M 5 HOH C 72 350 350 HOH HOH . M 5 HOH C 73 353 353 HOH HOH . M 5 HOH C 74 354 354 HOH HOH . M 5 HOH C 75 362 362 HOH HOH . M 5 HOH C 76 369 369 HOH HOH . M 5 HOH C 77 371 371 HOH HOH . M 5 HOH C 78 373 373 HOH HOH . M 5 HOH C 79 380 380 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 N1 DUT . . . D 2 -0.836 -1.061 -3.539 1 26.85 ? N1 DUT 2170 A 1 HETATM 2 C C2 DUT . . . D 2 -1.152 -0.641 -2.266 1 23.64 ? C2 DUT 2170 A 1 HETATM 3 N N3 DUT . . . D 2 -0.289 -0.752 -1.237 1 23.02 ? N3 DUT 2170 A 1 HETATM 4 C C4 DUT . . . D 2 0.945 -1.3 -1.464 1 26.17 ? C4 DUT 2170 A 1 HETATM 5 C C5 DUT . . . D 2 1.301 -1.734 -2.744 1 21.37 ? C5 DUT 2170 A 1 HETATM 6 C C6 DUT . . . D 2 0.397 -1.588 -3.738 1 23.76 ? C6 DUT 2170 A 1 HETATM 7 O O2 DUT . . . D 2 -2.244 -0.113 -1.949 1 23.42 ? O2 DUT 2170 A 1 HETATM 8 O O4 DUT . . . D 2 1.836 -1.462 -0.485 1 22.39 ? O4 DUT 2170 A 1 HETATM 9 C C1' DUT . . . D 2 -1.747 -0.883 -4.729 1 30.21 ? C1' DUT 2170 A 1 HETATM 10 C C2' DUT . . . D 2 -1.013 0.05 -5.663 1 31.66 ? C2' DUT 2170 A 1 HETATM 11 C C3' DUT . . . D 2 -0.673 -0.6 -7 1 34.94 ? C3' DUT 2170 A 1 HETATM 12 C C4' DUT . . . D 2 -1.489 -1.879 -6.914 1 37.85 ? C4' DUT 2170 A 1 HETATM 13 O O4' DUT . . . D 2 -1.979 -1.992 -5.556 1 34.61 ? O4' DUT 2170 A 1 HETATM 14 O O3' DUT . . . D 2 -0.699 0.149 -8.21 1 31.56 ? O3' DUT 2170 A 1 HETATM 15 C C5' DUT . . . D 2 -0.774 -3.138 -7.425 1 44.85 ? C5' DUT 2170 A 1 HETATM 16 O O5' DUT . . . D 2 0.515 -3.455 -6.847 1 52.99 ? O5' DUT 2170 A 1 HETATM 17 P PA DUT . . . D 2 1.502 -4.672 -7.349 1 60.15 ? PA DUT 2170 A 1 HETATM 18 O O1A DUT . . . D 2 1.679 -4.554 -8.878 1 60.84 ? O1A DUT 2170 A 1 HETATM 19 O O2A DUT . . . D 2 2.707 -4.612 -6.438 1 57.94 ? O2A DUT 2170 A 1 HETATM 20 O O3A DUT . . . D 2 0.654 -5.98 -6.945 1 61.35 ? O3A DUT 2170 A 1 HETATM 21 P PB DUT . . . D 2 -0.027 -7.078 -7.91 1 64.25 ? PB DUT 2170 A 1 HETATM 22 O O1B DUT . . . D 2 0.896 -7.149 -9.122 1 61.16 ? O1B DUT 2170 A 1 HETATM 23 O O2B DUT . . . D 2 -0.173 -8.36 -7.087 1 57.85 ? O2B DUT 2170 A 1 HETATM 24 O O3B DUT . . . D 2 -1.508 -6.436 -8.183 1 64.05 ? O3B DUT 2170 A 1 HETATM 25 P PG DUT . . . D 2 -1.958 -5.685 -9.563 1 68.88 ? PG DUT 2170 A 1 HETATM 26 O O1G DUT . . . D 2 -2.45 -6.768 -10.529 1 66.74 ? O1G DUT 2170 A 1 HETATM 27 O O2G DUT . . . D 2 -0.669 -5.061 -10.093 1 67.19 ? O2G DUT 2170 A 1 HETATM 28 O O3G DUT . . . D 2 -3.047 -4.726 -9.106 1 65.77 ? O3G DUT 2170 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #