data_5TPV # _model_server_result.job_id ZMml5uhdI4kixD6lBtuNqA _model_server_result.datetime_utc '2024-11-29 04:02:22' _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 5tpv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 5TPV # _exptl.entry_id 5TPV _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-5'-DIPHOSPHATE" _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 5TPV _cell.length_a 177.953 _cell.length_b 177.953 _cell.length_c 88.6 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TPV _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,F,G,I,J 1 1 C,H,K 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -177.953 0 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 E N N ? 2 H N N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 338 n n PA O2A TYD sing 339 n n PA O3A TYD sing 340 n n PA O5' TYD sing 341 n n O2A HOA2 TYD sing 342 n n O3A PB TYD sing 343 n n PB O1B TYD doub 344 n n PB O2B TYD sing 345 n n PB O3B TYD sing 346 n n O2B HOB2 TYD sing 347 n n O3B HOB3 TYD sing 348 n n O5' C5' TYD sing 349 n n C5' C4' TYD sing 350 n n C5' "H5'1" TYD sing 351 n n C5' "H5'2" TYD sing 352 n n C4' O4' TYD sing 353 n n C4' C3' TYD sing 354 n n C4' H4' TYD sing 355 n n O4' C1' TYD sing 356 n n C3' O3' TYD sing 357 n n C3' C2' TYD sing 358 n n C3' H3' TYD sing 359 n n O3' HO3' TYD sing 360 n n C2' C1' TYD sing 361 n n C2' "H2'1" TYD sing 362 n n C2' "H2'2" TYD sing 363 n n C1' N1 TYD sing 364 n n C1' H1' TYD sing 365 n n N1 C2 TYD sing 366 n y N1 C6 TYD sing 367 n y C2 O2 TYD doub 368 n n C2 N3 TYD sing 369 n y N3 C4 TYD sing 370 n y N3 HN3 TYD sing 371 n n C4 O4 TYD doub 372 n n C4 C5 TYD sing 373 n y C5 C5M TYD sing 374 n n C5 C6 TYD doub 375 n y C5M H51 TYD sing 376 n n C5M H52 TYD sing 377 n n C5M H53 TYD sing 378 n n C6 H6 TYD sing 379 n n # _atom_sites.entry_id 5TPV _atom_sites.fract_transf_matrix[1][1] 0.005619 _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] 0.005619 _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] 0.011287 _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 TYD A 1 201 150 TYD TYD . E 2 TYD B 1 201 150 TYD TYD . F 3 PO4 B 1 202 1 PO4 PO4 . G 3 PO4 B 1 203 2 PO4 PO4 . H 2 TYD C 1 201 150 TYD TYD . I 4 HOH A 1 301 343 HOH HOH . I 4 HOH A 2 302 231 HOH HOH . I 4 HOH A 3 303 279 HOH HOH . I 4 HOH A 4 304 355 HOH HOH . I 4 HOH A 5 305 88 HOH HOH . I 4 HOH A 6 306 161 HOH HOH . I 4 HOH A 7 307 98 HOH HOH . I 4 HOH A 8 308 277 HOH HOH . I 4 HOH A 9 309 184 HOH HOH . I 4 HOH A 10 310 314 HOH HOH . I 4 HOH A 11 311 91 HOH HOH . I 4 HOH A 12 312 21 HOH HOH . I 4 HOH A 13 313 336 HOH HOH . I 4 HOH A 14 314 152 HOH HOH . I 4 HOH A 15 315 12 HOH HOH . I 4 HOH A 16 316 3 HOH HOH . I 4 HOH A 17 317 327 HOH HOH . I 4 HOH A 18 318 255 HOH HOH . I 4 HOH A 19 319 87 HOH HOH . I 4 HOH A 20 320 40 HOH HOH . I 4 HOH A 21 321 11 HOH HOH . I 4 HOH A 22 322 177 HOH HOH . I 4 HOH A 23 323 246 HOH HOH . I 4 HOH A 24 324 90 HOH HOH . I 4 HOH A 25 325 19 HOH HOH . I 4 HOH A 26 326 325 HOH HOH . I 4 HOH A 27 327 266 HOH HOH . I 4 HOH A 28 328 268 HOH HOH . I 4 HOH A 29 329 32 HOH HOH . I 4 HOH A 30 330 337 HOH HOH . I 4 HOH A 31 331 349 HOH HOH . I 4 HOH A 32 332 276 HOH HOH . I 4 HOH A 33 333 52 HOH HOH . I 4 HOH A 34 334 35 HOH HOH . I 4 HOH A 35 335 243 HOH HOH . I 4 HOH A 36 336 274 HOH HOH . I 4 HOH A 37 337 29 HOH HOH . I 4 HOH A 38 338 240 HOH HOH . I 4 HOH A 39 339 330 HOH HOH . I 4 HOH A 40 340 350 HOH HOH . I 4 HOH A 41 341 165 HOH HOH . I 4 HOH A 42 342 248 HOH HOH . I 4 HOH A 43 343 28 HOH HOH . I 4 HOH A 44 344 114 HOH HOH . I 4 HOH A 45 345 45 HOH HOH . I 4 HOH A 46 346 267 HOH HOH . I 4 HOH A 47 347 68 HOH HOH . I 4 HOH A 48 348 70 HOH HOH . I 4 HOH A 49 349 82 HOH HOH . I 4 HOH A 50 350 47 HOH HOH . I 4 HOH A 51 351 83 HOH HOH . I 4 HOH A 52 352 72 HOH HOH . I 4 HOH A 53 353 356 HOH HOH . I 4 HOH A 54 354 164 HOH HOH . I 4 HOH A 55 355 238 HOH HOH . I 4 HOH A 56 356 308 HOH HOH . I 4 HOH A 57 357 64 HOH HOH . I 4 HOH A 58 358 92 HOH HOH . I 4 HOH A 59 359 73 HOH HOH . I 4 HOH A 60 360 56 HOH HOH . I 4 HOH A 61 361 196 HOH HOH . I 4 HOH A 62 362 74 HOH HOH . I 4 HOH A 63 363 338 HOH HOH . I 4 HOH A 64 364 15 HOH HOH . I 4 HOH A 65 365 326 HOH HOH . I 4 HOH A 66 366 75 HOH HOH . I 4 HOH A 67 367 353 HOH HOH . I 4 HOH A 68 368 153 HOH HOH . I 4 HOH A 69 369 280 HOH HOH . I 4 HOH A 70 370 62 HOH HOH . I 4 HOH A 71 371 245 HOH HOH . I 4 HOH A 72 372 239 HOH HOH . I 4 HOH A 73 373 102 HOH HOH . I 4 HOH A 74 374 307 HOH HOH . I 4 HOH A 75 375 351 HOH HOH . I 4 HOH A 76 376 168 HOH HOH . I 4 HOH A 77 377 143 HOH HOH . I 4 HOH A 78 378 101 HOH HOH . I 4 HOH A 79 379 254 HOH HOH . I 4 HOH A 80 380 303 HOH HOH . I 4 HOH A 81 381 145 HOH HOH . I 4 HOH A 82 382 69 HOH HOH . I 4 HOH A 83 383 318 HOH HOH . I 4 HOH A 84 384 332 HOH HOH . I 4 HOH A 85 385 244 HOH HOH . I 4 HOH A 86 386 331 HOH HOH . J 4 HOH B 1 301 348 HOH HOH . J 4 HOH B 2 302 80 HOH HOH . J 4 HOH B 3 303 39 HOH HOH . J 4 HOH B 4 304 198 HOH HOH . J 4 HOH B 5 305 57 HOH HOH . J 4 HOH B 6 306 310 HOH HOH . J 4 HOH B 7 307 6 HOH HOH . J 4 HOH B 8 308 345 HOH HOH . J 4 HOH B 9 309 339 HOH HOH . J 4 HOH B 10 310 113 HOH HOH . J 4 HOH B 11 311 44 HOH HOH . J 4 HOH B 12 312 169 HOH HOH . J 4 HOH B 13 313 278 HOH HOH . J 4 HOH B 14 314 283 HOH HOH . J 4 HOH B 15 315 258 HOH HOH . J 4 HOH B 16 316 256 HOH HOH . J 4 HOH B 17 317 346 HOH HOH . J 4 HOH B 18 318 119 HOH HOH . J 4 HOH B 19 319 84 HOH HOH . J 4 HOH B 20 320 273 HOH HOH . J 4 HOH B 21 321 287 HOH HOH . J 4 HOH B 22 322 116 HOH HOH . J 4 HOH B 23 323 172 HOH HOH . J 4 HOH B 24 324 85 HOH HOH . J 4 HOH B 25 325 282 HOH HOH . J 4 HOH B 26 326 25 HOH HOH . J 4 HOH B 27 327 262 HOH HOH . J 4 HOH B 28 328 126 HOH HOH . J 4 HOH B 29 329 191 HOH HOH . J 4 HOH B 30 330 251 HOH HOH . J 4 HOH B 31 331 157 HOH HOH . J 4 HOH B 32 332 334 HOH HOH . J 4 HOH B 33 333 250 HOH HOH . J 4 HOH B 34 334 259 HOH HOH . J 4 HOH B 35 335 341 HOH HOH . J 4 HOH B 36 336 188 HOH HOH . J 4 HOH B 37 337 335 HOH HOH . J 4 HOH B 38 338 289 HOH HOH . J 4 HOH B 39 339 86 HOH HOH . J 4 HOH B 40 340 53 HOH HOH . J 4 HOH B 41 341 323 HOH HOH . J 4 HOH B 42 342 120 HOH HOH . J 4 HOH B 43 343 315 HOH HOH . J 4 HOH B 44 344 344 HOH HOH . J 4 HOH B 45 345 340 HOH HOH . J 4 HOH B 46 346 357 HOH HOH . J 4 HOH B 47 347 242 HOH HOH . J 4 HOH B 48 348 16 HOH HOH . J 4 HOH B 49 349 352 HOH HOH . J 4 HOH B 50 350 269 HOH HOH . J 4 HOH B 51 351 200 HOH HOH . J 4 HOH B 52 352 115 HOH HOH . J 4 HOH B 53 353 270 HOH HOH . J 4 HOH B 54 354 112 HOH HOH . J 4 HOH B 55 355 13 HOH HOH . J 4 HOH B 56 356 123 HOH HOH . J 4 HOH B 57 357 95 HOH HOH . J 4 HOH B 58 358 96 HOH HOH . J 4 HOH B 59 359 281 HOH HOH . J 4 HOH B 60 360 271 HOH HOH . J 4 HOH B 61 361 9 HOH HOH . J 4 HOH B 62 362 97 HOH HOH . J 4 HOH B 63 363 195 HOH HOH . J 4 HOH B 64 364 79 HOH HOH . J 4 HOH B 65 365 121 HOH HOH . J 4 HOH B 66 366 183 HOH HOH . J 4 HOH B 67 367 122 HOH HOH . J 4 HOH B 68 368 288 HOH HOH . J 4 HOH B 69 369 328 HOH HOH . J 4 HOH B 70 370 5 HOH HOH . J 4 HOH B 71 371 125 HOH HOH . J 4 HOH B 72 372 252 HOH HOH . J 4 HOH B 73 373 354 HOH HOH . J 4 HOH B 74 374 342 HOH HOH . J 4 HOH B 75 375 285 HOH HOH . J 4 HOH B 76 376 127 HOH HOH . J 4 HOH B 77 377 20 HOH HOH . J 4 HOH B 78 378 186 HOH HOH . J 4 HOH B 79 379 67 HOH HOH . J 4 HOH B 80 380 76 HOH HOH . J 4 HOH B 81 381 261 HOH HOH . J 4 HOH B 82 382 284 HOH HOH . J 4 HOH B 83 383 194 HOH HOH . J 4 HOH B 84 384 347 HOH HOH . K 4 HOH C 1 301 293 HOH HOH . K 4 HOH C 2 302 301 HOH HOH . K 4 HOH C 3 303 49 HOH HOH . K 4 HOH C 4 304 8 HOH HOH . K 4 HOH C 5 305 275 HOH HOH . K 4 HOH C 6 306 135 HOH HOH . K 4 HOH C 7 307 324 HOH HOH . K 4 HOH C 8 308 117 HOH HOH . K 4 HOH C 9 309 132 HOH HOH . K 4 HOH C 10 310 136 HOH HOH . K 4 HOH C 11 311 130 HOH HOH . K 4 HOH C 12 312 139 HOH HOH . K 4 HOH C 13 313 81 HOH HOH . K 4 HOH C 14 314 159 HOH HOH . K 4 HOH C 15 315 205 HOH HOH . K 4 HOH C 16 316 297 HOH HOH . K 4 HOH C 17 317 189 HOH HOH . K 4 HOH C 18 318 291 HOH HOH . K 4 HOH C 19 319 26 HOH HOH . K 4 HOH C 20 320 10 HOH HOH . K 4 HOH C 21 321 78 HOH HOH . K 4 HOH C 22 322 128 HOH HOH . K 4 HOH C 23 323 131 HOH HOH . K 4 HOH C 24 324 134 HOH HOH . K 4 HOH C 25 325 2 HOH HOH . K 4 HOH C 26 326 201 HOH HOH . K 4 HOH C 27 327 140 HOH HOH . K 4 HOH C 28 328 290 HOH HOH . K 4 HOH C 29 329 24 HOH HOH . K 4 HOH C 30 330 129 HOH HOH . K 4 HOH C 31 331 204 HOH HOH . K 4 HOH C 32 332 296 HOH HOH . K 4 HOH C 33 333 50 HOH HOH . K 4 HOH C 34 334 199 HOH HOH . K 4 HOH C 35 335 148 HOH HOH . K 4 HOH C 36 336 237 HOH HOH . K 4 HOH C 37 337 77 HOH HOH . K 4 HOH C 38 338 63 HOH HOH . K 4 HOH C 39 339 118 HOH HOH . K 4 HOH C 40 340 147 HOH HOH . K 4 HOH C 41 341 149 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 PA TYD . . . D 2 -58.547 -31.87 10.132 1 43.53 ? PA TYD 201 A 1 HETATM 2 O O1A TYD . . . D 2 -58.918 -31.923 8.669 1 34.33 ? O1A TYD 201 A 1 HETATM 3 O O2A TYD . . . D 2 -59.561 -32.26 11.181 1 55.55 ? O2A TYD 201 A 1 HETATM 4 O O3A TYD . . . D 2 -57.226 -32.764 10.35 1 43.79 ? O3A TYD 201 A 1 HETATM 5 P PB TYD . . . D 2 -56.42 -33.353 9.087 1 39.89 ? PB TYD 201 A 1 HETATM 6 O O1B TYD . . . D 2 -57.491 -33.997 8.239 1 33.3 ? O1B TYD 201 A 1 HETATM 7 O O2B TYD . . . D 2 -55.441 -34.325 9.701 1 41.08 ? O2B TYD 201 A 1 HETATM 8 O O3B TYD . . . D 2 -55.781 -32.135 8.463 1 45.09 ? O3B TYD 201 A 1 HETATM 9 O O5' TYD . . . D 2 -58.024 -30.384 10.464 1 35.27 ? O5' TYD 201 A 1 HETATM 10 C C5' TYD . . . D 2 -57.078 -30.166 11.508 1 40.41 ? C5' TYD 201 A 1 HETATM 11 C C4' TYD . . . D 2 -57.54 -29.006 12.38 1 40.9 ? C4' TYD 201 A 1 HETATM 12 O O4' TYD . . . D 2 -57.233 -27.766 11.736 1 39.2 ? O4' TYD 201 A 1 HETATM 13 C C3' TYD . . . D 2 -59.043 -29.052 12.607 1 42.65 ? C3' TYD 201 A 1 HETATM 14 O O3' TYD . . . D 2 -59.324 -29.153 14.006 1 49.46 ? O3' TYD 201 A 1 HETATM 15 C C2' TYD . . . D 2 -59.6 -27.752 12.058 1 41.32 ? C2' TYD 201 A 1 HETATM 16 C C1' TYD . . . D 2 -58.406 -26.976 11.521 1 34.36 ? C1' TYD 201 A 1 HETATM 17 N N1 TYD . . . D 2 -58.58 -26.73 10.088 1 43.04 ? N1 TYD 201 A 1 HETATM 18 C C2 TYD . . . D 2 -59.052 -25.472 9.649 1 42.03 ? C2 TYD 201 A 1 HETATM 19 O O2 TYD . . . D 2 -59.313 -24.588 10.492 1 41.23 ? O2 TYD 201 A 1 HETATM 20 N N3 TYD . . . D 2 -59.224 -25.208 8.346 1 36.03 ? N3 TYD 201 A 1 HETATM 21 C C4 TYD . . . D 2 -58.952 -26.134 7.422 1 37.63 ? C4 TYD 201 A 1 HETATM 22 O O4 TYD . . . D 2 -59.114 -25.884 6.208 1 36.9 ? O4 TYD 201 A 1 HETATM 23 C C5 TYD . . . D 2 -58.456 -27.463 7.856 1 37.97 ? C5 TYD 201 A 1 HETATM 24 C C5M TYD . . . D 2 -58.138 -28.533 6.845 1 36.98 ? C5M TYD 201 A 1 HETATM 25 C C6 TYD . . . D 2 -58.29 -27.7 9.213 1 44.98 ? C6 TYD 201 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #