data_7S3U # _model_server_result.job_id 441xhoRRY70-L8PcYt5wYw _model_server_result.datetime_utc '2024-10-11 11:17:17' _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 7s3u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 7S3U # _exptl.entry_id 7S3U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 547.345 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate' _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 7S3U _cell.length_a 102.97 _cell.length_b 102.97 _cell.length_c 102.97 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7S3U _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 3 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H27 N3 O14 P2' _chem_comp.formula_weight 547.345 _chem_comp.id T3Q _chem_comp.mon_nstd_flag . _chem_comp.name '[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose" # 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 O4 C4 T3Q doub 385 n n N3 C4 T3Q sing 386 n n C4 C5 T3Q sing 387 n n N3 C2 T3Q sing 388 n n N3 HN3 T3Q sing 389 n n O2 C2 T3Q doub 390 n n C2 N1 T3Q sing 391 n n C5 C5M T3Q sing 392 n n C5 C6 T3Q doub 393 n n C5M H5M T3Q sing 394 n n C5M H5MA T3Q sing 395 n n C5M H5MB T3Q sing 396 n n N1 C6 T3Q sing 397 n n C6 H6 T3Q sing 398 n n N1 C1' T3Q sing 399 n n C1' O4' T3Q sing 400 n n C1' C2' T3Q sing 401 n n C1' H1' T3Q sing 402 n n O4' C4' T3Q sing 403 n n C2' C3' T3Q sing 404 n n C2' H2' T3Q sing 405 n n C2' "H2'A" T3Q sing 406 n n C4' C3' T3Q sing 407 n n C3' O3' T3Q sing 408 n n C3' H3' T3Q sing 409 n n O3' HO3' T3Q sing 410 n n C4' C5' T3Q sing 411 n n C4' H4' T3Q sing 412 n n O5' C5' T3Q sing 413 n n C5' H5' T3Q sing 414 n n C5' "H5'A" T3Q sing 415 n n O5' PA T3Q sing 416 n n O1A PA T3Q doub 417 n n O2A PA T3Q sing 418 n n PA O3A T3Q sing 419 n n O2A HO2A T3Q sing 420 n n O3A PB T3Q sing 421 n n O2B PB T3Q doub 422 n n O1B PB T3Q sing 423 n n PB O3B T3Q sing 424 n n O1B HO1B T3Q sing 425 n n O3B C1Q T3Q sing 426 n n C4Q O4Q T3Q sing 427 n n O4Q HO4Q T3Q sing 428 n n C5Q C4Q T3Q sing 429 n n C3Q C4Q T3Q sing 430 n n C4Q H4Q T3Q sing 431 n n O5Q C5Q T3Q sing 432 n n C5Q C6Q T3Q sing 433 n n C5Q H5Q T3Q sing 434 n n C1Q O5Q T3Q sing 435 n n C6Q H6Q T3Q sing 436 n n C6Q H6QA T3Q sing 437 n n C6Q H6QB T3Q sing 438 n n C2Q C3Q T3Q sing 439 n n C3Q N3Q T3Q sing 440 n n C3Q H3Q T3Q sing 441 n n N3Q HN3Q T3Q sing 442 n n N3Q HN3A T3Q sing 443 n n O2Q C2Q T3Q sing 444 n n C1Q C2Q T3Q sing 445 n n C2Q H2Q T3Q sing 446 n n O2Q HO2Q T3Q sing 447 n n C1Q H1Q T3Q sing 448 n n # _atom_sites.entry_id 7S3U _atom_sites.fract_transf_matrix[1][1] 0.009712 _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] 0.009712 _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] 0.009712 _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 COA A 1 201 201 COA COA . C 3 T3Q A 1 202 301 T3Q T3Q . D 4 EDO A 1 203 302 EDO EDO . E 5 HOH A 1 301 152 HOH HOH . E 5 HOH A 2 302 194 HOH HOH . E 5 HOH A 3 303 61 HOH HOH . E 5 HOH A 4 304 57 HOH HOH . E 5 HOH A 5 305 27 HOH HOH . E 5 HOH A 6 306 178 HOH HOH . E 5 HOH A 7 307 111 HOH HOH . E 5 HOH A 8 308 45 HOH HOH . E 5 HOH A 9 309 158 HOH HOH . E 5 HOH A 10 310 37 HOH HOH . E 5 HOH A 11 311 102 HOH HOH . E 5 HOH A 12 312 99 HOH HOH . E 5 HOH A 13 313 161 HOH HOH . E 5 HOH A 14 314 104 HOH HOH . E 5 HOH A 15 315 11 HOH HOH . E 5 HOH A 16 316 52 HOH HOH . E 5 HOH A 17 317 34 HOH HOH . E 5 HOH A 18 318 107 HOH HOH . E 5 HOH A 19 319 94 HOH HOH . E 5 HOH A 20 320 93 HOH HOH . E 5 HOH A 21 321 60 HOH HOH . E 5 HOH A 22 322 33 HOH HOH . E 5 HOH A 23 323 25 HOH HOH . E 5 HOH A 24 324 3 HOH HOH . E 5 HOH A 25 325 17 HOH HOH . E 5 HOH A 26 326 162 HOH HOH . E 5 HOH A 27 327 115 HOH HOH . E 5 HOH A 28 328 19 HOH HOH . E 5 HOH A 29 329 20 HOH HOH . E 5 HOH A 30 330 118 HOH HOH . E 5 HOH A 31 331 179 HOH HOH . E 5 HOH A 32 332 62 HOH HOH . E 5 HOH A 33 333 8 HOH HOH . E 5 HOH A 34 334 53 HOH HOH . E 5 HOH A 35 335 88 HOH HOH . E 5 HOH A 36 336 149 HOH HOH . E 5 HOH A 37 337 169 HOH HOH . E 5 HOH A 38 338 159 HOH HOH . E 5 HOH A 39 339 15 HOH HOH . E 5 HOH A 40 340 163 HOH HOH . E 5 HOH A 41 341 42 HOH HOH . E 5 HOH A 42 342 6 HOH HOH . E 5 HOH A 43 343 164 HOH HOH . E 5 HOH A 44 344 1 HOH HOH . E 5 HOH A 45 345 74 HOH HOH . E 5 HOH A 46 346 41 HOH HOH . E 5 HOH A 47 347 188 HOH HOH . E 5 HOH A 48 348 114 HOH HOH . E 5 HOH A 49 349 72 HOH HOH . E 5 HOH A 50 350 44 HOH HOH . E 5 HOH A 51 351 13 HOH HOH . E 5 HOH A 52 352 43 HOH HOH . E 5 HOH A 53 353 73 HOH HOH . E 5 HOH A 54 354 171 HOH HOH . E 5 HOH A 55 355 148 HOH HOH . E 5 HOH A 56 356 63 HOH HOH . E 5 HOH A 57 357 12 HOH HOH . E 5 HOH A 58 358 109 HOH HOH . E 5 HOH A 59 359 91 HOH HOH . E 5 HOH A 60 360 100 HOH HOH . E 5 HOH A 61 361 147 HOH HOH . E 5 HOH A 62 362 55 HOH HOH . E 5 HOH A 63 363 126 HOH HOH . E 5 HOH A 64 364 51 HOH HOH . E 5 HOH A 65 365 5 HOH HOH . E 5 HOH A 66 366 156 HOH HOH . E 5 HOH A 67 367 87 HOH HOH . E 5 HOH A 68 368 168 HOH HOH . E 5 HOH A 69 369 31 HOH HOH . E 5 HOH A 70 370 127 HOH HOH . E 5 HOH A 71 371 49 HOH HOH . E 5 HOH A 72 372 7 HOH HOH . E 5 HOH A 73 373 116 HOH HOH . E 5 HOH A 74 374 59 HOH HOH . E 5 HOH A 75 375 155 HOH HOH . E 5 HOH A 76 376 166 HOH HOH . E 5 HOH A 77 377 64 HOH HOH . E 5 HOH A 78 378 145 HOH HOH . E 5 HOH A 79 379 47 HOH HOH . E 5 HOH A 80 380 24 HOH HOH . E 5 HOH A 81 381 79 HOH HOH . E 5 HOH A 82 382 18 HOH HOH . E 5 HOH A 83 383 198 HOH HOH . E 5 HOH A 84 384 69 HOH HOH . E 5 HOH A 85 385 108 HOH HOH . E 5 HOH A 86 386 54 HOH HOH . E 5 HOH A 87 387 180 HOH HOH . E 5 HOH A 88 388 23 HOH HOH . E 5 HOH A 89 389 28 HOH HOH . E 5 HOH A 90 390 30 HOH HOH . E 5 HOH A 91 391 97 HOH HOH . E 5 HOH A 92 392 68 HOH HOH . E 5 HOH A 93 393 48 HOH HOH . E 5 HOH A 94 394 56 HOH HOH . E 5 HOH A 95 395 75 HOH HOH . E 5 HOH A 96 396 124 HOH HOH . E 5 HOH A 97 397 14 HOH HOH . E 5 HOH A 98 398 2 HOH HOH . E 5 HOH A 99 399 39 HOH HOH . E 5 HOH A 100 400 172 HOH HOH . E 5 HOH A 101 401 170 HOH HOH . E 5 HOH A 102 402 129 HOH HOH . E 5 HOH A 103 403 10 HOH HOH . E 5 HOH A 104 404 131 HOH HOH . E 5 HOH A 105 405 36 HOH HOH . E 5 HOH A 106 406 16 HOH HOH . E 5 HOH A 107 407 58 HOH HOH . E 5 HOH A 108 408 197 HOH HOH . E 5 HOH A 109 409 184 HOH HOH . E 5 HOH A 110 410 110 HOH HOH . E 5 HOH A 111 411 146 HOH HOH . E 5 HOH A 112 412 81 HOH HOH . E 5 HOH A 113 413 32 HOH HOH . E 5 HOH A 114 414 38 HOH HOH . E 5 HOH A 115 415 67 HOH HOH . E 5 HOH A 116 416 21 HOH HOH . E 5 HOH A 117 417 9 HOH HOH . E 5 HOH A 118 418 183 HOH HOH . E 5 HOH A 119 419 46 HOH HOH . E 5 HOH A 120 420 106 HOH HOH . E 5 HOH A 121 421 185 HOH HOH . E 5 HOH A 122 422 4 HOH HOH . E 5 HOH A 123 423 186 HOH HOH . E 5 HOH A 124 424 90 HOH HOH . E 5 HOH A 125 425 77 HOH HOH . E 5 HOH A 126 426 96 HOH HOH . E 5 HOH A 127 427 140 HOH HOH . E 5 HOH A 128 428 123 HOH HOH . E 5 HOH A 129 429 181 HOH HOH . E 5 HOH A 130 430 139 HOH HOH . E 5 HOH A 131 431 167 HOH HOH . E 5 HOH A 132 432 103 HOH HOH . E 5 HOH A 133 433 196 HOH HOH . E 5 HOH A 134 434 135 HOH HOH . E 5 HOH A 135 435 130 HOH HOH . E 5 HOH A 136 436 153 HOH HOH . E 5 HOH A 137 437 175 HOH HOH . E 5 HOH A 138 438 98 HOH HOH . E 5 HOH A 139 439 136 HOH HOH . E 5 HOH A 140 440 22 HOH HOH . E 5 HOH A 141 441 151 HOH HOH . E 5 HOH A 142 442 182 HOH HOH . E 5 HOH A 143 443 160 HOH HOH . E 5 HOH A 144 444 101 HOH HOH . E 5 HOH A 145 445 65 HOH HOH . E 5 HOH A 146 446 85 HOH HOH . E 5 HOH A 147 447 50 HOH HOH . E 5 HOH A 148 448 89 HOH HOH . E 5 HOH A 149 449 174 HOH HOH . E 5 HOH A 150 450 176 HOH HOH . E 5 HOH A 151 451 142 HOH HOH . E 5 HOH A 152 452 76 HOH HOH . E 5 HOH A 153 453 195 HOH HOH . E 5 HOH A 154 454 177 HOH HOH . E 5 HOH A 155 455 193 HOH HOH . E 5 HOH A 156 456 187 HOH HOH . E 5 HOH A 157 457 117 HOH HOH . E 5 HOH A 158 458 157 HOH HOH . E 5 HOH A 159 459 82 HOH HOH . E 5 HOH A 160 460 150 HOH HOH . E 5 HOH A 161 461 141 HOH HOH . E 5 HOH A 162 462 144 HOH HOH . E 5 HOH A 163 463 40 HOH HOH . E 5 HOH A 164 464 80 HOH HOH . E 5 HOH A 165 465 173 HOH HOH . E 5 HOH A 166 466 29 HOH HOH . E 5 HOH A 167 467 192 HOH HOH . E 5 HOH A 168 468 191 HOH HOH . E 5 HOH A 169 469 128 HOH HOH . E 5 HOH A 170 470 165 HOH HOH . E 5 HOH A 171 471 120 HOH HOH . E 5 HOH A 172 472 143 HOH HOH . E 5 HOH A 173 473 66 HOH HOH . E 5 HOH A 174 474 119 HOH HOH . E 5 HOH A 175 475 190 HOH HOH . E 5 HOH A 176 476 70 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 O O4 T3Q . . . C 3 23.019 -8.006 22.896 1 6.9 ? O4 T3Q 202 A 1 HETATM 2 C C4 T3Q . . . C 3 23.267 -8.437 23.967 1 5.9 ? C4 T3Q 202 A 1 HETATM 3 N N3 T3Q . . . C 3 22.951 -9.692 24.228 1 5.38 ? N3 T3Q 202 A 1 HETATM 4 C C2 T3Q . . . C 3 23.195 -10.271 25.432 1 6.12 ? C2 T3Q 202 A 1 HETATM 5 O O2 T3Q . . . C 3 22.912 -11.46 25.64 1 5.84 ? O2 T3Q 202 A 1 HETATM 6 C C5 T3Q . . . C 3 23.806 -7.694 24.974 1 5.57 ? C5 T3Q 202 A 1 HETATM 7 C C5M T3Q . . . C 3 24.163 -6.255 24.702 1 6.33 ? C5M T3Q 202 A 1 HETATM 8 C C6 T3Q . . . C 3 24.064 -8.254 26.181 1 5.75 ? C6 T3Q 202 A 1 HETATM 9 N N1 T3Q . . . C 3 23.769 -9.546 26.408 1 5.65 ? N1 T3Q 202 A 1 HETATM 10 C C1' T3Q . . . C 3 24.05 -10.239 27.683 1 5.99 ? C1' T3Q 202 A 1 HETATM 11 O O4' T3Q . . . C 3 24.284 -9.289 28.668 1 6.22 ? O4' T3Q 202 A 1 HETATM 12 C C2' T3Q . . . C 3 25.373 -11.006 27.544 1 6.34 ? C2' T3Q 202 A 1 HETATM 13 C C3' T3Q . . . C 3 26.429 -10.064 28.1 1 6.53 ? C3' T3Q 202 A 1 HETATM 14 O O3' T3Q . . . C 3 27.584 -10.78 28.545 1 6.45 ? O3' T3Q 202 A 1 HETATM 15 C C4' T3Q . . . C 3 25.609 -9.44 29.207 1 6.53 ? C4' T3Q 202 A 1 HETATM 16 C C5' T3Q . . . C 3 26.137 -8.056 29.634 1 7.1 ? C5' T3Q 202 A 1 HETATM 17 O O5' T3Q . . . C 3 25.433 -7.581 30.726 1 7.72 ? O5' T3Q 202 A 1 HETATM 18 P PA T3Q . . . C 3 26.178 -7.255 32.132 1 9.51 ? PA T3Q 202 A 1 HETATM 19 O O1A T3Q . . . C 3 25.143 -6.932 33.077 1 9.67 ? O1A T3Q 202 A 1 HETATM 20 O O2A T3Q . . . C 3 27.273 -6.33 31.839 1 11.32 ? O2A T3Q 202 A 1 HETATM 21 O O3A T3Q . . . C 3 26.95 -8.623 32.537 1 10.09 ? O3A T3Q 202 A 1 HETATM 22 P PB T3Q . . . C 3 26.486 -9.932 33.376 1 11.46 ? PB T3Q 202 A 1 HETATM 23 O O1B T3Q . . . C 3 26.084 -9.504 34.737 1 12.43 ? O1B T3Q 202 A 1 HETATM 24 O O2B T3Q . . . C 3 25.542 -10.758 32.588 1 10.49 ? O2B T3Q 202 A 1 HETATM 25 O O3B T3Q . . . C 3 27.906 -10.664 33.428 1 10.4 ? O3B T3Q 202 A 1 HETATM 26 O O4Q T3Q . . . C 3 30.687 -12.868 36.198 1 10.24 ? O4Q T3Q 202 A 1 HETATM 27 C C4Q T3Q . . . C 3 30.615 -11.736 35.342 1 10.69 ? C4Q T3Q 202 A 1 HETATM 28 C C5Q T3Q . . . C 3 29.506 -10.78 35.741 1 12.06 ? C5Q T3Q 202 A 1 HETATM 29 O O5Q T3Q . . . C 3 29.458 -9.731 34.838 1 10.76 ? O5Q T3Q 202 A 1 HETATM 30 C C6Q T3Q . . . C 3 29.726 -10.123 37.101 1 13.2 ? C6Q T3Q 202 A 1 HETATM 31 C C3Q T3Q . . . C 3 30.269 -12.256 33.955 1 11.1 ? C3Q T3Q 202 A 1 HETATM 32 N N3Q T3Q . . . C 3 31.255 -13.243 33.502 1 11.49 ? N3Q T3Q 202 A 1 HETATM 33 C C2Q T3Q . . . C 3 30.172 -11.069 33.008 1 11.96 ? C2Q T3Q 202 A 1 HETATM 34 O O2Q T3Q . . . C 3 29.776 -11.516 31.723 1 12.14 ? O2Q T3Q 202 A 1 HETATM 35 C C1Q T3Q . . . C 3 29.169 -10.06 33.482 1 11.71 ? C1Q T3Q 202 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 35 #