data_5K5P # _model_server_result.job_id 2a0MauEls9BBx0xc1496xA _model_server_result.datetime_utc '2024-10-20 00:31:55' _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 5k5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5K5P # _exptl.entry_id 5K5P _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 5K5P _cell.length_a 30.12 _cell.length_b 61.64 _cell.length_c 80.399 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K5P _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 _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 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 5K5P _atom_sites.fract_transf_matrix[1][1] 0.033201 _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] 0.016223 _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] 0.012438 _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 1 201 142 THP THP . C 3 HOH A 1 301 82 HOH HOH . C 3 HOH A 2 302 38 HOH HOH . C 3 HOH A 3 303 87 HOH HOH . C 3 HOH A 4 304 74 HOH HOH . C 3 HOH A 5 305 100 HOH HOH . C 3 HOH A 6 306 18 HOH HOH . C 3 HOH A 7 307 101 HOH HOH . C 3 HOH A 8 308 80 HOH HOH . C 3 HOH A 9 309 91 HOH HOH . C 3 HOH A 10 310 78 HOH HOH . C 3 HOH A 11 311 104 HOH HOH . C 3 HOH A 12 312 79 HOH HOH . C 3 HOH A 13 313 92 HOH HOH . C 3 HOH A 14 314 84 HOH HOH . C 3 HOH A 15 315 88 HOH HOH . C 3 HOH A 16 316 26 HOH HOH . C 3 HOH A 17 317 40 HOH HOH . C 3 HOH A 18 318 43 HOH HOH . C 3 HOH A 19 319 10 HOH HOH . C 3 HOH A 20 320 52 HOH HOH . C 3 HOH A 21 321 98 HOH HOH . C 3 HOH A 22 322 46 HOH HOH . C 3 HOH A 23 323 21 HOH HOH . C 3 HOH A 24 324 54 HOH HOH . C 3 HOH A 25 325 2 HOH HOH . C 3 HOH A 26 326 56 HOH HOH . C 3 HOH A 27 327 7 HOH HOH . C 3 HOH A 28 328 31 HOH HOH . C 3 HOH A 29 329 33 HOH HOH . C 3 HOH A 30 330 37 HOH HOH . C 3 HOH A 31 331 66 HOH HOH . C 3 HOH A 32 332 20 HOH HOH . C 3 HOH A 33 333 53 HOH HOH . C 3 HOH A 34 334 81 HOH HOH . C 3 HOH A 35 335 45 HOH HOH . C 3 HOH A 36 336 39 HOH HOH . C 3 HOH A 37 337 83 HOH HOH . C 3 HOH A 38 338 44 HOH HOH . C 3 HOH A 39 339 107 HOH HOH . C 3 HOH A 40 340 73 HOH HOH . C 3 HOH A 41 341 48 HOH HOH . C 3 HOH A 42 342 22 HOH HOH . C 3 HOH A 43 343 93 HOH HOH . C 3 HOH A 44 344 99 HOH HOH . C 3 HOH A 45 345 68 HOH HOH . C 3 HOH A 46 346 55 HOH HOH . C 3 HOH A 47 347 47 HOH HOH . C 3 HOH A 48 348 34 HOH HOH . C 3 HOH A 49 349 35 HOH HOH . C 3 HOH A 50 350 94 HOH HOH . C 3 HOH A 51 351 16 HOH HOH . C 3 HOH A 52 352 62 HOH HOH . C 3 HOH A 53 353 51 HOH HOH . C 3 HOH A 54 354 4 HOH HOH . C 3 HOH A 55 355 59 HOH HOH . C 3 HOH A 56 356 49 HOH HOH . C 3 HOH A 57 357 6 HOH HOH . C 3 HOH A 58 358 9 HOH HOH . C 3 HOH A 59 359 15 HOH HOH . C 3 HOH A 60 360 50 HOH HOH . C 3 HOH A 61 361 30 HOH HOH . C 3 HOH A 62 362 5 HOH HOH . C 3 HOH A 63 363 23 HOH HOH . C 3 HOH A 64 364 70 HOH HOH . C 3 HOH A 65 365 27 HOH HOH . C 3 HOH A 66 366 41 HOH HOH . C 3 HOH A 67 367 3 HOH HOH . C 3 HOH A 68 368 65 HOH HOH . C 3 HOH A 69 369 28 HOH HOH . C 3 HOH A 70 370 19 HOH HOH . C 3 HOH A 71 371 95 HOH HOH . C 3 HOH A 72 372 8 HOH HOH . C 3 HOH A 73 373 11 HOH HOH . C 3 HOH A 74 374 13 HOH HOH . C 3 HOH A 75 375 89 HOH HOH . C 3 HOH A 76 376 103 HOH HOH . C 3 HOH A 77 377 105 HOH HOH . C 3 HOH A 78 378 97 HOH HOH . C 3 HOH A 79 379 72 HOH HOH . C 3 HOH A 80 380 58 HOH HOH . C 3 HOH A 81 381 61 HOH HOH . C 3 HOH A 82 382 102 HOH HOH . C 3 HOH A 83 383 63 HOH HOH . C 3 HOH A 84 384 108 HOH HOH . C 3 HOH A 85 385 60 HOH HOH . C 3 HOH A 86 386 24 HOH HOH . C 3 HOH A 87 387 90 HOH HOH . C 3 HOH A 88 388 17 HOH HOH . C 3 HOH A 89 389 12 HOH HOH . C 3 HOH A 90 390 86 HOH HOH . C 3 HOH A 91 391 109 HOH HOH . C 3 HOH A 92 392 85 HOH HOH . C 3 HOH A 93 393 42 HOH HOH . C 3 HOH A 94 394 106 HOH HOH . C 3 HOH A 95 395 32 HOH HOH . C 3 HOH A 96 396 96 HOH HOH . C 3 HOH A 97 397 69 HOH HOH . C 3 HOH A 98 398 64 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 2.884 -20.306 14.884 1 16.22 ? P2 THP 201 A 1 HETATM 2 O O4P THP . . . B 2 1.737 -21.117 14.222 1 17.86 ? O4P THP 201 A 1 HETATM 3 O O5P THP . . . B 2 2.794 -18.8 14.723 1 13.11 ? O5P THP 201 A 1 HETATM 4 O O6P THP . . . B 2 4.211 -20.838 14.571 1 17.5 ? O6P THP 201 A 1 HETATM 5 P P1 THP . . . B 2 5.357 -24.525 19.459 1 30.48 ? P1 THP 201 A 1 HETATM 6 O O1P THP . . . B 2 5.252 -25.049 18.048 1 30.25 ? O1P THP 201 A 1 HETATM 7 O O2P THP . . . B 2 6.752 -24.216 19.939 1 34.22 ? O2P THP 201 A 1 HETATM 8 O O3P THP . . . B 2 4.527 -25.155 20.543 1 31.2 ? O3P THP 201 A 1 HETATM 9 O O5' THP . . . B 2 2.645 -20.536 16.387 1 17.81 ? O5' THP 201 A 1 HETATM 10 C C5' THP . . . B 2 2.57 -21.866 16.858 1 19.49 ? C5' THP 201 A 1 HETATM 11 C C4' THP . . . B 2 3.39 -21.765 18.06 1 21.09 ? C4' THP 201 A 1 HETATM 12 O O4' THP . . . B 2 2.849 -20.657 18.729 1 20.18 ? O4' THP 201 A 1 HETATM 13 C C3' THP . . . B 2 3.342 -22.962 18.997 1 24.69 ? C3' THP 201 A 1 HETATM 14 O O3' THP . . . B 2 4.671 -23.112 19.468 1 28.32 ? O3' THP 201 A 1 HETATM 15 C C2' THP . . . B 2 2.52 -22.534 20.143 1 22.54 ? C2' THP 201 A 1 HETATM 16 C C1' THP . . . B 2 2.594 -21.005 20.025 1 20.45 ? C1' THP 201 A 1 HETATM 17 N N1 THP . . . B 2 1.308 -20.601 20.375 1 16.77 ? N1 THP 201 A 1 HETATM 18 C C2 THP . . . B 2 1.054 -20.666 21.782 1 18.81 ? C2 THP 201 A 1 HETATM 19 O O2 THP . . . B 2 1.971 -20.916 22.617 1 24.43 ? O2 THP 201 A 1 HETATM 20 N N3 THP . . . B 2 -0.156 -20.4 22.263 1 13.26 ? N3 THP 201 A 1 HETATM 21 C C4 THP . . . B 2 -1.089 -20.14 21.36 1 12.22 ? C4 THP 201 A 1 HETATM 22 O O4 THP . . . B 2 -2.183 -19.929 21.806 1 10.72 ? O4 THP 201 A 1 HETATM 23 C C5 THP . . . B 2 -0.864 -20.107 19.859 1 12.66 ? C5 THP 201 A 1 HETATM 24 C C5M THP . . . B 2 -2.005 -19.817 18.892 1 11.46 ? C5M THP 201 A 1 HETATM 25 C C6 THP . . . B 2 0.379 -20.385 19.425 1 14.84 ? C6 THP 201 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #