data_4O7S # _model_server_result.job_id s8TLhIuOpF8-yn45_aVmCw _model_server_result.datetime_utc '2024-12-12 16:36:57' _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 4o7s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 4O7S # _exptl.entry_id 4O7S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-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 4O7S _cell.length_a 43.89 _cell.length_b 154.43 _cell.length_c 78.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O7S _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 43.89 0 39.05 # _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 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 316 n n P O2P TMP sing 317 n n P O3P TMP sing 318 n n P O5' TMP sing 319 n n O2P HOP2 TMP sing 320 n n O3P HOP3 TMP sing 321 n n O5' C5' TMP sing 322 n n C5' C4' TMP sing 323 n n C5' "H5'1" TMP sing 324 n n C5' "H5'2" TMP sing 325 n n C4' O4' TMP sing 326 n n C4' C3' TMP sing 327 n n C4' H4' TMP sing 328 n n O4' C1' TMP sing 329 n n C3' O3' TMP sing 330 n n C3' C2' TMP sing 331 n n C3' H3' TMP sing 332 n n O3' HO3' TMP sing 333 n n C2' C1' TMP sing 334 n n C2' "H2'1" TMP sing 335 n n C2' "H2'2" TMP sing 336 n n C1' N1 TMP sing 337 n n C1' H1' TMP sing 338 n n N1 C2 TMP sing 339 n n N1 C6 TMP sing 340 n n C2 O2 TMP doub 341 n n C2 N3 TMP sing 342 n n N3 C4 TMP sing 343 n n N3 HN3 TMP sing 344 n n C4 O4 TMP doub 345 n n C4 C5 TMP sing 346 n n C5 C5M TMP sing 347 n n C5 C6 TMP doub 348 n n C5M H51 TMP sing 349 n n C5M H52 TMP sing 350 n n C5M H53 TMP sing 351 n n C6 H6 TMP sing 352 n n # _atom_sites.entry_id 4O7S _atom_sites.fract_transf_matrix[1][1] 0.022784 _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] 0.006475 _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] 0.012804 _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 TYD A 1 301 420 TYD TYD . C 3 TMP A 1 302 430 TMP TMP . D 4 PO4 A 1 303 501 PO4 PO4 . E 5 ACT A 1 304 502 ACT ACT . F 6 HOH A 1 401 301 HOH HOH . F 6 HOH A 2 402 302 HOH HOH . F 6 HOH A 3 403 303 HOH HOH . F 6 HOH A 4 404 304 HOH HOH . F 6 HOH A 5 405 305 HOH HOH . F 6 HOH A 6 406 306 HOH HOH . F 6 HOH A 7 407 307 HOH HOH . F 6 HOH A 8 408 308 HOH HOH . F 6 HOH A 9 409 309 HOH HOH . F 6 HOH A 10 410 310 HOH HOH . F 6 HOH A 11 411 311 HOH HOH . F 6 HOH A 12 412 312 HOH HOH . F 6 HOH A 13 413 313 HOH HOH . F 6 HOH A 14 414 314 HOH HOH . F 6 HOH A 15 415 315 HOH HOH . F 6 HOH A 16 416 316 HOH HOH . F 6 HOH A 17 417 317 HOH HOH . F 6 HOH A 18 418 318 HOH HOH . F 6 HOH A 19 419 319 HOH HOH . F 6 HOH A 20 420 320 HOH HOH . F 6 HOH A 21 421 321 HOH HOH . F 6 HOH A 22 422 322 HOH HOH . F 6 HOH A 23 423 323 HOH HOH . F 6 HOH A 24 424 324 HOH HOH . F 6 HOH A 25 425 325 HOH HOH . F 6 HOH A 26 426 326 HOH HOH . F 6 HOH A 27 427 327 HOH HOH . F 6 HOH A 28 428 328 HOH HOH . F 6 HOH A 29 429 329 HOH HOH . F 6 HOH A 30 430 330 HOH HOH . F 6 HOH A 31 431 331 HOH HOH . F 6 HOH A 32 432 332 HOH HOH . F 6 HOH A 33 433 333 HOH HOH . F 6 HOH A 34 434 334 HOH HOH . F 6 HOH A 35 435 335 HOH HOH . F 6 HOH A 36 436 336 HOH HOH . F 6 HOH A 37 437 337 HOH HOH . F 6 HOH A 38 438 338 HOH HOH . F 6 HOH A 39 439 339 HOH HOH . F 6 HOH A 40 440 340 HOH HOH . F 6 HOH A 41 441 341 HOH HOH . F 6 HOH A 42 442 342 HOH HOH . F 6 HOH A 43 443 343 HOH HOH . F 6 HOH A 44 444 344 HOH HOH . F 6 HOH A 45 445 345 HOH HOH . F 6 HOH A 46 446 346 HOH HOH . F 6 HOH A 47 447 347 HOH HOH . F 6 HOH A 48 448 348 HOH HOH . F 6 HOH A 49 449 349 HOH HOH . F 6 HOH A 50 450 350 HOH HOH . F 6 HOH A 51 451 351 HOH HOH . F 6 HOH A 52 452 352 HOH HOH . F 6 HOH A 53 453 353 HOH HOH . F 6 HOH A 54 454 354 HOH HOH . F 6 HOH A 55 455 355 HOH HOH . F 6 HOH A 56 456 356 HOH HOH . F 6 HOH A 57 457 357 HOH HOH . F 6 HOH A 58 458 358 HOH HOH . F 6 HOH A 59 459 359 HOH HOH . F 6 HOH A 60 460 360 HOH HOH . F 6 HOH A 61 461 361 HOH HOH . F 6 HOH A 62 462 362 HOH HOH . F 6 HOH A 63 463 363 HOH HOH . F 6 HOH A 64 464 364 HOH HOH . F 6 HOH A 65 465 365 HOH HOH . F 6 HOH A 66 466 366 HOH HOH . F 6 HOH A 67 467 367 HOH HOH . F 6 HOH A 68 468 368 HOH HOH . F 6 HOH A 69 469 369 HOH HOH . F 6 HOH A 70 470 370 HOH HOH . F 6 HOH A 71 471 371 HOH HOH . F 6 HOH A 72 472 372 HOH HOH . F 6 HOH A 73 473 373 HOH HOH . F 6 HOH A 74 474 374 HOH HOH . F 6 HOH A 75 475 375 HOH HOH . F 6 HOH A 76 476 376 HOH HOH . F 6 HOH A 77 477 377 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 P TMP . B . C 3 14.233 15.21 10.65 0.4 20.18 ? P TMP 302 A 1 HETATM 2 O O1P TMP . B . C 3 15.342 15.758 11.519 0.4 19.79 ? O1P TMP 302 A 1 HETATM 3 O O2P TMP . B . C 3 12.86 15.37 11.263 0.4 19.57 ? O2P TMP 302 A 1 HETATM 4 O O3P TMP . B . C 3 14.514 13.863 10.035 0.4 19.86 ? O3P TMP 302 A 1 HETATM 5 O O5' TMP . B . C 3 14.19 16.195 9.383 0.4 20.93 ? O5' TMP 302 A 1 HETATM 6 C C5' TMP . B . C 3 13.321 17.324 9.396 0.4 22.23 ? C5' TMP 302 A 1 HETATM 7 C C4' TMP . B . C 3 13.093 17.804 7.968 0.4 23.6 ? C4' TMP 302 A 1 HETATM 8 O O4' TMP . B . C 3 14.343 18.169 7.39 0.4 24.37 ? O4' TMP 302 A 1 HETATM 9 C C3' TMP . B . C 3 12.498 16.723 7.076 0.4 23.74 ? C3' TMP 302 A 1 HETATM 10 O O3' TMP . B . C 3 11.602 17.36 6.17 0.4 23.23 ? O3' TMP 302 A 1 HETATM 11 C C2' TMP . B . C 3 13.655 16.182 6.271 0.4 24.68 ? C2' TMP 302 A 1 HETATM 12 C C1' TMP . B . C 3 14.623 17.351 6.249 0.4 25.69 ? C1' TMP 302 A 1 HETATM 13 N N1 TMP . B . C 3 16.014 16.908 6.309 0.4 27.39 ? N1 TMP 302 A 1 HETATM 14 C C2 TMP . B . C 3 16.611 16.346 5.156 0.4 27.57 ? C2 TMP 302 A 1 HETATM 15 O O2 TMP . B . C 3 15.93 16.23 4.117 0.4 26.67 ? O2 TMP 302 A 1 HETATM 16 N N3 TMP . B . C 3 17.888 15.939 5.172 0.4 28.23 ? N3 TMP 302 A 1 HETATM 17 C C4 TMP . B . C 3 18.626 16.073 6.286 0.4 29.14 ? C4 TMP 302 A 1 HETATM 18 O O4 TMP . B . C 3 19.814 15.698 6.299 0.4 30.18 ? O4 TMP 302 A 1 HETATM 19 C C5 TMP . B . C 3 18.028 16.674 7.507 0.4 28.74 ? C5 TMP 302 A 1 HETATM 20 C C5M TMP . B . C 3 18.825 16.848 8.776 0.4 27.88 ? C5M TMP 302 A 1 HETATM 21 C C6 TMP . B . C 3 16.703 17.077 7.446 0.4 28.12 ? C6 TMP 302 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #