data_5BSZ # _model_server_result.job_id 3ozBnKWche4QqcRyVNUj-Q _model_server_result.datetime_utc '2024-11-05 00:29:51' _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 5bsz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":306}' # _entry.id 5BSZ # _exptl.entry_id 5BSZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _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 5BSZ _cell.length_a 63.254 _cell.length_b 81.004 _cell.length_c 126.916 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BSZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # 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 O5' C5' THM sing 331 n n O5' HO5' THM sing 332 n n C5' C4' THM sing 333 n n C5' "H5'1" THM sing 334 n n C5' "H5'2" THM sing 335 n n C4' O4' THM sing 336 n n C4' C3' THM sing 337 n n C4' H4' THM sing 338 n n O4' C1' THM sing 339 n n C3' O3' THM sing 340 n n C3' C2' THM sing 341 n n C3' H3' THM sing 342 n n O3' HO3' THM sing 343 n n C2' C1' THM sing 344 n n C2' "H2'1" THM sing 345 n n C2' "H2'2" THM sing 346 n n C1' N1 THM sing 347 n n C1' H1' THM sing 348 n n N1 C2 THM sing 349 n n N1 C6 THM sing 350 n n C2 O2 THM doub 351 n n C2 N3 THM sing 352 n n N3 C4 THM sing 353 n n N3 HN3 THM sing 354 n n C4 O4 THM doub 355 n n C4 C5 THM sing 356 n n C5 C5M THM sing 357 n n C5 C6 THM doub 358 n n C5M HM51 THM sing 359 n n C5M HM52 THM sing 360 n n C5M HM53 THM sing 361 n n C6 H6 THM sing 362 n n # _atom_sites.entry_id 5BSZ _atom_sites.fract_transf_matrix[1][1] 0.015809 _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] 0.012345 _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] 0.007879 _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 SAH A 1 301 1 SAH SAH . C 3 EDO A 1 302 1 EDO EDO . D 3 EDO A 1 303 2 EDO EDO . E 3 EDO A 1 304 3 EDO EDO . F 3 EDO A 1 305 1 EDO EDO . G 4 THM A 1 306 1 THM THM . H 5 HOH A 1 401 217 HOH HOH . H 5 HOH A 2 402 200 HOH HOH . H 5 HOH A 3 403 204 HOH HOH . H 5 HOH A 4 404 64 HOH HOH . H 5 HOH A 5 405 111 HOH HOH . H 5 HOH A 6 406 85 HOH HOH . H 5 HOH A 7 407 104 HOH HOH . H 5 HOH A 8 408 235 HOH HOH . H 5 HOH A 9 409 132 HOH HOH . H 5 HOH A 10 410 59 HOH HOH . H 5 HOH A 11 411 38 HOH HOH . H 5 HOH A 12 412 196 HOH HOH . H 5 HOH A 13 413 135 HOH HOH . H 5 HOH A 14 414 213 HOH HOH . H 5 HOH A 15 415 97 HOH HOH . H 5 HOH A 16 416 11 HOH HOH . H 5 HOH A 17 417 16 HOH HOH . H 5 HOH A 18 418 220 HOH HOH . H 5 HOH A 19 419 5 HOH HOH . H 5 HOH A 20 420 6 HOH HOH . H 5 HOH A 21 421 137 HOH HOH . H 5 HOH A 22 422 161 HOH HOH . H 5 HOH A 23 423 25 HOH HOH . H 5 HOH A 24 424 8 HOH HOH . H 5 HOH A 25 425 46 HOH HOH . H 5 HOH A 26 426 3 HOH HOH . H 5 HOH A 27 427 31 HOH HOH . H 5 HOH A 28 428 22 HOH HOH . H 5 HOH A 29 429 114 HOH HOH . H 5 HOH A 30 430 138 HOH HOH . H 5 HOH A 31 431 103 HOH HOH . H 5 HOH A 32 432 42 HOH HOH . H 5 HOH A 33 433 210 HOH HOH . H 5 HOH A 34 434 47 HOH HOH . H 5 HOH A 35 435 61 HOH HOH . H 5 HOH A 36 436 142 HOH HOH . H 5 HOH A 37 437 108 HOH HOH . H 5 HOH A 38 438 78 HOH HOH . H 5 HOH A 39 439 216 HOH HOH . H 5 HOH A 40 440 75 HOH HOH . H 5 HOH A 41 441 125 HOH HOH . H 5 HOH A 42 442 26 HOH HOH . H 5 HOH A 43 443 57 HOH HOH . H 5 HOH A 44 444 84 HOH HOH . H 5 HOH A 45 445 50 HOH HOH . H 5 HOH A 46 446 199 HOH HOH . H 5 HOH A 47 447 20 HOH HOH . H 5 HOH A 48 448 9 HOH HOH . H 5 HOH A 49 449 33 HOH HOH . H 5 HOH A 50 450 58 HOH HOH . H 5 HOH A 51 451 1 HOH HOH . H 5 HOH A 52 452 239 HOH HOH . H 5 HOH A 53 453 209 HOH HOH . H 5 HOH A 54 454 2 HOH HOH . H 5 HOH A 55 455 65 HOH HOH . H 5 HOH A 56 456 12 HOH HOH . H 5 HOH A 57 457 90 HOH HOH . H 5 HOH A 58 458 237 HOH HOH . H 5 HOH A 59 459 105 HOH HOH . H 5 HOH A 60 460 93 HOH HOH . H 5 HOH A 61 461 91 HOH HOH . H 5 HOH A 62 462 60 HOH HOH . H 5 HOH A 63 463 146 HOH HOH . H 5 HOH A 64 464 41 HOH HOH . H 5 HOH A 65 465 71 HOH HOH . H 5 HOH A 66 466 27 HOH HOH . H 5 HOH A 67 467 177 HOH HOH . H 5 HOH A 68 468 68 HOH HOH . H 5 HOH A 69 469 43 HOH HOH . H 5 HOH A 70 470 73 HOH HOH . H 5 HOH A 71 471 24 HOH HOH . H 5 HOH A 72 472 66 HOH HOH . H 5 HOH A 73 473 190 HOH HOH . H 5 HOH A 74 474 69 HOH HOH . H 5 HOH A 75 475 198 HOH HOH . H 5 HOH A 76 476 34 HOH HOH . H 5 HOH A 77 477 242 HOH HOH . H 5 HOH A 78 478 29 HOH HOH . H 5 HOH A 79 479 106 HOH HOH . H 5 HOH A 80 480 228 HOH HOH . H 5 HOH A 81 481 133 HOH HOH . H 5 HOH A 82 482 147 HOH HOH . H 5 HOH A 83 483 225 HOH HOH . H 5 HOH A 84 484 70 HOH HOH . H 5 HOH A 85 485 159 HOH HOH . H 5 HOH A 86 486 51 HOH HOH . H 5 HOH A 87 487 44 HOH HOH . H 5 HOH A 88 488 100 HOH HOH . H 5 HOH A 89 489 173 HOH HOH . H 5 HOH A 90 490 74 HOH HOH . H 5 HOH A 91 491 243 HOH HOH . H 5 HOH A 92 492 110 HOH HOH . H 5 HOH A 93 493 101 HOH HOH . H 5 HOH A 94 494 52 HOH HOH . H 5 HOH A 95 495 53 HOH HOH . H 5 HOH A 96 496 36 HOH HOH . H 5 HOH A 97 497 82 HOH HOH . H 5 HOH A 98 498 23 HOH HOH . H 5 HOH A 99 499 152 HOH HOH . H 5 HOH A 100 500 56 HOH HOH . H 5 HOH A 101 501 80 HOH HOH . H 5 HOH A 102 502 94 HOH HOH . H 5 HOH A 103 503 77 HOH HOH . H 5 HOH A 104 504 32 HOH HOH . H 5 HOH A 105 505 87 HOH HOH . H 5 HOH A 106 506 120 HOH HOH . H 5 HOH A 107 507 21 HOH HOH . H 5 HOH A 108 508 30 HOH HOH . H 5 HOH A 109 509 39 HOH HOH . H 5 HOH A 110 510 107 HOH HOH . H 5 HOH A 111 511 185 HOH HOH . H 5 HOH A 112 512 221 HOH HOH . H 5 HOH A 113 513 10 HOH HOH . H 5 HOH A 114 514 37 HOH HOH . H 5 HOH A 115 515 72 HOH HOH . H 5 HOH A 116 516 19 HOH HOH . H 5 HOH A 117 517 113 HOH HOH . H 5 HOH A 118 518 7 HOH HOH . H 5 HOH A 119 519 218 HOH HOH . H 5 HOH A 120 520 55 HOH HOH . H 5 HOH A 121 521 13 HOH HOH . H 5 HOH A 122 522 28 HOH HOH . H 5 HOH A 123 523 35 HOH HOH . H 5 HOH A 124 524 231 HOH HOH . H 5 HOH A 125 525 168 HOH HOH . H 5 HOH A 126 526 226 HOH HOH . H 5 HOH A 127 527 136 HOH HOH . H 5 HOH A 128 528 48 HOH HOH . H 5 HOH A 129 529 246 HOH HOH . H 5 HOH A 130 530 232 HOH HOH . H 5 HOH A 131 531 127 HOH HOH . H 5 HOH A 132 532 17 HOH HOH . H 5 HOH A 133 533 45 HOH HOH . H 5 HOH A 134 534 54 HOH HOH . H 5 HOH A 135 535 98 HOH HOH . H 5 HOH A 136 536 40 HOH HOH . H 5 HOH A 137 537 49 HOH HOH . H 5 HOH A 138 538 79 HOH HOH . H 5 HOH A 139 539 67 HOH HOH . H 5 HOH A 140 540 240 HOH HOH . H 5 HOH A 141 541 81 HOH HOH . H 5 HOH A 142 542 112 HOH HOH . H 5 HOH A 143 543 201 HOH HOH . H 5 HOH A 144 544 89 HOH HOH . H 5 HOH A 145 545 102 HOH HOH . H 5 HOH A 146 546 131 HOH HOH . H 5 HOH A 147 547 116 HOH HOH . H 5 HOH A 148 548 92 HOH HOH . H 5 HOH A 149 549 163 HOH HOH . H 5 HOH A 150 550 187 HOH HOH . H 5 HOH A 151 551 182 HOH HOH . H 5 HOH A 152 552 134 HOH HOH . H 5 HOH A 153 553 234 HOH HOH . H 5 HOH A 154 554 99 HOH HOH . H 5 HOH A 155 555 145 HOH HOH . H 5 HOH A 156 556 193 HOH HOH . H 5 HOH A 157 557 233 HOH HOH . H 5 HOH A 158 558 158 HOH HOH . H 5 HOH A 159 559 186 HOH HOH . H 5 HOH A 160 560 95 HOH HOH . H 5 HOH A 161 561 219 HOH HOH . H 5 HOH A 162 562 144 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 O5' THM . . . G 4 -19.353 -0.085 -17.288 1 59.63 ? O5' THM 306 A 1 HETATM 2 C C5' THM . . . G 4 -18.82 1.203 -16.917 1 54.59 ? C5' THM 306 A 1 HETATM 3 C C4' THM . . . G 4 -17.904 1.766 -18.009 1 39.91 ? C4' THM 306 A 1 HETATM 4 O O4' THM . . . G 4 -18.822 1.994 -19.081 1 47.64 ? O4' THM 306 A 1 HETATM 5 C C3' THM . . . G 4 -17.218 3.133 -17.73 1 37.92 ? C3' THM 306 A 1 HETATM 6 O O3' THM . . . G 4 -15.782 3.059 -17.86 1 27.46 ? O3' THM 306 A 1 HETATM 7 C C2' THM . . . G 4 -17.793 4.168 -18.718 1 44.49 ? C2' THM 306 A 1 HETATM 8 C C1' THM . . . G 4 -18.523 3.244 -19.708 1 39.06 ? C1' THM 306 A 1 HETATM 9 N N1 THM . . . G 4 -19.723 3.686 -20.438 1 38.77 ? N1 THM 306 A 1 HETATM 10 C C2 THM . . . G 4 -19.352 4.461 -21.553 1 27.99 ? C2 THM 306 A 1 HETATM 11 O O2 THM . . . G 4 -18.138 4.685 -21.671 1 25.39 ? O2 THM 306 A 1 HETATM 12 N N3 THM . . . G 4 -20.228 4.96 -22.421 1 33.09 ? N3 THM 306 A 1 HETATM 13 C C4 THM . . . G 4 -21.529 4.698 -22.298 1 32.94 ? C4 THM 306 A 1 HETATM 14 O O4 THM . . . G 4 -22.363 5.16 -23.145 1 41.89 ? O4 THM 306 A 1 HETATM 15 C C5 THM . . . G 4 -21.941 3.866 -21.149 1 32.72 ? C5 THM 306 A 1 HETATM 16 C C5M THM . . . G 4 -23.426 3.628 -21.064 1 46.53 ? C5M THM 306 A 1 HETATM 17 C C6 THM . . . G 4 -21.01 3.355 -20.251 1 31.76 ? C6 THM 306 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 17 #