data_3IK1 # _model_server_result.job_id eM30NhoIhQpibNXPDsQAgw _model_server_result.datetime_utc '2024-10-10 21:23:37' _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 3ik1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":491}' # _entry.id 3IK1 # _exptl.entry_id 3IK1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 120 _cell.entry_id 3IK1 _cell.length_a 77.985 _cell.length_b 77.985 _cell.length_c 224.718 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IK1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -38.9925 67.536991 37.453 # _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 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 393 n n N1 C6 UMP sing 394 n n N1 C1' UMP sing 395 n n C2 N3 UMP sing 396 n n C2 O2 UMP doub 397 n n N3 C4 UMP sing 398 n n N3 HN3 UMP sing 399 n n C4 C5 UMP sing 400 n n C4 O4 UMP doub 401 n n C5 C6 UMP doub 402 n n C5 H5 UMP sing 403 n n C6 H6 UMP sing 404 n n C1' C2' UMP sing 405 n n C1' O4' UMP sing 406 n n C1' H1' UMP sing 407 n n C2' C3' UMP sing 408 n n C2' H2' UMP sing 409 n n C2' "H2''" UMP sing 410 n n C3' C4' UMP sing 411 n n C3' O3' UMP sing 412 n n C3' H3' UMP sing 413 n n C4' O4' UMP sing 414 n n C4' C5' UMP sing 415 n n C4' H4' UMP sing 416 n n O3' HO3' UMP sing 417 n n C5' O5' UMP sing 418 n n C5' H5' UMP sing 419 n n C5' "H5''" UMP sing 420 n n O5' P UMP sing 421 n n P OP1 UMP doub 422 n n P OP2 UMP sing 423 n n P OP3 UMP sing 424 n n OP2 HOP2 UMP sing 425 n n OP3 HOP3 UMP sing 426 n n # _atom_sites.entry_id 3IK1 _atom_sites.fract_transf_matrix[1][1] 0.012823 _atom_sites.fract_transf_matrix[1][2] 0.007403 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014807 _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] 0.00445 _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 20C A 1 490 490 20C 20A . C 3 UMP A 1 491 491 UMP UMP . D 4 HOH A 1 321 321 HOH HOH . D 4 HOH A 2 322 322 HOH HOH . D 4 HOH A 3 323 323 HOH HOH . D 4 HOH A 4 324 324 HOH HOH . D 4 HOH A 5 325 325 HOH HOH . D 4 HOH A 6 326 326 HOH HOH . D 4 HOH A 7 327 327 HOH HOH . D 4 HOH A 8 328 328 HOH HOH . D 4 HOH A 9 329 329 HOH HOH . D 4 HOH A 10 340 340 HOH HOH . D 4 HOH A 11 341 341 HOH HOH . D 4 HOH A 12 342 342 HOH HOH . D 4 HOH A 13 343 343 HOH HOH . D 4 HOH A 14 344 344 HOH HOH . D 4 HOH A 15 345 345 HOH HOH . D 4 HOH A 16 346 346 HOH HOH . D 4 HOH A 17 347 347 HOH HOH . D 4 HOH A 18 348 348 HOH HOH . D 4 HOH A 19 349 349 HOH HOH . D 4 HOH A 20 350 350 HOH HOH . D 4 HOH A 21 351 351 HOH HOH . D 4 HOH A 22 352 352 HOH HOH . D 4 HOH A 23 353 353 HOH HOH . D 4 HOH A 24 354 354 HOH HOH . D 4 HOH A 25 355 355 HOH HOH . D 4 HOH A 26 356 356 HOH HOH . D 4 HOH A 27 357 357 HOH HOH . D 4 HOH A 28 358 358 HOH HOH . D 4 HOH A 29 359 359 HOH HOH . D 4 HOH A 30 360 360 HOH HOH . D 4 HOH A 31 361 361 HOH HOH . D 4 HOH A 32 362 362 HOH HOH . D 4 HOH A 33 363 363 HOH HOH . D 4 HOH A 34 364 364 HOH HOH . D 4 HOH A 35 365 365 HOH HOH . D 4 HOH A 36 366 366 HOH HOH . D 4 HOH A 37 367 367 HOH HOH . D 4 HOH A 38 368 368 HOH HOH . D 4 HOH A 39 369 369 HOH HOH . D 4 HOH A 40 370 370 HOH HOH . D 4 HOH A 41 371 371 HOH HOH . D 4 HOH A 42 372 372 HOH HOH . D 4 HOH A 43 373 373 HOH HOH . D 4 HOH A 44 374 374 HOH HOH . D 4 HOH A 45 375 375 HOH HOH . D 4 HOH A 46 376 376 HOH HOH . D 4 HOH A 47 377 377 HOH HOH . D 4 HOH A 48 378 378 HOH HOH . D 4 HOH A 49 379 379 HOH HOH . D 4 HOH A 50 380 380 HOH HOH . D 4 HOH A 51 381 381 HOH HOH . D 4 HOH A 52 382 382 HOH HOH . D 4 HOH A 53 383 383 HOH HOH . D 4 HOH A 54 384 384 HOH HOH . D 4 HOH A 55 385 385 HOH HOH . D 4 HOH A 56 386 386 HOH HOH . D 4 HOH A 57 387 387 HOH HOH . D 4 HOH A 58 388 388 HOH HOH . D 4 HOH A 59 389 389 HOH HOH . D 4 HOH A 60 390 390 HOH HOH . D 4 HOH A 61 391 391 HOH HOH . D 4 HOH A 62 392 392 HOH HOH . D 4 HOH A 63 393 393 HOH HOH . D 4 HOH A 64 394 394 HOH HOH . D 4 HOH A 65 395 395 HOH HOH . D 4 HOH A 66 396 396 HOH HOH . D 4 HOH A 67 397 397 HOH HOH . D 4 HOH A 68 398 398 HOH HOH . D 4 HOH A 69 399 399 HOH HOH . D 4 HOH A 70 400 400 HOH HOH . D 4 HOH A 71 401 401 HOH HOH . D 4 HOH A 72 402 402 HOH HOH . D 4 HOH A 73 403 403 HOH HOH . D 4 HOH A 74 404 404 HOH HOH . D 4 HOH A 75 405 405 HOH HOH . D 4 HOH A 76 406 406 HOH HOH . D 4 HOH A 77 407 407 HOH HOH . D 4 HOH A 78 408 408 HOH HOH . D 4 HOH A 79 409 409 HOH HOH . D 4 HOH A 80 410 410 HOH HOH . D 4 HOH A 81 411 411 HOH HOH . D 4 HOH A 82 412 412 HOH HOH . D 4 HOH A 83 413 413 HOH HOH . D 4 HOH A 84 414 414 HOH HOH . D 4 HOH A 85 415 415 HOH HOH . D 4 HOH A 86 416 416 HOH HOH . D 4 HOH A 87 417 417 HOH HOH . D 4 HOH A 88 418 418 HOH HOH . D 4 HOH A 89 419 419 HOH HOH . D 4 HOH A 90 420 420 HOH HOH . D 4 HOH A 91 421 421 HOH HOH . D 4 HOH A 92 422 422 HOH HOH . D 4 HOH A 93 423 423 HOH HOH . D 4 HOH A 94 424 424 HOH HOH . D 4 HOH A 95 425 425 HOH HOH . D 4 HOH A 96 426 426 HOH HOH . D 4 HOH A 97 427 427 HOH HOH . D 4 HOH A 98 428 428 HOH HOH . D 4 HOH A 99 429 429 HOH HOH . D 4 HOH A 100 430 430 HOH HOH . D 4 HOH A 101 431 431 HOH HOH . D 4 HOH A 102 432 432 HOH HOH . D 4 HOH A 103 433 433 HOH HOH . D 4 HOH A 104 434 434 HOH HOH . D 4 HOH A 105 435 435 HOH HOH . D 4 HOH A 106 436 436 HOH HOH . D 4 HOH A 107 437 437 HOH HOH . D 4 HOH A 108 438 438 HOH HOH . D 4 HOH A 109 439 439 HOH HOH . D 4 HOH A 110 440 440 HOH HOH . D 4 HOH A 111 441 441 HOH HOH . D 4 HOH A 112 442 442 HOH HOH . D 4 HOH A 113 443 443 HOH HOH . D 4 HOH A 114 444 444 HOH HOH . D 4 HOH A 115 445 445 HOH HOH . D 4 HOH A 116 446 446 HOH HOH . D 4 HOH A 117 447 447 HOH HOH . D 4 HOH A 118 448 448 HOH HOH . D 4 HOH A 119 449 449 HOH HOH . D 4 HOH A 120 450 450 HOH HOH . D 4 HOH A 121 451 451 HOH HOH . D 4 HOH A 122 452 452 HOH HOH . D 4 HOH A 123 453 453 HOH HOH . D 4 HOH A 124 454 454 HOH HOH . D 4 HOH A 125 455 455 HOH HOH . D 4 HOH A 126 456 456 HOH HOH . D 4 HOH A 127 457 457 HOH HOH . D 4 HOH A 128 458 458 HOH HOH . D 4 HOH A 129 459 459 HOH HOH . D 4 HOH A 130 460 460 HOH HOH . D 4 HOH A 131 461 461 HOH HOH . D 4 HOH A 132 462 462 HOH HOH . D 4 HOH A 133 463 463 HOH HOH . D 4 HOH A 134 464 464 HOH HOH . D 4 HOH A 135 465 465 HOH HOH . D 4 HOH A 136 466 466 HOH HOH . D 4 HOH A 137 467 467 HOH HOH . D 4 HOH A 138 468 468 HOH HOH . D 4 HOH A 139 469 469 HOH HOH . D 4 HOH A 140 470 470 HOH HOH . D 4 HOH A 141 471 471 HOH HOH . D 4 HOH A 142 472 472 HOH HOH . D 4 HOH A 143 473 473 HOH HOH . D 4 HOH A 144 474 474 HOH HOH . D 4 HOH A 145 475 475 HOH HOH . D 4 HOH A 146 476 476 HOH HOH . D 4 HOH A 147 477 477 HOH HOH . D 4 HOH A 148 478 478 HOH HOH . D 4 HOH A 149 479 479 HOH HOH . D 4 HOH A 150 480 480 HOH HOH . D 4 HOH A 151 481 481 HOH HOH . D 4 HOH A 152 482 482 HOH HOH . D 4 HOH A 153 483 483 HOH HOH . D 4 HOH A 154 484 484 HOH HOH . D 4 HOH A 155 485 485 HOH HOH . D 4 HOH A 156 486 486 HOH HOH . D 4 HOH A 157 487 487 HOH HOH . D 4 HOH A 158 488 488 HOH HOH . D 4 HOH A 159 489 489 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 N N1 UMP . . . C 3 -31.399 9.893 23.902 1 71.9 ? N1 UMP 491 A 1 HETATM 2 C C2 UMP . . . C 3 -32.605 9.742 24.645 1 71.16 ? C2 UMP 491 A 1 HETATM 3 N N3 UMP . . . C 3 -32.872 10.558 25.709 1 71.63 ? N3 UMP 491 A 1 HETATM 4 C C4 UMP . . . C 3 -31.943 11.509 26.059 1 73.33 ? C4 UMP 491 A 1 HETATM 5 C C5 UMP . . . C 3 -30.756 11.669 25.378 1 73.2 ? C5 UMP 491 A 1 HETATM 6 C C6 UMP . . . C 3 -30.498 10.841 24.306 1 73.25 ? C6 UMP 491 A 1 HETATM 7 O O2 UMP . . . C 3 -33.499 8.936 24.432 1 69.94 ? O2 UMP 491 A 1 HETATM 8 O O4 UMP . . . C 3 -32.151 12.237 27.006 1 76.82 ? O4 UMP 491 A 1 HETATM 9 C C1' UMP . . . C 3 -30.923 9.071 22.736 1 70.11 ? C1' UMP 491 A 1 HETATM 10 C C2' UMP . . . C 3 -31.605 9.234 21.391 1 68.76 ? C2' UMP 491 A 1 HETATM 11 C C3' UMP . . . C 3 -30.6 8.515 20.487 1 67.39 ? C3' UMP 491 A 1 HETATM 12 C C4' UMP . . . C 3 -29.241 8.787 21.091 1 65.77 ? C4' UMP 491 A 1 HETATM 13 O O3' UMP . . . C 3 -30.755 7.109 20.565 1 68.18 ? O3' UMP 491 A 1 HETATM 14 O O4' UMP . . . C 3 -29.544 9.286 22.396 1 68.62 ? O4' UMP 491 A 1 HETATM 15 C C5' UMP . . . C 3 -28.378 9.754 20.256 1 60.38 ? C5' UMP 491 A 1 HETATM 16 O O5' UMP . . . C 3 -28.061 9.364 18.906 1 52.83 ? O5' UMP 491 A 1 HETATM 17 P P UMP . . . C 3 -28.318 10.463 17.773 1 35.78 ? P UMP 491 A 1 HETATM 18 O OP1 UMP . . . C 3 -27.556 10.282 16.543 1 39.08 ? OP1 UMP 491 A 1 HETATM 19 O OP2 UMP . . . C 3 -27.884 11.707 18.456 1 41.81 ? OP2 UMP 491 A 1 HETATM 20 O OP3 UMP . . . C 3 -29.76 10.445 17.583 1 41.35 ? OP3 UMP 491 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #