data_1VZE # _model_server_result.job_id g567xzKRZN-RyPWV71n34g _model_server_result.datetime_utc '2024-11-23 19:31:21' _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 1vze # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1VZE # _exptl.entry_id 1VZE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _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 1VZE _cell.length_a 78.9 _cell.length_b 78.9 _cell.length_c 230.7 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VZE _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -115.35 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 198 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 198 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C6 _struct_conn.ptnr2_label_comp_id UMP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id UMP _struct_conn.ptnr2_auth_seq_id 317 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.819 _struct_conn.pdbx_value_order ? # _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 418 n n N1 C6 UMP sing 419 n n N1 C1' UMP sing 420 n n C2 N3 UMP sing 421 n n C2 O2 UMP doub 422 n n N3 C4 UMP sing 423 n n N3 HN3 UMP sing 424 n n C4 C5 UMP sing 425 n n C4 O4 UMP doub 426 n n C5 C6 UMP doub 427 n n C5 H5 UMP sing 428 n n C6 H6 UMP sing 429 n n C1' C2' UMP sing 430 n n C1' O4' UMP sing 431 n n C1' H1' UMP sing 432 n n C2' C3' UMP sing 433 n n C2' H2' UMP sing 434 n n C2' "H2''" UMP sing 435 n n C3' C4' UMP sing 436 n n C3' O3' UMP sing 437 n n C3' H3' UMP sing 438 n n C4' O4' UMP sing 439 n n C4' C5' UMP sing 440 n n C4' H4' UMP sing 441 n n O3' HO3' UMP sing 442 n n C5' O5' UMP sing 443 n n C5' H5' UMP sing 444 n n C5' "H5''" UMP sing 445 n n O5' P UMP sing 446 n n P OP1 UMP doub 447 n n P OP2 UMP sing 448 n n P OP3 UMP sing 449 n n OP2 HOP2 UMP sing 450 n n OP3 HOP3 UMP sing 451 n n # _atom_sites.entry_id 1VZE _atom_sites.fract_transf_matrix[1][1] 0.012674 _atom_sites.fract_transf_matrix[1][2] 0.007317 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014635 _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] 0.004335 _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 UMP A 1 317 317 UMP UMP . C 3 CB3 A 1 318 318 CB3 CB3 . D 4 HOH A 1 319 319 HOH HOH . D 4 HOH A 2 320 320 HOH HOH . D 4 HOH A 3 321 321 HOH HOH . D 4 HOH A 4 322 322 HOH HOH . D 4 HOH A 5 323 323 HOH HOH . D 4 HOH A 6 324 324 HOH HOH . D 4 HOH A 7 325 325 HOH HOH . D 4 HOH A 8 326 326 HOH HOH . D 4 HOH A 9 327 327 HOH HOH . D 4 HOH A 10 328 328 HOH HOH . D 4 HOH A 11 329 329 HOH HOH . D 4 HOH A 12 330 330 HOH HOH . D 4 HOH A 13 331 331 HOH HOH . D 4 HOH A 14 332 332 HOH HOH . D 4 HOH A 15 333 333 HOH HOH . D 4 HOH A 16 334 334 HOH HOH . D 4 HOH A 17 335 335 HOH HOH . D 4 HOH A 18 336 336 HOH HOH . D 4 HOH A 19 337 337 HOH HOH . D 4 HOH A 20 338 338 HOH HOH . D 4 HOH A 21 339 339 HOH HOH . D 4 HOH A 22 340 340 HOH HOH . D 4 HOH A 23 341 341 HOH HOH . D 4 HOH A 24 342 342 HOH HOH . D 4 HOH A 25 343 343 HOH HOH . D 4 HOH A 26 344 344 HOH HOH . D 4 HOH A 27 345 345 HOH HOH . D 4 HOH A 28 346 346 HOH HOH . D 4 HOH A 29 347 347 HOH HOH . D 4 HOH A 30 348 348 HOH HOH . D 4 HOH A 31 349 349 HOH HOH . D 4 HOH A 32 350 350 HOH HOH . D 4 HOH A 33 351 351 HOH HOH . D 4 HOH A 34 352 352 HOH HOH . D 4 HOH A 35 353 353 HOH HOH . D 4 HOH A 36 354 354 HOH HOH . D 4 HOH A 37 355 355 HOH HOH . D 4 HOH A 38 356 356 HOH HOH . D 4 HOH A 39 357 357 HOH HOH . D 4 HOH A 40 358 358 HOH HOH . D 4 HOH A 41 359 359 HOH HOH . D 4 HOH A 42 360 360 HOH HOH . D 4 HOH A 43 361 361 HOH HOH . D 4 HOH A 44 362 362 HOH HOH . D 4 HOH A 45 363 363 HOH HOH . D 4 HOH A 46 364 364 HOH HOH . D 4 HOH A 47 365 365 HOH HOH . D 4 HOH A 48 366 366 HOH HOH . D 4 HOH A 49 367 367 HOH HOH . D 4 HOH A 50 368 368 HOH HOH . D 4 HOH A 51 369 369 HOH HOH . D 4 HOH A 52 370 370 HOH HOH . D 4 HOH A 53 371 371 HOH HOH . D 4 HOH A 54 372 372 HOH HOH . D 4 HOH A 55 373 373 HOH HOH . D 4 HOH A 56 374 374 HOH HOH . D 4 HOH A 57 375 375 HOH HOH . D 4 HOH A 58 376 376 HOH HOH . D 4 HOH A 59 377 377 HOH HOH . D 4 HOH A 60 378 378 HOH HOH . D 4 HOH A 61 379 379 HOH HOH . D 4 HOH A 62 380 380 HOH HOH . D 4 HOH A 63 381 381 HOH HOH . D 4 HOH A 64 382 382 HOH HOH . D 4 HOH A 65 383 383 HOH HOH . D 4 HOH A 66 384 384 HOH HOH . D 4 HOH A 67 385 385 HOH HOH . D 4 HOH A 68 386 386 HOH HOH . D 4 HOH A 69 387 387 HOH HOH . D 4 HOH A 70 388 388 HOH HOH . D 4 HOH A 71 389 389 HOH HOH . D 4 HOH A 72 390 390 HOH HOH . D 4 HOH A 73 391 391 HOH HOH . D 4 HOH A 74 392 392 HOH HOH . D 4 HOH A 75 393 393 HOH HOH . D 4 HOH A 76 394 394 HOH HOH . D 4 HOH A 77 395 395 HOH HOH . D 4 HOH A 78 396 396 HOH HOH . D 4 HOH A 79 397 397 HOH HOH . D 4 HOH A 80 398 398 HOH HOH . D 4 HOH A 81 399 399 HOH HOH . D 4 HOH A 82 400 400 HOH HOH . D 4 HOH A 83 401 401 HOH HOH . D 4 HOH A 84 402 402 HOH HOH . D 4 HOH A 85 403 403 HOH HOH . D 4 HOH A 86 404 404 HOH HOH . D 4 HOH A 87 405 405 HOH HOH . D 4 HOH A 88 406 406 HOH HOH . D 4 HOH A 89 407 407 HOH HOH . D 4 HOH A 90 408 408 HOH HOH . D 4 HOH A 91 409 409 HOH HOH . D 4 HOH A 92 410 410 HOH HOH . D 4 HOH A 93 411 411 HOH HOH . D 4 HOH A 94 412 412 HOH HOH . D 4 HOH A 95 413 413 HOH HOH . D 4 HOH A 96 414 414 HOH HOH . D 4 HOH A 97 415 415 HOH HOH . D 4 HOH A 98 416 416 HOH HOH . D 4 HOH A 99 417 417 HOH HOH . D 4 HOH A 100 418 418 HOH HOH . D 4 HOH A 101 419 419 HOH HOH . D 4 HOH A 102 420 420 HOH HOH . D 4 HOH A 103 421 421 HOH HOH . D 4 HOH A 104 422 422 HOH HOH . D 4 HOH A 105 423 423 HOH HOH . D 4 HOH A 106 424 424 HOH HOH . D 4 HOH A 107 425 425 HOH HOH . D 4 HOH A 108 426 426 HOH HOH . D 4 HOH A 109 427 427 HOH HOH . D 4 HOH A 110 428 428 HOH HOH . D 4 HOH A 111 429 429 HOH HOH . D 4 HOH A 112 430 430 HOH HOH . D 4 HOH A 113 431 431 HOH HOH . D 4 HOH A 114 432 432 HOH HOH . D 4 HOH A 115 433 433 HOH HOH . D 4 HOH A 116 434 434 HOH HOH . D 4 HOH A 117 435 435 HOH HOH . D 4 HOH A 118 436 436 HOH HOH . D 4 HOH A 119 437 437 HOH HOH . D 4 HOH A 120 438 438 HOH HOH . D 4 HOH A 121 439 439 HOH HOH . D 4 HOH A 122 440 440 HOH HOH . D 4 HOH A 123 441 441 HOH HOH . D 4 HOH A 124 442 442 HOH HOH . D 4 HOH A 125 443 443 HOH HOH . D 4 HOH A 126 444 444 HOH HOH . D 4 HOH A 127 445 445 HOH HOH . D 4 HOH A 128 446 446 HOH HOH . D 4 HOH A 129 447 447 HOH HOH . D 4 HOH A 130 448 448 HOH HOH . D 4 HOH A 131 449 449 HOH HOH . D 4 HOH A 132 450 450 HOH HOH . D 4 HOH A 133 451 451 HOH HOH . D 4 HOH A 134 452 452 HOH HOH . D 4 HOH A 135 453 453 HOH HOH . D 4 HOH A 136 454 454 HOH HOH . D 4 HOH A 137 455 455 HOH HOH . D 4 HOH A 138 456 456 HOH HOH . D 4 HOH A 139 457 457 HOH HOH . D 4 HOH A 140 458 458 HOH HOH . D 4 HOH A 141 459 459 HOH HOH . D 4 HOH A 142 460 460 HOH HOH . D 4 HOH A 143 461 461 HOH HOH . D 4 HOH A 144 462 462 HOH HOH . D 4 HOH A 145 463 463 HOH HOH . D 4 HOH A 146 464 464 HOH HOH . D 4 HOH A 147 465 465 HOH HOH . D 4 HOH A 148 466 466 HOH HOH . D 4 HOH A 149 467 467 HOH HOH . D 4 HOH A 150 468 468 HOH HOH . D 4 HOH A 151 469 469 HOH HOH . D 4 HOH A 152 470 470 HOH HOH . D 4 HOH A 153 471 471 HOH HOH . D 4 HOH A 154 472 472 HOH HOH . D 4 HOH A 155 473 473 HOH HOH . D 4 HOH A 156 474 474 HOH HOH . D 4 HOH A 157 475 475 HOH HOH . D 4 HOH A 158 476 476 HOH HOH . D 4 HOH A 159 477 477 HOH HOH . D 4 HOH A 160 478 478 HOH HOH . D 4 HOH A 161 479 479 HOH HOH . D 4 HOH A 162 480 480 HOH HOH . D 4 HOH A 163 481 481 HOH HOH . D 4 HOH A 164 482 482 HOH HOH . D 4 HOH A 165 483 483 HOH HOH . D 4 HOH A 166 484 484 HOH HOH . D 4 HOH A 167 485 485 HOH HOH . D 4 HOH A 168 486 486 HOH HOH . D 4 HOH A 169 487 487 HOH HOH . D 4 HOH A 170 488 488 HOH HOH . D 4 HOH A 171 489 489 HOH HOH . D 4 HOH A 172 490 490 HOH HOH . D 4 HOH A 173 491 491 HOH HOH . D 4 HOH A 174 492 492 HOH HOH . D 4 HOH A 175 493 493 HOH HOH . D 4 HOH A 176 494 494 HOH HOH . D 4 HOH A 177 495 495 HOH HOH . D 4 HOH A 178 496 496 HOH HOH . D 4 HOH A 179 497 497 HOH HOH . D 4 HOH A 180 498 498 HOH HOH . D 4 HOH A 181 499 499 HOH HOH . D 4 HOH A 182 500 500 HOH HOH . D 4 HOH A 183 501 501 HOH HOH . D 4 HOH A 184 502 502 HOH HOH . D 4 HOH A 185 503 503 HOH HOH . D 4 HOH A 186 504 504 HOH HOH . D 4 HOH A 187 505 505 HOH HOH . D 4 HOH A 188 506 506 HOH HOH . D 4 HOH A 189 507 507 HOH HOH . D 4 HOH A 190 508 508 HOH HOH . D 4 HOH A 191 509 509 HOH HOH . D 4 HOH A 192 510 510 HOH HOH . D 4 HOH A 193 511 511 HOH HOH . D 4 HOH A 194 512 512 HOH HOH . D 4 HOH A 195 513 513 HOH HOH . D 4 HOH A 196 514 514 HOH HOH . D 4 HOH A 197 515 515 HOH HOH . D 4 HOH A 198 516 516 HOH HOH . D 4 HOH A 199 517 517 HOH HOH . D 4 HOH A 200 518 518 HOH HOH . D 4 HOH A 201 519 519 HOH HOH . D 4 HOH A 202 520 520 HOH HOH . D 4 HOH A 203 521 521 HOH HOH . D 4 HOH A 204 522 522 HOH HOH . D 4 HOH A 205 523 523 HOH HOH . D 4 HOH A 206 524 524 HOH HOH . D 4 HOH A 207 525 525 HOH HOH . D 4 HOH A 208 526 526 HOH HOH . D 4 HOH A 209 527 527 HOH HOH . D 4 HOH A 210 528 528 HOH HOH . D 4 HOH A 211 529 529 HOH HOH . D 4 HOH A 212 530 530 HOH HOH . D 4 HOH A 213 531 531 HOH HOH . D 4 HOH A 214 532 532 HOH HOH . D 4 HOH A 215 533 533 HOH HOH . D 4 HOH A 216 534 534 HOH HOH . D 4 HOH A 217 535 535 HOH HOH . D 4 HOH A 218 536 536 HOH HOH . D 4 HOH A 219 537 537 HOH HOH . D 4 HOH A 220 538 538 HOH HOH . D 4 HOH A 221 539 539 HOH HOH . D 4 HOH A 222 540 540 HOH HOH . D 4 HOH A 223 541 541 HOH HOH . D 4 HOH A 224 542 542 HOH HOH . D 4 HOH A 225 543 543 HOH HOH . D 4 HOH A 226 544 544 HOH HOH . D 4 HOH A 227 545 545 HOH HOH . D 4 HOH A 228 546 546 HOH HOH . D 4 HOH A 229 547 547 HOH HOH . D 4 HOH A 230 548 548 HOH HOH . D 4 HOH A 231 549 549 HOH HOH . D 4 HOH A 232 550 550 HOH HOH . D 4 HOH A 233 551 551 HOH HOH . D 4 HOH A 234 552 552 HOH HOH . D 4 HOH A 235 553 553 HOH HOH . D 4 HOH A 236 554 554 HOH HOH . D 4 HOH A 237 555 555 HOH HOH . D 4 HOH A 238 556 556 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 . . . B 2 14.609 48.159 -52.532 1 20.58 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 14.327 47.516 -51.306 1 21.54 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 14.125 48.4 -50.198 1 20.92 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 13.642 49.742 -50.289 1 21.75 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 13.667 50.341 -51.647 1 21.16 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 13.761 49.361 -52.801 1 20.82 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 14.263 46.276 -51.229 1 16.09 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 13.189 50.334 -49.288 1 20.62 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 15.704 47.626 -53.407 1 20.08 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.141 47.059 -54.696 1 19.37 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 16.376 46.825 -55.567 1 21.26 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 17.127 48.127 -55.33 1 18.78 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 17.152 45.717 -55.046 1 22.71 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 16.937 48.34 -53.869 1 19.4 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 16.507 49.335 -56.083 1 18.69 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 15.885 48.914 -57.345 1 16.99 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 16.071 49.765 -58.649 1 18.76 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 16.068 51.18 -58.337 1 17.19 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 17.367 49.461 -59.301 1 18.96 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 15.017 49.466 -59.615 1 17.36 ? OP3 UMP 317 A 1 HETATM 21 H HN3 UMP . . . B 2 14.518 48.143 -49.338 1 15 ? HN3 UMP 317 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #