data_3WK1 # _model_server_result.job_id -9a9o4DPmm0OFqxyS_nz_A _model_server_result.datetime_utc '2024-11-13 07:40:23' _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 3wk1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3WK1 # _exptl.entry_id 3WK1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 396.244 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-(ethoxycarbonyl)uridine 5'-(dihydrogen 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 3WK1 _cell.length_a 57.8 _cell.length_b 103.49 _cell.length_c 73.59 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WK1 _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 _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' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 103.49 73.59 # _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 'C12 H17 N2 O11 P' _chem_comp.formula_weight 396.244 _chem_comp.id O7E _chem_comp.mon_nstd_flag . _chem_comp.name "6-(ethoxycarbonyl)uridine 5'-(dihydrogen 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 O71 C7 O7E doub 250 n n C7 O72 O7E sing 251 n n C7 C6 O7E sing 252 n n O72 C8 O7E sing 253 n n C5 C6 O7E doub 254 n n C5 C4 O7E sing 255 n n C6 N1 O7E sing 256 n n C9 C8 O7E sing 257 n n O4' C1' O7E sing 258 n n O4' C4' O7E sing 259 n n O4 C4 O7E doub 260 n n C4 N3 O7E sing 261 n n N1 C1' O7E sing 262 n n N1 C2 O7E sing 263 n n C1' C2' O7E sing 264 n n C4' C5' O7E sing 265 n n C4' C3' O7E sing 266 n n N3 C2 O7E sing 267 n n C2 O2 O7E doub 268 n n O3' C3' O7E sing 269 n n C5' O5' O7E sing 270 n n C3' C2' O7E sing 271 n n C2' O2' O7E sing 272 n n O3P P O7E doub 273 n n O5' P O7E sing 274 n n P O1P O7E sing 275 n n P O2P O7E sing 276 n n O1P H1 O7E sing 277 n n O2P H2 O7E sing 278 n n C5' H3 O7E sing 279 n n C5' H4 O7E sing 280 n n C4' H5 O7E sing 281 n n C3' H6 O7E sing 282 n n O3' H7 O7E sing 283 n n C2' H8 O7E sing 284 n n O2' H9 O7E sing 285 n n C1' H10 O7E sing 286 n n N3 H11 O7E sing 287 n n C5 H12 O7E sing 288 n n C8 H13 O7E sing 289 n n C8 H14 O7E sing 290 n n C9 H15 O7E sing 291 n n C9 H16 O7E sing 292 n n C9 H17 O7E sing 293 n n # _atom_sites.entry_id 3WK1 _atom_sites.fract_transf_matrix[1][1] 0.017301 _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] 0.009663 _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] 0.013589 _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 O7E A 1 301 301 O7E O7E . C 3 GOL A 1 302 311 GOL GOL . D 3 GOL A 1 303 312 GOL GOL . E 4 HOH A 1 401 401 HOH HOH . E 4 HOH A 2 402 402 HOH HOH . E 4 HOH A 3 403 403 HOH HOH . E 4 HOH A 4 404 404 HOH HOH . E 4 HOH A 5 405 405 HOH HOH . E 4 HOH A 6 406 406 HOH HOH . E 4 HOH A 7 407 407 HOH HOH . E 4 HOH A 8 408 408 HOH HOH . E 4 HOH A 9 409 409 HOH HOH . E 4 HOH A 10 410 410 HOH HOH . E 4 HOH A 11 411 411 HOH HOH . E 4 HOH A 12 412 412 HOH HOH . E 4 HOH A 13 413 413 HOH HOH . E 4 HOH A 14 414 414 HOH HOH . E 4 HOH A 15 415 451 HOH HOH . E 4 HOH A 16 416 501 HOH HOH . E 4 HOH A 17 417 502 HOH HOH . E 4 HOH A 18 418 503 HOH HOH . E 4 HOH A 19 419 504 HOH HOH . E 4 HOH A 20 420 505 HOH HOH . E 4 HOH A 21 421 506 HOH HOH . E 4 HOH A 22 422 507 HOH HOH . E 4 HOH A 23 423 508 HOH HOH . E 4 HOH A 24 424 509 HOH HOH . E 4 HOH A 25 425 510 HOH HOH . E 4 HOH A 26 426 511 HOH HOH . E 4 HOH A 27 427 512 HOH HOH . E 4 HOH A 28 428 513 HOH HOH . E 4 HOH A 29 429 514 HOH HOH . E 4 HOH A 30 430 515 HOH HOH . E 4 HOH A 31 431 516 HOH HOH . E 4 HOH A 32 432 517 HOH HOH . E 4 HOH A 33 433 518 HOH HOH . E 4 HOH A 34 434 519 HOH HOH . E 4 HOH A 35 435 520 HOH HOH . E 4 HOH A 36 436 521 HOH HOH . E 4 HOH A 37 437 522 HOH HOH . E 4 HOH A 38 438 523 HOH HOH . E 4 HOH A 39 439 524 HOH HOH . E 4 HOH A 40 440 525 HOH HOH . E 4 HOH A 41 441 526 HOH HOH . E 4 HOH A 42 442 527 HOH HOH . E 4 HOH A 43 443 528 HOH HOH . E 4 HOH A 44 444 529 HOH HOH . E 4 HOH A 45 445 530 HOH HOH . E 4 HOH A 46 446 531 HOH HOH . E 4 HOH A 47 447 532 HOH HOH . E 4 HOH A 48 448 533 HOH HOH . E 4 HOH A 49 449 534 HOH HOH . E 4 HOH A 50 450 535 HOH HOH . E 4 HOH A 51 451 536 HOH HOH . E 4 HOH A 52 452 537 HOH HOH . E 4 HOH A 53 453 538 HOH HOH . E 4 HOH A 54 454 539 HOH HOH . E 4 HOH A 55 455 540 HOH HOH . E 4 HOH A 56 456 541 HOH HOH . E 4 HOH A 57 457 542 HOH HOH . E 4 HOH A 58 458 543 HOH HOH . E 4 HOH A 59 459 544 HOH HOH . E 4 HOH A 60 460 545 HOH HOH . E 4 HOH A 61 461 546 HOH HOH . E 4 HOH A 62 462 547 HOH HOH . E 4 HOH A 63 463 548 HOH HOH . E 4 HOH A 64 464 549 HOH HOH . E 4 HOH A 65 465 550 HOH HOH . E 4 HOH A 66 466 551 HOH HOH . E 4 HOH A 67 467 552 HOH HOH . E 4 HOH A 68 468 553 HOH HOH . E 4 HOH A 69 469 554 HOH HOH . E 4 HOH A 70 470 555 HOH HOH . E 4 HOH A 71 471 556 HOH HOH . E 4 HOH A 72 472 557 HOH HOH . E 4 HOH A 73 473 558 HOH HOH . E 4 HOH A 74 474 559 HOH HOH . E 4 HOH A 75 475 560 HOH HOH . E 4 HOH A 76 476 561 HOH HOH . E 4 HOH A 77 477 562 HOH HOH . E 4 HOH A 78 478 563 HOH HOH . E 4 HOH A 79 479 564 HOH HOH . E 4 HOH A 80 480 565 HOH HOH . E 4 HOH A 81 481 566 HOH HOH . E 4 HOH A 82 482 567 HOH HOH . E 4 HOH A 83 483 568 HOH HOH . E 4 HOH A 84 484 569 HOH HOH . E 4 HOH A 85 485 570 HOH HOH . E 4 HOH A 86 486 571 HOH HOH . E 4 HOH A 87 487 572 HOH HOH . E 4 HOH A 88 488 573 HOH HOH . E 4 HOH A 89 489 574 HOH HOH . E 4 HOH A 90 490 575 HOH HOH . E 4 HOH A 91 491 576 HOH HOH . E 4 HOH A 92 492 577 HOH HOH . E 4 HOH A 93 493 578 HOH HOH . E 4 HOH A 94 494 579 HOH HOH . E 4 HOH A 95 495 580 HOH HOH . E 4 HOH A 96 496 581 HOH HOH . E 4 HOH A 97 497 582 HOH HOH . E 4 HOH A 98 498 583 HOH HOH . E 4 HOH A 99 499 584 HOH HOH . E 4 HOH A 100 500 585 HOH HOH . E 4 HOH A 101 501 586 HOH HOH . E 4 HOH A 102 502 587 HOH HOH . E 4 HOH A 103 503 588 HOH HOH . E 4 HOH A 104 504 589 HOH HOH . E 4 HOH A 105 505 590 HOH HOH . E 4 HOH A 106 506 591 HOH HOH . E 4 HOH A 107 507 592 HOH HOH . E 4 HOH A 108 508 593 HOH HOH . E 4 HOH A 109 509 594 HOH HOH . E 4 HOH A 110 510 595 HOH HOH . E 4 HOH A 111 511 596 HOH HOH . E 4 HOH A 112 512 597 HOH HOH . E 4 HOH A 113 513 598 HOH HOH . E 4 HOH A 114 514 599 HOH HOH . E 4 HOH A 115 515 600 HOH HOH . E 4 HOH A 116 516 601 HOH HOH . E 4 HOH A 117 517 602 HOH HOH . E 4 HOH A 118 518 603 HOH HOH . E 4 HOH A 119 519 604 HOH HOH . E 4 HOH A 120 520 605 HOH HOH . E 4 HOH A 121 521 606 HOH HOH . E 4 HOH A 122 522 607 HOH HOH . E 4 HOH A 123 523 608 HOH HOH . E 4 HOH A 124 524 609 HOH HOH . E 4 HOH A 125 525 610 HOH HOH . E 4 HOH A 126 526 611 HOH HOH . E 4 HOH A 127 527 612 HOH HOH . E 4 HOH A 128 528 613 HOH HOH . E 4 HOH A 129 529 614 HOH HOH . E 4 HOH A 130 530 615 HOH HOH . E 4 HOH A 131 531 616 HOH HOH . E 4 HOH A 132 532 617 HOH HOH . E 4 HOH A 133 533 618 HOH HOH . E 4 HOH A 134 534 619 HOH HOH . E 4 HOH A 135 535 620 HOH HOH . E 4 HOH A 136 536 621 HOH HOH . E 4 HOH A 137 537 622 HOH HOH . E 4 HOH A 138 538 623 HOH HOH . E 4 HOH A 139 539 624 HOH HOH . E 4 HOH A 140 540 625 HOH HOH . E 4 HOH A 141 541 626 HOH HOH . E 4 HOH A 142 542 627 HOH HOH . E 4 HOH A 143 543 628 HOH HOH . E 4 HOH A 144 544 629 HOH HOH . E 4 HOH A 145 545 630 HOH HOH . E 4 HOH A 146 546 631 HOH HOH . E 4 HOH A 147 547 632 HOH HOH . E 4 HOH A 148 548 633 HOH HOH . E 4 HOH A 149 549 634 HOH HOH . E 4 HOH A 150 550 635 HOH HOH . E 4 HOH A 151 551 636 HOH HOH . E 4 HOH A 152 552 637 HOH HOH . E 4 HOH A 153 553 638 HOH HOH . E 4 HOH A 154 554 639 HOH HOH . E 4 HOH A 155 555 640 HOH HOH . E 4 HOH A 156 556 641 HOH HOH . E 4 HOH A 157 557 642 HOH HOH . E 4 HOH A 158 558 643 HOH HOH . E 4 HOH A 159 559 644 HOH HOH . E 4 HOH A 160 560 645 HOH HOH . E 4 HOH A 161 561 646 HOH HOH . E 4 HOH A 162 562 647 HOH HOH . E 4 HOH A 163 563 648 HOH HOH . E 4 HOH A 164 564 649 HOH HOH . E 4 HOH A 165 565 650 HOH HOH . E 4 HOH A 166 566 651 HOH HOH . E 4 HOH A 167 567 652 HOH HOH . E 4 HOH A 168 568 653 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 O3P O7E . . . B 2 18.899 33.524 37.431 1 6.8 ? O3P O7E 301 A 1 HETATM 2 P P O7E . . . B 2 19.013 34.65 38.403 1 6.23 ? P O7E 301 A 1 HETATM 3 O O1P O7E . . . B 2 17.728 34.847 39.136 1 7.46 ? O1P O7E 301 A 1 HETATM 4 O O2P O7E . . . B 2 20.204 34.507 39.314 1 7.28 ? O2P O7E 301 A 1 HETATM 5 O O5' O7E . . . B 2 19.385 35.977 37.551 1 6.66 ? O5' O7E 301 A 1 HETATM 6 C C5' O7E . . . B 2 18.31 36.735 36.933 1 7.02 ? C5' O7E 301 A 1 HETATM 7 C C4' O7E . . . B 2 19.063 37.896 36.282 1 4.71 ? C4' O7E 301 A 1 HETATM 8 O O4' O7E . . . B 2 18.141 38.607 35.42 1 5.58 ? O4' O7E 301 A 1 HETATM 9 C C3' O7E . . . B 2 19.566 38.916 37.266 1 6.39 ? C3' O7E 301 A 1 HETATM 10 O O3' O7E . . . B 2 20.676 39.611 36.664 1 6.91 ? O3' O7E 301 A 1 HETATM 11 C C2' O7E . . . B 2 18.384 39.866 37.354 1 7.62 ? C2' O7E 301 A 1 HETATM 12 O O2' O7E . . . B 2 18.849 41.144 37.758 1 11.16 ? O2' O7E 301 A 1 HETATM 13 C C1' O7E . . . B 2 17.884 39.918 35.914 1 5.95 ? C1' O7E 301 A 1 HETATM 14 N N1 O7E . . . B 2 16.425 40.198 35.814 1 5.84 ? N1 O7E 301 A 1 HETATM 15 C C2 O7E . . . B 2 15.502 39.504 36.486 1 6.88 ? C2 O7E 301 A 1 HETATM 16 O O2 O7E . . . B 2 15.825 38.554 37.207 1 6.77 ? O2 O7E 301 A 1 HETATM 17 N N3 O7E . . . B 2 14.197 39.834 36.408 1 5.95 ? N3 O7E 301 A 1 HETATM 18 C C4 O7E . . . B 2 13.75 40.845 35.657 1 8.45 ? C4 O7E 301 A 1 HETATM 19 O O4 O7E . . . B 2 12.509 41.071 35.65 1 8.28 ? O4 O7E 301 A 1 HETATM 20 C C5 O7E . . . B 2 14.653 41.597 34.926 1 7.03 ? C5 O7E 301 A 1 HETATM 21 C C6 O7E . . . B 2 15.981 41.226 35.028 1 7.14 ? C6 O7E 301 A 1 HETATM 22 C C7 O7E . D . B 2 16.873 41.827 34.056 0.5 6.25 ? C7 O7E 301 A 1 HETATM 23 O O71 O7E . D . B 2 17.481 41.114 33.27 0.5 7.58 ? O71 O7E 301 A 1 HETATM 24 O O72 O7E . D . B 2 16.953 43.283 34.146 0.5 10.34 ? O72 O7E 301 A 1 HETATM 25 C C8 O7E . D . B 2 17.047 43.945 35.396 0.25 8.23 ? C8 O7E 301 A 1 HETATM 26 C C9 O7E . D . B 2 16.319 45.27 35.334 0.25 7.46 ? C9 O7E 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #