data_3WK3 # _model_server_result.job_id JG1V6O-m1MLN0XDXDpoRNg _model_server_result.datetime_utc '2024-11-08 03:04:56' _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 3wk3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3WK3 # _exptl.entry_id 3WK3 _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 3WK3 _cell.length_a 57.985 _cell.length_b 103.466 _cell.length_c 73.628 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WK3 _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 0 103.466 73.628 # _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 3WK3 _atom_sites.fract_transf_matrix[1][1] 0.017246 _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] 0.009665 _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] 0.013582 _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 16 416 477 HOH HOH . E 4 HOH A 17 417 501 HOH HOH . E 4 HOH A 18 418 502 HOH HOH . E 4 HOH A 19 419 503 HOH HOH . E 4 HOH A 20 420 504 HOH HOH . E 4 HOH A 21 421 505 HOH HOH . E 4 HOH A 22 422 506 HOH HOH . E 4 HOH A 23 423 507 HOH HOH . E 4 HOH A 24 424 508 HOH HOH . E 4 HOH A 25 425 509 HOH HOH . E 4 HOH A 26 426 510 HOH HOH . E 4 HOH A 27 427 511 HOH HOH . E 4 HOH A 28 428 512 HOH HOH . E 4 HOH A 29 429 513 HOH HOH . E 4 HOH A 30 430 514 HOH HOH . E 4 HOH A 31 431 515 HOH HOH . E 4 HOH A 32 432 516 HOH HOH . E 4 HOH A 33 433 517 HOH HOH . E 4 HOH A 34 434 518 HOH HOH . E 4 HOH A 35 435 519 HOH HOH . E 4 HOH A 36 436 520 HOH HOH . E 4 HOH A 37 437 521 HOH HOH . E 4 HOH A 38 438 522 HOH HOH . E 4 HOH A 39 439 523 HOH HOH . E 4 HOH A 40 440 524 HOH HOH . E 4 HOH A 41 441 525 HOH HOH . E 4 HOH A 42 442 526 HOH HOH . E 4 HOH A 43 443 527 HOH HOH . E 4 HOH A 44 444 528 HOH HOH . E 4 HOH A 45 445 529 HOH HOH . E 4 HOH A 46 446 530 HOH HOH . E 4 HOH A 47 447 531 HOH HOH . E 4 HOH A 48 448 532 HOH HOH . E 4 HOH A 49 449 533 HOH HOH . E 4 HOH A 50 450 534 HOH HOH . E 4 HOH A 51 451 535 HOH HOH . E 4 HOH A 52 452 536 HOH HOH . E 4 HOH A 53 453 537 HOH HOH . E 4 HOH A 54 454 538 HOH HOH . E 4 HOH A 55 455 539 HOH HOH . E 4 HOH A 56 456 540 HOH HOH . E 4 HOH A 57 457 541 HOH HOH . E 4 HOH A 58 458 542 HOH HOH . E 4 HOH A 59 459 543 HOH HOH . E 4 HOH A 60 460 544 HOH HOH . E 4 HOH A 61 461 545 HOH HOH . E 4 HOH A 62 462 546 HOH HOH . E 4 HOH A 63 463 547 HOH HOH . E 4 HOH A 64 464 548 HOH HOH . E 4 HOH A 65 465 549 HOH HOH . E 4 HOH A 66 466 550 HOH HOH . E 4 HOH A 67 467 551 HOH HOH . E 4 HOH A 68 468 552 HOH HOH . E 4 HOH A 69 469 553 HOH HOH . E 4 HOH A 70 470 554 HOH HOH . E 4 HOH A 71 471 555 HOH HOH . E 4 HOH A 72 472 556 HOH HOH . E 4 HOH A 73 473 557 HOH HOH . E 4 HOH A 74 474 558 HOH HOH . E 4 HOH A 75 475 559 HOH HOH . E 4 HOH A 76 476 560 HOH HOH . E 4 HOH A 77 477 561 HOH HOH . E 4 HOH A 78 478 562 HOH HOH . E 4 HOH A 79 479 563 HOH HOH . E 4 HOH A 80 480 564 HOH HOH . E 4 HOH A 81 481 565 HOH HOH . E 4 HOH A 82 482 566 HOH HOH . E 4 HOH A 83 483 567 HOH HOH . E 4 HOH A 84 484 568 HOH HOH . E 4 HOH A 85 485 569 HOH HOH . E 4 HOH A 86 486 570 HOH HOH . E 4 HOH A 87 487 571 HOH HOH . E 4 HOH A 88 488 572 HOH HOH . E 4 HOH A 89 489 573 HOH HOH . E 4 HOH A 90 490 574 HOH HOH . E 4 HOH A 91 491 575 HOH HOH . E 4 HOH A 92 492 576 HOH HOH . E 4 HOH A 93 493 577 HOH HOH . E 4 HOH A 94 494 578 HOH HOH . E 4 HOH A 95 495 579 HOH HOH . E 4 HOH A 96 496 580 HOH HOH . E 4 HOH A 97 497 581 HOH HOH . E 4 HOH A 98 498 582 HOH HOH . E 4 HOH A 99 499 583 HOH HOH . E 4 HOH A 100 500 584 HOH HOH . E 4 HOH A 101 501 585 HOH HOH . E 4 HOH A 102 502 586 HOH HOH . E 4 HOH A 103 503 587 HOH HOH . E 4 HOH A 104 504 588 HOH HOH . E 4 HOH A 105 505 589 HOH HOH . E 4 HOH A 106 506 590 HOH HOH . E 4 HOH A 107 507 591 HOH HOH . E 4 HOH A 108 508 592 HOH HOH . E 4 HOH A 109 509 593 HOH HOH . E 4 HOH A 110 510 594 HOH HOH . E 4 HOH A 111 511 595 HOH HOH . E 4 HOH A 112 512 596 HOH HOH . E 4 HOH A 113 513 597 HOH HOH . E 4 HOH A 114 514 598 HOH HOH . E 4 HOH A 115 515 599 HOH HOH . E 4 HOH A 116 516 600 HOH HOH . E 4 HOH A 117 517 601 HOH HOH . E 4 HOH A 118 518 602 HOH HOH . E 4 HOH A 119 519 603 HOH HOH . E 4 HOH A 120 520 604 HOH HOH . E 4 HOH A 121 521 605 HOH HOH . E 4 HOH A 122 522 606 HOH HOH . E 4 HOH A 123 523 607 HOH HOH . E 4 HOH A 124 524 608 HOH HOH . E 4 HOH A 125 525 609 HOH HOH . E 4 HOH A 126 526 610 HOH HOH . E 4 HOH A 127 527 611 HOH HOH . E 4 HOH A 128 528 612 HOH HOH . E 4 HOH A 129 529 613 HOH HOH . E 4 HOH A 130 530 614 HOH HOH . E 4 HOH A 131 531 615 HOH HOH . E 4 HOH A 132 532 616 HOH HOH . E 4 HOH A 133 533 617 HOH HOH . E 4 HOH A 134 534 618 HOH HOH . E 4 HOH A 135 535 619 HOH HOH . E 4 HOH A 136 536 620 HOH HOH . E 4 HOH A 137 537 621 HOH HOH . E 4 HOH A 138 538 622 HOH HOH . E 4 HOH A 139 539 623 HOH HOH . E 4 HOH A 140 540 624 HOH HOH . E 4 HOH A 141 541 625 HOH HOH . E 4 HOH A 142 542 626 HOH HOH . E 4 HOH A 143 543 627 HOH HOH . E 4 HOH A 144 544 628 HOH HOH . E 4 HOH A 145 545 629 HOH HOH . E 4 HOH A 146 546 630 HOH HOH . E 4 HOH A 147 547 631 HOH HOH . E 4 HOH A 148 548 632 HOH HOH . E 4 HOH A 149 549 633 HOH HOH . E 4 HOH A 150 550 634 HOH HOH . E 4 HOH A 151 551 635 HOH HOH . E 4 HOH A 152 552 636 HOH HOH . E 4 HOH A 153 553 637 HOH HOH . E 4 HOH A 154 554 638 HOH HOH . E 4 HOH A 155 555 639 HOH HOH . E 4 HOH A 156 556 640 HOH HOH . E 4 HOH A 157 557 641 HOH HOH . E 4 HOH A 158 558 642 HOH HOH . E 4 HOH A 159 559 643 HOH HOH . E 4 HOH A 160 560 644 HOH HOH . E 4 HOH A 161 561 645 HOH HOH . E 4 HOH A 162 562 646 HOH HOH . E 4 HOH A 163 563 647 HOH HOH . E 4 HOH A 164 564 648 HOH HOH . E 4 HOH A 165 565 649 HOH HOH . E 4 HOH A 166 566 650 HOH HOH . E 4 HOH A 167 567 651 HOH HOH . E 4 HOH A 168 568 652 HOH HOH . E 4 HOH A 169 569 653 HOH HOH . E 4 HOH A 170 570 654 HOH HOH . E 4 HOH A 171 571 655 HOH HOH . E 4 HOH A 172 572 656 HOH HOH . E 4 HOH A 173 573 657 HOH HOH . E 4 HOH A 174 574 658 HOH HOH . E 4 HOH A 175 575 659 HOH HOH . E 4 HOH A 176 576 660 HOH HOH . E 4 HOH A 177 577 661 HOH HOH . E 4 HOH A 178 578 662 HOH HOH . E 4 HOH A 179 579 663 HOH HOH . E 4 HOH A 180 580 664 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 18.942 33.545 37.405 1 6.83 ? O3P O7E 301 A 1 HETATM 2 P P O7E . . . B 2 19.038 34.685 38.385 1 6.76 ? P O7E 301 A 1 HETATM 3 O O1P O7E . . . B 2 17.74 34.899 39.108 1 7.26 ? O1P O7E 301 A 1 HETATM 4 O O2P O7E . . . B 2 20.224 34.574 39.322 1 7.14 ? O2P O7E 301 A 1 HETATM 5 O O5' O7E . . . B 2 19.391 36.022 37.548 1 6.62 ? O5' O7E 301 A 1 HETATM 6 C C5' O7E . . . B 2 18.359 36.808 36.932 1 6.88 ? C5' O7E 301 A 1 HETATM 7 C C4' O7E . . . B 2 19.085 37.965 36.276 1 7.09 ? C4' O7E 301 A 1 HETATM 8 O O4' O7E . . . B 2 18.181 38.693 35.41 1 6.45 ? O4' O7E 301 A 1 HETATM 9 C C3' O7E . . . B 2 19.583 38.998 37.27 1 6.92 ? C3' O7E 301 A 1 HETATM 10 O O3' O7E . . . B 2 20.71 39.724 36.724 1 6.63 ? O3' O7E 301 A 1 HETATM 11 C C2' O7E . . . B 2 18.409 39.95 37.387 1 6.38 ? C2' O7E 301 A 1 HETATM 12 O O2' O7E . . . B 2 18.819 41.233 37.859 1 8.07 ? O2' O7E 301 A 1 HETATM 13 C C1' O7E . . . B 2 17.892 39.948 35.972 1 6.42 ? C1' O7E 301 A 1 HETATM 14 N N1 O7E . . . B 2 16.445 40.25 35.845 1 6.5 ? N1 O7E 301 A 1 HETATM 15 C C2 O7E . . . B 2 15.516 39.498 36.487 1 6.51 ? C2 O7E 301 A 1 HETATM 16 O O2 O7E . . . B 2 15.835 38.507 37.162 1 7.03 ? O2 O7E 301 A 1 HETATM 17 N N3 O7E . . . B 2 14.206 39.859 36.409 1 6.67 ? N3 O7E 301 A 1 HETATM 18 C C4 O7E . . . B 2 13.758 40.947 35.751 1 7.1 ? C4 O7E 301 A 1 HETATM 19 O O4 O7E . . . B 2 12.521 41.148 35.738 1 8.35 ? O4 O7E 301 A 1 HETATM 20 C C5 O7E . . . B 2 14.679 41.737 35.09 1 8.38 ? C5 O7E 301 A 1 HETATM 21 C C6 O7E . . . B 2 16.018 41.351 35.103 1 9.36 ? C6 O7E 301 A 1 HETATM 22 C C7 O7E . A . B 2 16.914 42.07 34.184 0.5 9.61 ? C7 O7E 301 A 1 HETATM 23 C C7 O7E . B . B 2 16.681 41.447 33.715 0.5 12.86 ? C7 O7E 301 A 1 HETATM 24 O O71 O7E . A . B 2 17.371 41.509 33.221 0.5 9.32 ? O71 O7E 301 A 1 HETATM 25 O O71 O7E . B . B 2 17.564 40.693 33.255 0.5 12.66 ? O71 O7E 301 A 1 HETATM 26 O O72 O7E . A . B 2 17.255 43.429 34.438 0.5 13.11 ? O72 O7E 301 A 1 HETATM 27 O O72 O7E . B . B 2 16.365 42.535 32.829 0.5 16.49 ? O72 O7E 301 A 1 HETATM 28 C C8 O7E . A . B 2 16.762 44.765 34.754 0.5 8.59 ? C8 O7E 301 A 1 HETATM 29 C C8 O7E . B . B 2 17.18 43.714 32.927 0.5 22.5 ? C8 O7E 301 A 1 HETATM 30 C C9 O7E . A . B 2 16.005 44.815 36.093 0.5 11.27 ? C9 O7E 301 A 1 HETATM 31 C C9 O7E . B . B 2 16.486 44.807 33.722 0.5 24.31 ? C9 O7E 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #