data_3WK2 # _model_server_result.job_id yb0CMMV_ETEafaB8FXD2SA _model_server_result.datetime_utc '2024-11-29 21:39:59' _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 3wk2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3WK2 # _exptl.entry_id 3WK2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 382.217 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-(methoxycarbonyl)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 3WK2 _cell.length_a 57.833 _cell.length_b 103.388 _cell.length_c 73.27 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WK2 _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 0 103.388 73.27 # _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 'C11 H15 N2 O11 P' _chem_comp.formula_weight 382.217 _chem_comp.id O7M _chem_comp.mon_nstd_flag . _chem_comp.name "6-(methoxycarbonyl)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 C8 O72 O7M sing 250 n n O72 C7 O7M sing 251 n n O71 C7 O7M doub 252 n n C7 C6 O7M sing 253 n n C5 C6 O7M doub 254 n n C5 C4 O7M sing 255 n n C6 N1 O7M sing 256 n n O4' C1' O7M sing 257 n n O4' C4' O7M sing 258 n n O4 C4 O7M doub 259 n n C4 N3 O7M sing 260 n n N1 C1' O7M sing 261 n n N1 C2 O7M sing 262 n n C1' C2' O7M sing 263 n n C4' C5' O7M sing 264 n n C4' C3' O7M sing 265 n n N3 C2 O7M sing 266 n n C2 O2 O7M doub 267 n n O3' C3' O7M sing 268 n n C5' O5' O7M sing 269 n n C3' C2' O7M sing 270 n n C2' O2' O7M sing 271 n n O3P P O7M doub 272 n n O5' P O7M sing 273 n n P O1P O7M sing 274 n n P O2P O7M sing 275 n n O1P H1 O7M sing 276 n n O2P H2 O7M sing 277 n n C5' H3 O7M sing 278 n n C5' H4 O7M sing 279 n n C4' H5 O7M sing 280 n n C3' H6 O7M sing 281 n n O3' H7 O7M sing 282 n n C2' H8 O7M sing 283 n n O2' H9 O7M sing 284 n n C1' H10 O7M sing 285 n n N3 H11 O7M sing 286 n n C5 H12 O7M sing 287 n n C8 H15 O7M sing 288 n n C8 H16 O7M sing 289 n n C8 H17 O7M sing 290 n n # _atom_sites.entry_id 3WK2 _atom_sites.fract_transf_matrix[1][1] 0.017291 _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] 0.009672 _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] 0.013648 _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 O7M A 1 301 301 O7M O7M . 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 . # 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 O7M . . . B 2 18.816 33.521 37.218 1 8.61 ? O3P O7M 301 A 1 HETATM 2 P P O7M . . . B 2 18.929 34.647 38.215 1 8.61 ? P O7M 301 A 1 HETATM 3 O O1P O7M . . . B 2 17.656 34.884 38.985 1 10.66 ? O1P O7M 301 A 1 HETATM 4 O O2P O7M . . . B 2 20.098 34.49 39.187 1 9.94 ? O2P O7M 301 A 1 HETATM 5 O O5' O7M . . . B 2 19.274 35.949 37.355 1 9.26 ? O5' O7M 301 A 1 HETATM 6 C C5' O7M . . . B 2 18.251 36.778 36.764 1 9.16 ? C5' O7M 301 A 1 HETATM 7 C C4' O7M . . . B 2 19.007 37.944 36.122 1 6.99 ? C4' O7M 301 A 1 HETATM 8 O O4' O7M . . . B 2 18.073 38.63 35.257 1 8.14 ? O4' O7M 301 A 1 HETATM 9 C C3' O7M . . . B 2 19.48 38.945 37.132 1 9.3 ? C3' O7M 301 A 1 HETATM 10 O O3' O7M . . . B 2 20.581 39.656 36.55 1 9.41 ? O3' O7M 301 A 1 HETATM 11 C C2' O7M . . . B 2 18.274 39.86 37.21 1 8.06 ? C2' O7M 301 A 1 HETATM 12 O O2' O7M . . . B 2 18.681 41.138 37.711 1 9.34 ? O2' O7M 301 A 1 HETATM 13 C C1' O7M . . . B 2 17.78 39.916 35.762 1 8.49 ? C1' O7M 301 A 1 HETATM 14 N N1 O7M . . . B 2 16.331 40.217 35.684 1 8.85 ? N1 O7M 301 A 1 HETATM 15 C C2 O7M . . . B 2 15.424 39.489 36.321 1 9.32 ? C2 O7M 301 A 1 HETATM 16 O O2 O7M . . . B 2 15.751 38.495 36.987 1 8.7 ? O2 O7M 301 A 1 HETATM 17 N N3 O7M . . . B 2 14.121 39.806 36.264 1 7.86 ? N3 O7M 301 A 1 HETATM 18 C C4 O7M . . . B 2 13.661 40.871 35.574 1 9.92 ? C4 O7M 301 A 1 HETATM 19 O O4 O7M . . . B 2 12.435 41.134 35.557 1 10.73 ? O4 O7M 301 A 1 HETATM 20 C C5 O7M . . . B 2 14.583 41.668 34.921 1 9.21 ? C5 O7M 301 A 1 HETATM 21 C C6 O7M . . . B 2 15.922 41.274 34.964 1 10.16 ? C6 O7M 301 A 1 HETATM 22 C C7 O7M . A . B 2 16.795 42.016 34.005 0.5 10.96 ? C7 O7M 301 A 1 HETATM 23 C C7 O7M . B . B 2 16.652 41.472 33.65 0.5 16.58 ? C7 O7M 301 A 1 HETATM 24 O O71 O7M . A . B 2 17.215 41.483 32.982 0.5 8.17 ? O71 O7M 301 A 1 HETATM 25 O O71 O7M . B . B 2 17.39 40.64 33.136 0.5 16.71 ? O71 O7M 301 A 1 HETATM 26 O O72 O7M . A . B 2 17.194 43.364 34.319 0.5 12.55 ? O72 O7M 301 A 1 HETATM 27 O O72 O7M . B . B 2 16.497 42.728 32.952 0.5 18.92 ? O72 O7M 301 A 1 HETATM 28 C C8 O7M . A . B 2 16.418 44.485 34.765 0.5 15.47 ? C8 O7M 301 A 1 HETATM 29 C C8 O7M . B . B 2 16.439 43.9 33.758 0.5 21.86 ? C8 O7M 301 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 947 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 29 #