data_3WJW # _model_server_result.job_id rkq2bJXOmtHWo8csr04H1Q _model_server_result.datetime_utc '2024-11-13 07:54:04' _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 3wjw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3WJW # _exptl.entry_id 3WJW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 338.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-methyluridine 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 3WJW _cell.length_a 58.025 _cell.length_b 103.573 _cell.length_c 73.508 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WJW _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 _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 0 103.573 73.508 # _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 'C10 H15 N2 O9 P' _chem_comp.formula_weight 338.208 _chem_comp.id U6M _chem_comp.mon_nstd_flag . _chem_comp.name "6-methyluridine 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 C7 C6 U6M sing 330 n n C6 C5 U6M doub 331 n n C6 N1 U6M sing 332 n n C5 C4 U6M sing 333 n n O4' C1' U6M sing 334 n n O4' C4' U6M sing 335 n n O4 C4 U6M doub 336 n n C4 N3 U6M sing 337 n n N1 C1' U6M sing 338 n n N1 C2 U6M sing 339 n n C1' C2' U6M sing 340 n n C4' C5' U6M sing 341 n n C4' C3' U6M sing 342 n n N3 C2 U6M sing 343 n n C2 O2 U6M doub 344 n n O3' C3' U6M sing 345 n n C5' O5' U6M sing 346 n n C3' C2' U6M sing 347 n n C2' O2' U6M sing 348 n n O3P P U6M doub 349 n n O5' P U6M sing 350 n n P O1P U6M sing 351 n n P O2P U6M sing 352 n n N3 H1 U6M sing 353 n n C5 H2 U6M sing 354 n n C7 H5 U6M sing 355 n n C7 H6 U6M sing 356 n n C7 H7 U6M sing 357 n n C1' H8 U6M sing 358 n n C2' H9 U6M sing 359 n n O2' H10 U6M sing 360 n n C3' H11 U6M sing 361 n n O3' H12 U6M sing 362 n n C4' H13 U6M sing 363 n n C5' H14 U6M sing 364 n n C5' H15 U6M sing 365 n n O1P H16 U6M sing 366 n n O2P H17 U6M sing 367 n n # _atom_sites.entry_id 3WJW _atom_sites.fract_transf_matrix[1][1] 0.017234 _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] 0.009655 _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] 0.013604 _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 U6M A 1 301 301 U6M U6M . C 3 HOH A 1 401 401 HOH HOH . C 3 HOH A 2 402 402 HOH HOH . C 3 HOH A 3 403 403 HOH HOH . C 3 HOH A 4 404 404 HOH HOH . C 3 HOH A 5 405 405 HOH HOH . C 3 HOH A 6 406 406 HOH HOH . C 3 HOH A 7 407 407 HOH HOH . C 3 HOH A 8 408 408 HOH HOH . C 3 HOH A 9 409 409 HOH HOH . C 3 HOH A 10 410 410 HOH HOH . C 3 HOH A 11 411 411 HOH HOH . C 3 HOH A 12 412 412 HOH HOH . C 3 HOH A 13 413 413 HOH HOH . C 3 HOH A 14 414 414 HOH HOH . C 3 HOH A 15 415 415 HOH HOH . C 3 HOH A 16 416 416 HOH HOH . C 3 HOH A 17 417 417 HOH HOH . C 3 HOH A 18 418 451 HOH HOH . C 3 HOH A 19 419 501 HOH HOH . C 3 HOH A 20 420 502 HOH HOH . C 3 HOH A 21 421 503 HOH HOH . C 3 HOH A 22 422 504 HOH HOH . C 3 HOH A 23 423 505 HOH HOH . C 3 HOH A 24 424 506 HOH HOH . C 3 HOH A 25 425 507 HOH HOH . C 3 HOH A 26 426 508 HOH HOH . C 3 HOH A 27 427 509 HOH HOH . C 3 HOH A 28 428 510 HOH HOH . C 3 HOH A 29 429 511 HOH HOH . C 3 HOH A 30 430 512 HOH HOH . C 3 HOH A 31 431 513 HOH HOH . C 3 HOH A 32 432 514 HOH HOH . C 3 HOH A 33 433 515 HOH HOH . C 3 HOH A 34 434 516 HOH HOH . C 3 HOH A 35 435 517 HOH HOH . C 3 HOH A 36 436 518 HOH HOH . C 3 HOH A 37 437 519 HOH HOH . C 3 HOH A 38 438 520 HOH HOH . C 3 HOH A 39 439 521 HOH HOH . C 3 HOH A 40 440 522 HOH HOH . C 3 HOH A 41 441 523 HOH HOH . C 3 HOH A 42 442 524 HOH HOH . C 3 HOH A 43 443 525 HOH HOH . C 3 HOH A 44 444 526 HOH HOH . C 3 HOH A 45 445 527 HOH HOH . C 3 HOH A 46 446 528 HOH HOH . C 3 HOH A 47 447 529 HOH HOH . C 3 HOH A 48 448 530 HOH HOH . C 3 HOH A 49 449 531 HOH HOH . C 3 HOH A 50 450 532 HOH HOH . C 3 HOH A 51 451 533 HOH HOH . C 3 HOH A 52 452 534 HOH HOH . C 3 HOH A 53 453 535 HOH HOH . C 3 HOH A 54 454 536 HOH HOH . C 3 HOH A 55 455 537 HOH HOH . C 3 HOH A 56 456 538 HOH HOH . C 3 HOH A 57 457 539 HOH HOH . C 3 HOH A 58 458 540 HOH HOH . C 3 HOH A 59 459 541 HOH HOH . C 3 HOH A 60 460 542 HOH HOH . C 3 HOH A 61 461 543 HOH HOH . C 3 HOH A 62 462 544 HOH HOH . C 3 HOH A 63 463 545 HOH HOH . C 3 HOH A 64 464 546 HOH HOH . C 3 HOH A 65 465 547 HOH HOH . C 3 HOH A 66 466 548 HOH HOH . C 3 HOH A 67 467 549 HOH HOH . C 3 HOH A 68 468 550 HOH HOH . C 3 HOH A 69 469 551 HOH HOH . C 3 HOH A 70 470 552 HOH HOH . C 3 HOH A 71 471 553 HOH HOH . C 3 HOH A 72 472 554 HOH HOH . C 3 HOH A 73 473 555 HOH HOH . C 3 HOH A 74 474 556 HOH HOH . C 3 HOH A 75 475 557 HOH HOH . C 3 HOH A 76 476 558 HOH HOH . C 3 HOH A 77 477 559 HOH HOH . C 3 HOH A 78 478 560 HOH HOH . C 3 HOH A 79 479 561 HOH HOH . C 3 HOH A 80 480 562 HOH HOH . C 3 HOH A 81 481 563 HOH HOH . C 3 HOH A 82 482 564 HOH HOH . C 3 HOH A 83 483 565 HOH HOH . C 3 HOH A 84 484 566 HOH HOH . C 3 HOH A 85 485 567 HOH HOH . C 3 HOH A 86 486 568 HOH HOH . C 3 HOH A 87 487 569 HOH HOH . C 3 HOH A 88 488 570 HOH HOH . C 3 HOH A 89 489 571 HOH HOH . C 3 HOH A 90 490 572 HOH HOH . C 3 HOH A 91 491 573 HOH HOH . C 3 HOH A 92 492 574 HOH HOH . C 3 HOH A 93 493 575 HOH HOH . C 3 HOH A 94 494 576 HOH HOH . C 3 HOH A 95 495 577 HOH HOH . C 3 HOH A 96 496 578 HOH HOH . C 3 HOH A 97 497 579 HOH HOH . C 3 HOH A 98 498 580 HOH HOH . C 3 HOH A 99 499 581 HOH HOH . C 3 HOH A 100 500 582 HOH HOH . C 3 HOH A 101 501 583 HOH HOH . C 3 HOH A 102 502 584 HOH HOH . C 3 HOH A 103 503 585 HOH HOH . C 3 HOH A 104 504 586 HOH HOH . C 3 HOH A 105 505 587 HOH HOH . C 3 HOH A 106 506 588 HOH HOH . C 3 HOH A 107 507 589 HOH HOH . C 3 HOH A 108 508 590 HOH HOH . C 3 HOH A 109 509 591 HOH HOH . C 3 HOH A 110 510 592 HOH HOH . C 3 HOH A 111 511 593 HOH HOH . C 3 HOH A 112 512 594 HOH HOH . C 3 HOH A 113 513 595 HOH HOH . C 3 HOH A 114 514 596 HOH HOH . C 3 HOH A 115 515 597 HOH HOH . C 3 HOH A 116 516 598 HOH HOH . C 3 HOH A 117 517 599 HOH HOH . C 3 HOH A 118 518 600 HOH HOH . C 3 HOH A 119 519 601 HOH HOH . C 3 HOH A 120 520 602 HOH HOH . C 3 HOH A 121 521 603 HOH HOH . C 3 HOH A 122 522 604 HOH HOH . C 3 HOH A 123 523 605 HOH HOH . C 3 HOH A 124 524 606 HOH HOH . C 3 HOH A 125 525 607 HOH HOH . C 3 HOH A 126 526 608 HOH HOH . C 3 HOH A 127 527 609 HOH HOH . C 3 HOH A 128 528 610 HOH HOH . C 3 HOH A 129 529 611 HOH HOH . C 3 HOH A 130 530 612 HOH HOH . C 3 HOH A 131 531 613 HOH HOH . C 3 HOH A 132 532 614 HOH HOH . C 3 HOH A 133 533 615 HOH HOH . C 3 HOH A 134 534 616 HOH HOH . C 3 HOH A 135 535 617 HOH HOH . C 3 HOH A 136 536 618 HOH HOH . C 3 HOH A 137 537 619 HOH HOH . C 3 HOH A 138 538 620 HOH HOH . C 3 HOH A 139 539 621 HOH HOH . C 3 HOH A 140 540 622 HOH HOH . C 3 HOH A 141 541 623 HOH HOH . C 3 HOH A 142 542 624 HOH HOH . C 3 HOH A 143 543 625 HOH HOH . C 3 HOH A 144 544 626 HOH HOH . C 3 HOH A 145 545 627 HOH HOH . C 3 HOH A 146 546 628 HOH HOH . C 3 HOH A 147 547 629 HOH HOH . C 3 HOH A 148 548 630 HOH HOH . C 3 HOH A 149 549 631 HOH HOH . C 3 HOH A 150 550 632 HOH HOH . C 3 HOH A 151 551 633 HOH HOH . C 3 HOH A 152 552 634 HOH HOH . C 3 HOH A 153 553 635 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 O2 U6M . . . B 2 15.916 38.626 37.102 1 10.38 ? O2 U6M 301 A 1 HETATM 2 C C2 U6M . . . B 2 15.574 39.582 36.385 1 11.66 ? C2 U6M 301 A 1 HETATM 3 N N3 U6M . . . B 2 14.258 39.887 36.297 1 10.04 ? N3 U6M 301 A 1 HETATM 4 C C4 U6M . . . B 2 13.845 40.929 35.56 1 13.2 ? C4 U6M 301 A 1 HETATM 5 O O4 U6M . . . B 2 12.598 41.105 35.478 1 13.46 ? O4 U6M 301 A 1 HETATM 6 C C5 U6M . . . B 2 14.716 41.501 34.645 1 15.44 ? C5 U6M 301 A 1 HETATM 7 C C6 U6M . . . B 2 16.058 41.129 34.598 1 14.96 ? C6 U6M 301 A 1 HETATM 8 C C7 U6M . . . B 2 16.799 41.286 33.289 1 16.73 ? C7 U6M 301 A 1 HETATM 9 N N1 U6M . . . B 2 16.53 40.266 35.655 1 12.21 ? N1 U6M 301 A 1 HETATM 10 C C1' U6M . . . B 2 17.978 40.011 35.851 1 11.88 ? C1' U6M 301 A 1 HETATM 11 O O4' U6M . . . B 2 18.208 38.674 35.337 1 11.09 ? O4' U6M 301 A 1 HETATM 12 C C2' U6M . . . B 2 18.473 39.996 37.264 1 13.04 ? C2' U6M 301 A 1 HETATM 13 O O2' U6M . . . B 2 18.928 41.308 37.575 1 17.51 ? O2' U6M 301 A 1 HETATM 14 C C3' U6M . . . B 2 19.629 39.028 37.189 1 11.51 ? C3' U6M 301 A 1 HETATM 15 O O3' U6M . . . B 2 20.758 39.683 36.579 1 11.75 ? O3' U6M 301 A 1 HETATM 16 C C4' U6M . . . B 2 19.132 37.988 36.21 1 9.49 ? C4' U6M 301 A 1 HETATM 17 C C5' U6M . . . B 2 18.386 36.824 36.853 1 12.23 ? C5' U6M 301 A 1 HETATM 18 O O5' U6M . . . B 2 19.431 36.041 37.461 1 10.63 ? O5' U6M 301 A 1 HETATM 19 P P U6M . . . B 2 19.074 34.705 38.298 1 10.62 ? P U6M 301 A 1 HETATM 20 O O3P U6M . . . B 2 18.964 33.592 37.315 1 11.32 ? O3P U6M 301 A 1 HETATM 21 O O1P U6M . . . B 2 17.781 34.892 39.007 1 12.28 ? O1P U6M 301 A 1 HETATM 22 O O2P U6M . . . B 2 20.25 34.57 39.236 1 11.83 ? O2P U6M 301 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #