data_3W07 # _model_server_result.job_id Q4R5yUXFZRTYqODrx0Wfuw _model_server_result.datetime_utc '2025-01-25 07:29:10' _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 3w07 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3W07 # _exptl.entry_id 3W07 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 90 _cell.entry_id 3W07 _cell.length_a 57.943 _cell.length_b 103.233 _cell.length_c 73.567 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3W07 _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 _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 0 103.233 73.567 # _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 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 343 n n N1 C6 U5P sing 344 n n N1 C1' U5P sing 345 n n C2 N3 U5P sing 346 n n C2 O2 U5P doub 347 n n N3 C4 U5P sing 348 n n N3 HN3 U5P sing 349 n n C4 C5 U5P sing 350 n n C4 O4 U5P doub 351 n n C5 C6 U5P doub 352 n n C5 H5 U5P sing 353 n n C6 H6 U5P sing 354 n n C1' C2' U5P sing 355 n n C1' O4' U5P sing 356 n n C1' H1' U5P sing 357 n n C2' O2' U5P sing 358 n n C2' C3' U5P sing 359 n n C2' H2' U5P sing 360 n n O2' HO2' U5P sing 361 n n C3' C4' U5P sing 362 n n C3' O3' U5P sing 363 n n C3' H3' U5P sing 364 n n C4' O4' U5P sing 365 n n C4' C5' U5P sing 366 n n C4' H4' U5P sing 367 n n O3' HO3' U5P sing 368 n n C5' O5' U5P sing 369 n n C5' "H5'1" U5P sing 370 n n C5' "H5'2" U5P sing 371 n n O5' P U5P sing 372 n n P O1P U5P doub 373 n n P O2P U5P sing 374 n n P O3P U5P sing 375 n n O2P HOP2 U5P sing 376 n n O3P HOP3 U5P sing 377 n n # _atom_sites.entry_id 3W07 _atom_sites.fract_transf_matrix[1][1] 0.017258 _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] 0.009687 _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] 0.013593 _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 U5P A 1 301 301 U5P U5P . C 3 GOL A 1 302 311 GOL GOL . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 404 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 HOH HOH . D 4 HOH A 10 410 410 HOH HOH . D 4 HOH A 11 411 411 HOH HOH . D 4 HOH A 12 412 412 HOH HOH . D 4 HOH A 13 413 413 HOH HOH . D 4 HOH A 14 414 414 HOH HOH . D 4 HOH A 15 415 415 HOH HOH . D 4 HOH A 16 416 416 HOH HOH . D 4 HOH A 17 417 501 HOH HOH . D 4 HOH A 18 418 502 HOH HOH . D 4 HOH A 19 419 503 HOH HOH . D 4 HOH A 20 420 504 HOH HOH . D 4 HOH A 21 421 505 HOH HOH . D 4 HOH A 22 422 506 HOH HOH . D 4 HOH A 23 423 507 HOH HOH . D 4 HOH A 24 424 508 HOH HOH . D 4 HOH A 25 425 509 HOH HOH . D 4 HOH A 26 426 510 HOH HOH . D 4 HOH A 27 427 511 HOH HOH . D 4 HOH A 28 428 512 HOH HOH . D 4 HOH A 29 429 513 HOH HOH . D 4 HOH A 30 430 514 HOH HOH . D 4 HOH A 31 431 515 HOH HOH . D 4 HOH A 32 432 516 HOH HOH . D 4 HOH A 33 433 517 HOH HOH . D 4 HOH A 34 434 518 HOH HOH . D 4 HOH A 35 435 519 HOH HOH . D 4 HOH A 36 436 520 HOH HOH . D 4 HOH A 37 437 521 HOH HOH . D 4 HOH A 38 438 522 HOH HOH . D 4 HOH A 39 439 523 HOH HOH . D 4 HOH A 40 440 524 HOH HOH . D 4 HOH A 41 441 525 HOH HOH . D 4 HOH A 42 442 526 HOH HOH . D 4 HOH A 43 443 527 HOH HOH . D 4 HOH A 44 444 528 HOH HOH . D 4 HOH A 45 445 529 HOH HOH . D 4 HOH A 46 446 530 HOH HOH . D 4 HOH A 47 447 531 HOH HOH . D 4 HOH A 48 448 532 HOH HOH . D 4 HOH A 49 449 533 HOH HOH . D 4 HOH A 50 450 534 HOH HOH . D 4 HOH A 51 451 535 HOH HOH . D 4 HOH A 52 452 536 HOH HOH . D 4 HOH A 53 453 537 HOH HOH . D 4 HOH A 54 454 538 HOH HOH . D 4 HOH A 55 455 539 HOH HOH . D 4 HOH A 56 456 540 HOH HOH . D 4 HOH A 57 457 541 HOH HOH . D 4 HOH A 58 458 542 HOH HOH . D 4 HOH A 59 459 543 HOH HOH . D 4 HOH A 60 460 544 HOH HOH . D 4 HOH A 61 461 545 HOH HOH . D 4 HOH A 62 462 546 HOH HOH . D 4 HOH A 63 463 547 HOH HOH . D 4 HOH A 64 464 548 HOH HOH . D 4 HOH A 65 465 549 HOH HOH . D 4 HOH A 66 466 550 HOH HOH . D 4 HOH A 67 467 551 HOH HOH . D 4 HOH A 68 468 552 HOH HOH . D 4 HOH A 69 469 553 HOH HOH . D 4 HOH A 70 470 554 HOH HOH . D 4 HOH A 71 471 555 HOH HOH . D 4 HOH A 72 472 556 HOH HOH . D 4 HOH A 73 473 557 HOH HOH . D 4 HOH A 74 474 558 HOH HOH . D 4 HOH A 75 475 559 HOH HOH . D 4 HOH A 76 476 560 HOH HOH . D 4 HOH A 77 477 561 HOH HOH . D 4 HOH A 78 478 562 HOH HOH . D 4 HOH A 79 479 563 HOH HOH . D 4 HOH A 80 480 564 HOH HOH . D 4 HOH A 81 481 565 HOH HOH . D 4 HOH A 82 482 566 HOH HOH . D 4 HOH A 83 483 567 HOH HOH . D 4 HOH A 84 484 568 HOH HOH . D 4 HOH A 85 485 569 HOH HOH . D 4 HOH A 86 486 570 HOH HOH . D 4 HOH A 87 487 571 HOH HOH . D 4 HOH A 88 488 572 HOH HOH . D 4 HOH A 89 489 573 HOH HOH . D 4 HOH A 90 490 574 HOH HOH . D 4 HOH A 91 491 575 HOH HOH . D 4 HOH A 92 492 576 HOH HOH . D 4 HOH A 93 493 577 HOH HOH . D 4 HOH A 94 494 578 HOH HOH . D 4 HOH A 95 495 579 HOH HOH . D 4 HOH A 96 496 580 HOH HOH . D 4 HOH A 97 497 581 HOH HOH . D 4 HOH A 98 498 582 HOH HOH . D 4 HOH A 99 499 583 HOH HOH . D 4 HOH A 100 500 584 HOH HOH . D 4 HOH A 101 501 585 HOH HOH . D 4 HOH A 102 502 586 HOH HOH . D 4 HOH A 103 503 587 HOH HOH . D 4 HOH A 104 504 588 HOH HOH . D 4 HOH A 105 505 589 HOH HOH . D 4 HOH A 106 506 590 HOH HOH . D 4 HOH A 107 507 591 HOH HOH . D 4 HOH A 108 508 592 HOH HOH . D 4 HOH A 109 509 593 HOH HOH . D 4 HOH A 110 510 594 HOH HOH . D 4 HOH A 111 511 595 HOH HOH . D 4 HOH A 112 512 596 HOH HOH . D 4 HOH A 113 513 597 HOH HOH . D 4 HOH A 114 514 598 HOH HOH . D 4 HOH A 115 515 599 HOH HOH . D 4 HOH A 116 516 600 HOH HOH . D 4 HOH A 117 517 601 HOH HOH . D 4 HOH A 118 518 602 HOH HOH . D 4 HOH A 119 519 603 HOH HOH . D 4 HOH A 120 520 604 HOH HOH . D 4 HOH A 121 521 605 HOH HOH . D 4 HOH A 122 522 606 HOH HOH . D 4 HOH A 123 523 607 HOH HOH . D 4 HOH A 124 524 608 HOH HOH . D 4 HOH A 125 525 609 HOH HOH . D 4 HOH A 126 526 610 HOH HOH . D 4 HOH A 127 527 611 HOH HOH . D 4 HOH A 128 528 612 HOH HOH . D 4 HOH A 129 529 613 HOH HOH . D 4 HOH A 130 530 614 HOH HOH . D 4 HOH A 131 531 615 HOH HOH . D 4 HOH A 132 532 616 HOH HOH . D 4 HOH A 133 533 617 HOH HOH . D 4 HOH A 134 534 618 HOH HOH . D 4 HOH A 135 535 619 HOH HOH . D 4 HOH A 136 536 620 HOH HOH . D 4 HOH A 137 537 621 HOH HOH . D 4 HOH A 138 538 622 HOH HOH . D 4 HOH A 139 539 623 HOH HOH . D 4 HOH A 140 540 624 HOH HOH . D 4 HOH A 141 541 625 HOH HOH . D 4 HOH A 142 542 626 HOH HOH . D 4 HOH A 143 543 627 HOH HOH . D 4 HOH A 144 544 628 HOH HOH . D 4 HOH A 145 545 629 HOH HOH . D 4 HOH A 146 546 630 HOH HOH . D 4 HOH A 147 547 631 HOH HOH . D 4 HOH A 148 548 632 HOH HOH . D 4 HOH A 149 549 633 HOH HOH . D 4 HOH A 150 550 634 HOH HOH . D 4 HOH A 151 551 635 HOH HOH . D 4 HOH A 152 552 636 HOH HOH . D 4 HOH A 153 553 637 HOH HOH . D 4 HOH A 154 554 638 HOH HOH . D 4 HOH A 155 555 639 HOH HOH . D 4 HOH A 156 556 640 HOH HOH . D 4 HOH A 157 557 641 HOH HOH . D 4 HOH A 158 558 642 HOH HOH . D 4 HOH A 159 559 643 HOH HOH . D 4 HOH A 160 560 644 HOH HOH . D 4 HOH A 161 561 645 HOH HOH . D 4 HOH A 162 562 646 HOH HOH . D 4 HOH A 163 563 647 HOH HOH . D 4 HOH A 164 564 648 HOH HOH . D 4 HOH A 165 565 649 HOH HOH . D 4 HOH A 166 566 650 HOH HOH . D 4 HOH A 167 567 651 HOH HOH . D 4 HOH A 168 568 652 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 U5P . . . B 2 16.613 40.22 35.865 1 7.66 ? N1 U5P 301 A 1 HETATM 2 C C2 U5P . . . B 2 15.66 39.466 36.532 1 6.98 ? C2 U5P 301 A 1 HETATM 3 N N3 U5P . . . B 2 14.364 39.81 36.348 1 7.35 ? N3 U5P 301 A 1 HETATM 4 C C4 U5P . . . B 2 13.908 40.837 35.542 1 8.77 ? C4 U5P 301 A 1 HETATM 5 C C5 U5P . . . B 2 14.901 41.59 34.897 1 10.96 ? C5 U5P 301 A 1 HETATM 6 C C6 U5P . . . B 2 16.218 41.237 34.962 1 11.59 ? C6 U5P 301 A 1 HETATM 7 O O2 U5P . . . B 2 15.97 38.516 37.228 1 7.54 ? O2 U5P 301 A 1 HETATM 8 O O4 U5P . . . B 2 12.673 41.002 35.475 1 9.67 ? O4 U5P 301 A 1 HETATM 9 C C1' U5P . . . B 2 18.024 39.899 35.971 1 7.23 ? C1' U5P 301 A 1 HETATM 10 C C2' U5P . . . B 2 18.614 39.902 37.37 1 7.94 ? C2' U5P 301 A 1 HETATM 11 O O2' U5P . . . B 2 19.103 41.159 37.737 1 12.1 ? O2' U5P 301 A 1 HETATM 12 C C3' U5P . . . B 2 19.743 38.895 37.221 1 6.99 ? C3' U5P 301 A 1 HETATM 13 C C4' U5P . . . B 2 19.156 37.886 36.272 1 7 ? C4' U5P 301 A 1 HETATM 14 O O3' U5P . . . B 2 20.841 39.553 36.594 1 7.69 ? O3' U5P 301 A 1 HETATM 15 O O4' U5P . . . B 2 18.26 38.616 35.418 1 6.93 ? O4' U5P 301 A 1 HETATM 16 C C5' U5P . . . B 2 18.44 36.736 36.958 1 8.14 ? C5' U5P 301 A 1 HETATM 17 O O5' U5P . . . B 2 19.46 35.943 37.515 1 8.07 ? O5' U5P 301 A 1 HETATM 18 P P U5P . . . B 2 19.129 34.601 38.352 1 7.26 ? P U5P 301 A 1 HETATM 19 O O1P U5P . . . B 2 17.818 34.81 39.086 1 7.68 ? O1P U5P 301 A 1 HETATM 20 O O2P U5P . . . B 2 20.327 34.495 39.257 1 7.71 ? O2P U5P 301 A 1 HETATM 21 O O3P U5P . . . B 2 19.04 33.47 37.367 1 7.35 ? O3P U5P 301 A 1 HETATM 22 H H1' U5P . . . B 2 18.521 40.552 35.435 1 8.67 ? H1' U5P 301 A 1 HETATM 23 H H4' U5P . . . B 2 19.879 37.518 35.722 1 8.4 ? H4' U5P 301 A 1 HETATM 24 H "H5'1" U5P . . . B 2 17.846 37.067 37.651 1 9.77 ? "H5'1" U5P 301 A 1 HETATM 25 H "H5'2" U5P . . . B 2 17.919 36.226 36.319 1 9.77 ? "H5'2" U5P 301 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #