data_8RZ3 # _model_server_result.job_id dmTlOiNdH2911rQIhqgaMw _model_server_result.datetime_utc '2024-11-23 11:55:09' _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 8rz3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8RZ3 # _exptl.entry_id 8RZ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 607.354 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.94 _cell.angle_gamma 90 _cell.entry_id 8RZ3 _cell.length_a 107.898 _cell.length_b 56.323 _cell.length_c 108.045 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RZ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C17 H27 N3 O17 P2' _chem_comp.formula_weight 607.354 _chem_comp.id UD1 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE _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 C1' C2' UD1 sing 358 n n C1' O1' UD1 sing 359 n n C1' O5' UD1 sing 360 n n C1' H1' UD1 sing 361 n n C2' C3' UD1 sing 362 n n C2' N2' UD1 sing 363 n n C2' H2' UD1 sing 364 n n C3' C4' UD1 sing 365 n n C3' O3' UD1 sing 366 n n C3' H3' UD1 sing 367 n n C4' C5' UD1 sing 368 n n C4' O4' UD1 sing 369 n n C4' H4' UD1 sing 370 n n C5' C6' UD1 sing 371 n n C5' O5' UD1 sing 372 n n C5' H5' UD1 sing 373 n n C6' O6' UD1 sing 374 n n C6' "H6'1" UD1 sing 375 n n C6' "H6'2" UD1 sing 376 n n C7' C8' UD1 sing 377 n n C7' N2' UD1 sing 378 n n C7' O7' UD1 doub 379 n n C8' "H8'1" UD1 sing 380 n n C8' "H8'2" UD1 sing 381 n n C8' "H8'3" UD1 sing 382 n n N2' HN2' UD1 sing 383 n n O1' PB UD1 sing 384 n n O3' HO3' UD1 sing 385 n n O4' HO4' UD1 sing 386 n n O6' HO6' UD1 sing 387 n n N1 C2 UD1 sing 388 n n N1 C6 UD1 sing 389 n n N1 C1B UD1 sing 390 n n C2 N3 UD1 sing 391 n n C2 O2 UD1 doub 392 n n N3 C4 UD1 sing 393 n n N3 HN3 UD1 sing 394 n n C4 C5 UD1 sing 395 n n C4 O4 UD1 doub 396 n n C5 C6 UD1 doub 397 n n C5 H5 UD1 sing 398 n n C6 H6 UD1 sing 399 n n C1B C2B UD1 sing 400 n n C1B O4B UD1 sing 401 n n C1B H1B UD1 sing 402 n n C2B O2' UD1 sing 403 n n C2B C3B UD1 sing 404 n n C2B H2B UD1 sing 405 n n O2' HO2' UD1 sing 406 n n C3B C4B UD1 sing 407 n n C3B O3B UD1 sing 408 n n C3B H3B UD1 sing 409 n n C4B O4B UD1 sing 410 n n C4B C5B UD1 sing 411 n n C4B H4B UD1 sing 412 n n O3B HO3A UD1 sing 413 n n C5B O5B UD1 sing 414 n n C5B "H5'1" UD1 sing 415 n n C5B "H5'2" UD1 sing 416 n n O5B PA UD1 sing 417 n n PA O1A UD1 doub 418 n n PA O2A UD1 sing 419 n n PA O3A UD1 sing 420 n n O2A HOA2 UD1 sing 421 n n O3A PB UD1 sing 422 n n PB O1B UD1 doub 423 n n PB O2B UD1 sing 424 n n O2B HOB2 UD1 sing 425 n n # _atom_sites.entry_id 8RZ3 _atom_sites.fract_transf_matrix[1][1] 0.009268 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000152 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017755 _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] 0.009257 _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 D 2 UD1 A 1 401 4 UD1 UD1 . E 2 UD1 B 1 401 5 UD1 UD1 . F 2 UD1 C 1 401 6 UD1 UD1 . G 3 HOH A 1 501 698 HOH HOH . G 3 HOH A 2 502 711 HOH HOH . G 3 HOH A 3 503 706 HOH HOH . G 3 HOH A 4 504 431 HOH HOH . G 3 HOH A 5 505 705 HOH HOH . G 3 HOH A 6 506 578 HOH HOH . G 3 HOH A 7 507 667 HOH HOH . G 3 HOH A 8 508 607 HOH HOH . G 3 HOH A 9 509 589 HOH HOH . G 3 HOH A 10 510 583 HOH HOH . G 3 HOH A 11 511 486 HOH HOH . G 3 HOH A 12 512 585 HOH HOH . G 3 HOH A 13 513 701 HOH HOH . G 3 HOH A 14 514 580 HOH HOH . G 3 HOH A 15 515 581 HOH HOH . G 3 HOH A 16 516 576 HOH HOH . G 3 HOH A 17 517 708 HOH HOH . G 3 HOH A 18 518 476 HOH HOH . G 3 HOH A 19 519 702 HOH HOH . G 3 HOH A 20 520 596 HOH HOH . G 3 HOH A 21 521 601 HOH HOH . G 3 HOH A 22 522 549 HOH HOH . G 3 HOH A 23 523 713 HOH HOH . G 3 HOH A 24 524 704 HOH HOH . G 3 HOH A 25 525 469 HOH HOH . G 3 HOH A 26 526 609 HOH HOH . G 3 HOH A 27 527 606 HOH HOH . G 3 HOH A 28 528 541 HOH HOH . G 3 HOH A 29 529 595 HOH HOH . G 3 HOH A 30 530 669 HOH HOH . G 3 HOH A 31 531 547 HOH HOH . G 3 HOH A 32 532 611 HOH HOH . G 3 HOH A 33 533 464 HOH HOH . G 3 HOH A 34 534 468 HOH HOH . G 3 HOH A 35 535 539 HOH HOH . G 3 HOH A 36 536 597 HOH HOH . G 3 HOH A 37 537 707 HOH HOH . G 3 HOH A 38 538 673 HOH HOH . G 3 HOH A 39 539 477 HOH HOH . G 3 HOH A 40 540 588 HOH HOH . G 3 HOH A 41 541 615 HOH HOH . G 3 HOH A 42 542 712 HOH HOH . G 3 HOH A 43 543 610 HOH HOH . G 3 HOH A 44 544 470 HOH HOH . G 3 HOH A 45 545 614 HOH HOH . G 3 HOH A 46 546 700 HOH HOH . G 3 HOH A 47 547 148 HOH HOH . G 3 HOH A 48 548 613 HOH HOH . G 3 HOH A 49 549 600 HOH HOH . G 3 HOH A 50 550 699 HOH HOH . G 3 HOH A 51 551 603 HOH HOH . G 3 HOH A 52 552 640 HOH HOH . G 3 HOH A 53 553 584 HOH HOH . G 3 HOH A 54 554 473 HOH HOH . G 3 HOH A 55 555 283 HOH HOH . G 3 HOH A 56 556 651 HOH HOH . G 3 HOH A 57 557 612 HOH HOH . G 3 HOH A 58 558 668 HOH HOH . G 3 HOH A 59 559 474 HOH HOH . G 3 HOH A 60 560 592 HOH HOH . G 3 HOH A 61 561 598 HOH HOH . G 3 HOH A 62 562 666 HOH HOH . H 3 HOH B 1 501 299 HOH HOH . H 3 HOH B 2 502 322 HOH HOH . H 3 HOH B 3 503 680 HOH HOH . H 3 HOH B 4 504 528 HOH HOH . H 3 HOH B 5 505 36 HOH HOH . H 3 HOH B 6 506 553 HOH HOH . H 3 HOH B 7 507 709 HOH HOH . H 3 HOH B 8 508 532 HOH HOH . H 3 HOH B 9 509 681 HOH HOH . H 3 HOH B 10 510 379 HOH HOH . H 3 HOH B 11 511 642 HOH HOH . H 3 HOH B 12 512 644 HOH HOH . H 3 HOH B 13 513 525 HOH HOH . H 3 HOH B 14 514 555 HOH HOH . H 3 HOH B 15 515 621 HOH HOH . H 3 HOH B 16 516 490 HOH HOH . H 3 HOH B 17 517 526 HOH HOH . H 3 HOH B 18 518 627 HOH HOH . H 3 HOH B 19 519 684 HOH HOH . H 3 HOH B 20 520 685 HOH HOH . H 3 HOH B 21 521 626 HOH HOH . H 3 HOH B 22 522 513 HOH HOH . H 3 HOH B 23 523 560 HOH HOH . H 3 HOH B 24 524 635 HOH HOH . H 3 HOH B 25 525 432 HOH HOH . H 3 HOH B 26 526 562 HOH HOH . H 3 HOH B 27 527 623 HOH HOH . H 3 HOH B 28 528 312 HOH HOH . H 3 HOH B 29 529 634 HOH HOH . H 3 HOH B 30 530 636 HOH HOH . H 3 HOH B 31 531 682 HOH HOH . H 3 HOH B 32 532 638 HOH HOH . H 3 HOH B 33 533 622 HOH HOH . H 3 HOH B 34 534 683 HOH HOH . H 3 HOH B 35 535 639 HOH HOH . H 3 HOH B 36 536 524 HOH HOH . H 3 HOH B 37 537 437 HOH HOH . H 3 HOH B 38 538 678 HOH HOH . H 3 HOH B 39 539 629 HOH HOH . H 3 HOH B 40 540 643 HOH HOH . H 3 HOH B 41 541 533 HOH HOH . H 3 HOH B 42 542 625 HOH HOH . H 3 HOH B 43 543 658 HOH HOH . H 3 HOH B 44 544 616 HOH HOH . H 3 HOH B 45 545 376 HOH HOH . H 3 HOH B 46 546 569 HOH HOH . H 3 HOH B 47 547 530 HOH HOH . H 3 HOH B 48 548 620 HOH HOH . H 3 HOH B 49 549 632 HOH HOH . H 3 HOH B 50 550 675 HOH HOH . H 3 HOH B 51 551 619 HOH HOH . H 3 HOH B 52 552 558 HOH HOH . H 3 HOH B 53 553 637 HOH HOH . H 3 HOH B 54 554 214 HOH HOH . H 3 HOH B 55 555 538 HOH HOH . H 3 HOH B 56 556 95 HOH HOH . H 3 HOH B 57 557 628 HOH HOH . H 3 HOH B 58 558 679 HOH HOH . H 3 HOH B 59 559 633 HOH HOH . H 3 HOH B 60 560 660 HOH HOH . H 3 HOH B 61 561 563 HOH HOH . H 3 HOH B 62 562 412 HOH HOH . H 3 HOH B 63 563 630 HOH HOH . H 3 HOH B 64 564 677 HOH HOH . H 3 HOH B 65 565 641 HOH HOH . H 3 HOH B 66 566 565 HOH HOH . I 3 HOH C 1 501 692 HOH HOH . I 3 HOH C 2 502 689 HOH HOH . I 3 HOH C 3 503 442 HOH HOH . I 3 HOH C 4 504 686 HOH HOH . I 3 HOH C 5 505 695 HOH HOH . I 3 HOH C 6 506 691 HOH HOH . I 3 HOH C 7 507 697 HOH HOH . I 3 HOH C 8 508 531 HOH HOH . I 3 HOH C 9 509 511 HOH HOH . I 3 HOH C 10 510 571 HOH HOH . I 3 HOH C 11 511 661 HOH HOH . I 3 HOH C 12 512 665 HOH HOH . I 3 HOH C 13 513 465 HOH HOH . I 3 HOH C 14 514 56 HOH HOH . I 3 HOH C 15 515 338 HOH HOH . I 3 HOH C 16 516 566 HOH HOH . I 3 HOH C 17 517 694 HOH HOH . I 3 HOH C 18 518 690 HOH HOH . I 3 HOH C 19 519 55 HOH HOH . I 3 HOH C 20 520 572 HOH HOH . I 3 HOH C 21 521 573 HOH HOH . I 3 HOH C 22 522 657 HOH HOH . I 3 HOH C 23 523 655 HOH HOH . I 3 HOH C 24 524 462 HOH HOH . I 3 HOH C 25 525 348 HOH HOH . I 3 HOH C 26 526 688 HOH HOH . I 3 HOH C 27 527 664 HOH HOH . I 3 HOH C 28 528 499 HOH HOH . I 3 HOH C 29 529 557 HOH HOH . I 3 HOH C 30 530 647 HOH HOH . I 3 HOH C 31 531 645 HOH HOH . I 3 HOH C 32 532 567 HOH HOH . I 3 HOH C 33 533 650 HOH HOH . I 3 HOH C 34 534 570 HOH HOH . I 3 HOH C 35 535 439 HOH HOH . I 3 HOH C 36 536 521 HOH HOH . I 3 HOH C 37 537 212 HOH HOH . I 3 HOH C 38 538 649 HOH HOH . I 3 HOH C 39 539 696 HOH HOH . I 3 HOH C 40 540 522 HOH HOH . I 3 HOH C 41 541 536 HOH HOH . I 3 HOH C 42 542 311 HOH HOH . I 3 HOH C 43 543 295 HOH HOH . I 3 HOH C 44 544 646 HOH HOH . I 3 HOH C 45 545 158 HOH HOH . I 3 HOH C 46 546 687 HOH HOH . I 3 HOH C 47 547 653 HOH HOH . I 3 HOH C 48 548 518 HOH HOH . I 3 HOH C 49 549 618 HOH HOH . I 3 HOH C 50 550 365 HOH HOH . I 3 HOH C 51 551 652 HOH HOH . I 3 HOH C 52 552 693 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 C C1' UD1 . . . D 2 18.463 6.22 1.815 1 52.26 ? C1' UD1 401 A 1 HETATM 2 C C2' UD1 . . . D 2 18.183 5.198 2.893 1 55.43 ? C2' UD1 401 A 1 HETATM 3 C C3' UD1 . . . D 2 17.989 3.89 2.207 1 51.53 ? C3' UD1 401 A 1 HETATM 4 C C4' UD1 . . . D 2 16.809 3.92 1.344 1 51.72 ? C4' UD1 401 A 1 HETATM 5 C C5' UD1 . . . D 2 16.876 5.076 0.369 1 51.68 ? C5' UD1 401 A 1 HETATM 6 C C6' UD1 . . . D 2 15.54 5.228 -0.262 1 48.33 ? C6' UD1 401 A 1 HETATM 7 C C7' UD1 . . . D 2 19.086 5.305 5.29 1 56.29 ? C7' UD1 401 A 1 HETATM 8 C C8' UD1 . . . D 2 17.628 5.478 5.764 1 51.54 ? C8' UD1 401 A 1 HETATM 9 N N2' UD1 . . . D 2 19.335 5.175 3.85 1 53.44 ? N2' UD1 401 A 1 HETATM 10 O O1' UD1 . . . D 2 19.489 5.712 0.986 1 54.62 ? O1' UD1 401 A 1 HETATM 11 O O3' UD1 . . . D 2 17.798 2.803 3.16 1 48.5 ? O3' UD1 401 A 1 HETATM 12 O O4' UD1 . . . D 2 16.763 2.683 0.578 1 51.96 ? O4' UD1 401 A 1 HETATM 13 O O5' UD1 . . . D 2 17.257 6.346 1.041 1 52.33 ? O5' UD1 401 A 1 HETATM 14 O O6' UD1 . . . D 2 15.634 6.232 -1.23 1 48.61 ? O6' UD1 401 A 1 HETATM 15 O O7' UD1 . . . D 2 19.958 5.283 6.096 1 58.31 ? O7' UD1 401 A 1 HETATM 16 N N1 UD1 . . . D 2 26.894 5.08 -3.944 1 48.26 ? N1 UD1 401 A 1 HETATM 17 C C2 UD1 . . . D 2 27.903 5.102 -5.053 1 47.46 ? C2 UD1 401 A 1 HETATM 18 N N3 UD1 . . . D 2 29.257 5.722 -4.648 1 49.49 ? N3 UD1 401 A 1 HETATM 19 C C4 UD1 . . . D 2 29.49 6.234 -3.318 1 47.43 ? C4 UD1 401 A 1 HETATM 20 C C5 UD1 . . . D 2 28.466 6.187 -2.309 1 49.59 ? C5 UD1 401 A 1 HETATM 21 C C6 UD1 . . . D 2 27.156 5.62 -2.617 1 50.02 ? C6 UD1 401 A 1 HETATM 22 O O2 UD1 . . . D 2 27.656 4.66 -6.127 1 48.98 ? O2 UD1 401 A 1 HETATM 23 O O4 UD1 . . . D 2 30.534 6.705 -3.066 1 50.8 ? O4 UD1 401 A 1 HETATM 24 C C1B UD1 . . . D 2 25.577 4.516 -4.261 1 49.65 ? C1B UD1 401 A 1 HETATM 25 C C2B UD1 . . . D 2 25.344 3.137 -3.592 1 47.18 ? C2B UD1 401 A 1 HETATM 26 O O2' UD1 . . . D 2 25.689 2.131 -4.402 1 45.88 ? O2' UD1 401 A 1 HETATM 27 C C3B UD1 . . . D 2 23.785 3.154 -3.442 1 48.07 ? C3B UD1 401 A 1 HETATM 28 C C4B UD1 . . . D 2 23.478 4.381 -3.175 1 49.62 ? C4B UD1 401 A 1 HETATM 29 O O4B UD1 . . . D 2 24.708 5.326 -3.741 1 52.11 ? O4B UD1 401 A 1 HETATM 30 O O3B UD1 . . . D 2 23.198 2.741 -4.732 1 43.23 ? O3B UD1 401 A 1 HETATM 31 C C5B UD1 . . . D 2 23.359 4.595 -1.688 1 47.4 ? C5B UD1 401 A 1 HETATM 32 O O5B UD1 . . . D 2 22.011 4.174 -1.395 1 53.26 ? O5B UD1 401 A 1 HETATM 33 P PA UD1 . . . D 2 21.717 3.539 0.08 1 45.49 ? PA UD1 401 A 1 HETATM 34 O O1A UD1 . . . D 2 20.275 3.137 0.133 1 48.59 -1 O1A UD1 401 A 1 HETATM 35 O O2A UD1 . . . D 2 22.629 2.382 0.356 1 49.35 ? O2A UD1 401 A 1 HETATM 36 O O3A UD1 . . . D 2 22.072 4.728 1.197 1 51.68 ? O3A UD1 401 A 1 HETATM 37 P PB UD1 . . . D 2 21.113 6.085 1.268 1 52.03 ? PB UD1 401 A 1 HETATM 38 O O1B UD1 . . . D 2 21.59 6.992 0.195 1 51.64 -1 O1B UD1 401 A 1 HETATM 39 O O2B UD1 . . . D 2 21.294 6.595 2.659 1 56.37 ? O2B UD1 401 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #