data_8DVZ # _model_server_result.job_id VLRTGEmfLRUndP6AT60fjA _model_server_result.datetime_utc '2024-11-27 18:01:23' _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 8dvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8DVZ # _exptl.entry_id 8DVZ _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-ACETYLGALACTOSAMINE _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 120 _cell.entry_id 8DVZ _cell.length_a 97.971 _cell.length_b 97.971 _cell.length_c 100.768 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _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 'C17 H27 N3 O17 P2' _chem_comp.formula_weight 607.354 _chem_comp.id UD2 _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' # 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 O4 C4 UD2 doub 358 n n C4 N3 UD2 sing 359 n n C4 C5 UD2 sing 360 n n N3 C2 UD2 sing 361 n n C5 C6 UD2 doub 362 n n C2 O2 UD2 doub 363 n n C2 N1 UD2 sing 364 n n C6 N1 UD2 sing 365 n n N1 C1B UD2 sing 366 n n O2' C2B UD2 sing 367 n n C1B C2B UD2 sing 368 n n C1B O4B UD2 sing 369 n n C2B C3B UD2 sing 370 n n O2A PA UD2 doub 371 n n O4B C4B UD2 sing 372 n n O6' C6' UD2 sing 373 n n O5B PA UD2 sing 374 n n O5B C5B UD2 sing 375 n n C3B C4B UD2 sing 376 n n C3B O3B UD2 sing 377 n n PA O3A UD2 sing 378 n n PA O1A UD2 sing 379 n n C4B C5B UD2 sing 380 n n O3A PB UD2 sing 381 n n C6' C5' UD2 sing 382 n n O2B PB UD2 doub 383 n n C5' O5' UD2 sing 384 n n C5' C4' UD2 sing 385 n n PB O1B UD2 sing 386 n n PB O1' UD2 sing 387 n n O5' C1' UD2 sing 388 n n C4' O4' UD2 sing 389 n n C4' C3' UD2 sing 390 n n O1' C1' UD2 sing 391 n n C1' C2' UD2 sing 392 n n C3' C2' UD2 sing 393 n n C3' O3' UD2 sing 394 n n C2' N2' UD2 sing 395 n n N2' C7' UD2 sing 396 n n C7' O7' UD2 doub 397 n n C7' C8' UD2 sing 398 n n C1' H1' UD2 sing 399 n n C2' H2' UD2 sing 400 n n C3' H3' UD2 sing 401 n n C4' H4' UD2 sing 402 n n C5' H5' UD2 sing 403 n n C6' "H6'1" UD2 sing 404 n n C6' "H6'2" UD2 sing 405 n n C8' "H8'1" UD2 sing 406 n n C8' "H8'2" UD2 sing 407 n n C8' "H8'3" UD2 sing 408 n n N2' HN2' UD2 sing 409 n n O3' HO3' UD2 sing 410 n n O4' HO4' UD2 sing 411 n n O6' HO6' UD2 sing 412 n n N3 HN3 UD2 sing 413 n n C5 H5 UD2 sing 414 n n C6 H6 UD2 sing 415 n n C1B H1B UD2 sing 416 n n C2B H2B UD2 sing 417 n n O2' HO2' UD2 sing 418 n n C3B H3B UD2 sing 419 n n C4B H4B UD2 sing 420 n n O3B HO3A UD2 sing 421 n n C5B "H5'1" UD2 sing 422 n n C5B "H5'2" UD2 sing 423 n n O1A HOA2 UD2 sing 424 n n O1B HOB2 UD2 sing 425 n n # _atom_sites.entry_id 8DVZ _atom_sites.fract_transf_matrix[1][1] 0.010207 _atom_sites.fract_transf_matrix[1][2] 0.005893 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011786 _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] 0.009924 _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 UD2 A 1 401 401 UD2 UD2 . C 3 HOH A 1 501 14 HOH HOH . C 3 HOH A 2 502 49 HOH HOH . C 3 HOH A 3 503 111 HOH HOH . C 3 HOH A 4 504 40 HOH HOH . C 3 HOH A 5 505 9 HOH HOH . C 3 HOH A 6 506 37 HOH HOH . C 3 HOH A 7 507 67 HOH HOH . C 3 HOH A 8 508 20 HOH HOH . C 3 HOH A 9 509 28 HOH HOH . C 3 HOH A 10 510 15 HOH HOH . C 3 HOH A 11 511 51 HOH HOH . C 3 HOH A 12 512 89 HOH HOH . C 3 HOH A 13 513 124 HOH HOH . C 3 HOH A 14 514 73 HOH HOH . C 3 HOH A 15 515 78 HOH HOH . C 3 HOH A 16 516 4 HOH HOH . C 3 HOH A 17 517 17 HOH HOH . C 3 HOH A 18 518 101 HOH HOH . C 3 HOH A 19 519 13 HOH HOH . C 3 HOH A 20 520 10 HOH HOH . C 3 HOH A 21 521 109 HOH HOH . C 3 HOH A 22 522 23 HOH HOH . C 3 HOH A 23 523 21 HOH HOH . C 3 HOH A 24 524 65 HOH HOH . C 3 HOH A 25 525 32 HOH HOH . C 3 HOH A 26 526 6 HOH HOH . C 3 HOH A 27 527 2 HOH HOH . C 3 HOH A 28 528 79 HOH HOH . C 3 HOH A 29 529 114 HOH HOH . C 3 HOH A 30 530 47 HOH HOH . C 3 HOH A 31 531 11 HOH HOH . C 3 HOH A 32 532 62 HOH HOH . C 3 HOH A 33 533 97 HOH HOH . C 3 HOH A 34 534 12 HOH HOH . C 3 HOH A 35 535 38 HOH HOH . C 3 HOH A 36 536 120 HOH HOH . C 3 HOH A 37 537 1 HOH HOH . C 3 HOH A 38 538 34 HOH HOH . C 3 HOH A 39 539 31 HOH HOH . C 3 HOH A 40 540 57 HOH HOH . C 3 HOH A 41 541 59 HOH HOH . C 3 HOH A 42 542 24 HOH HOH . C 3 HOH A 43 543 35 HOH HOH . C 3 HOH A 44 544 107 HOH HOH . C 3 HOH A 45 545 44 HOH HOH . C 3 HOH A 46 546 8 HOH HOH . C 3 HOH A 47 547 50 HOH HOH . C 3 HOH A 48 548 7 HOH HOH . C 3 HOH A 49 549 5 HOH HOH . C 3 HOH A 50 550 105 HOH HOH . C 3 HOH A 51 551 45 HOH HOH . C 3 HOH A 52 552 33 HOH HOH . C 3 HOH A 53 553 113 HOH HOH . C 3 HOH A 54 554 60 HOH HOH . C 3 HOH A 55 555 72 HOH HOH . C 3 HOH A 56 556 19 HOH HOH . C 3 HOH A 57 557 16 HOH HOH . C 3 HOH A 58 558 26 HOH HOH . C 3 HOH A 59 559 52 HOH HOH . C 3 HOH A 60 560 25 HOH HOH . C 3 HOH A 61 561 94 HOH HOH . C 3 HOH A 62 562 3 HOH HOH . C 3 HOH A 63 563 71 HOH HOH . C 3 HOH A 64 564 121 HOH HOH . C 3 HOH A 65 565 29 HOH HOH . C 3 HOH A 66 566 39 HOH HOH . C 3 HOH A 67 567 22 HOH HOH . C 3 HOH A 68 568 48 HOH HOH . C 3 HOH A 69 569 54 HOH HOH . C 3 HOH A 70 570 108 HOH HOH . C 3 HOH A 71 571 95 HOH HOH . C 3 HOH A 72 572 127 HOH HOH . C 3 HOH A 73 573 90 HOH HOH . C 3 HOH A 74 574 83 HOH HOH . C 3 HOH A 75 575 77 HOH HOH . C 3 HOH A 76 576 82 HOH HOH . C 3 HOH A 77 577 46 HOH HOH . C 3 HOH A 78 578 30 HOH HOH . C 3 HOH A 79 579 74 HOH HOH . C 3 HOH A 80 580 70 HOH HOH . C 3 HOH A 81 581 85 HOH HOH . C 3 HOH A 82 582 56 HOH HOH . C 3 HOH A 83 583 36 HOH HOH . C 3 HOH A 84 584 41 HOH HOH . C 3 HOH A 85 585 64 HOH HOH . C 3 HOH A 86 586 27 HOH HOH . C 3 HOH A 87 587 66 HOH HOH . C 3 HOH A 88 588 58 HOH HOH . C 3 HOH A 89 589 86 HOH HOH . C 3 HOH A 90 590 42 HOH HOH . C 3 HOH A 91 591 106 HOH HOH . C 3 HOH A 92 592 98 HOH HOH . C 3 HOH A 93 593 123 HOH HOH . C 3 HOH A 94 594 118 HOH HOH . C 3 HOH A 95 595 18 HOH HOH . C 3 HOH A 96 596 76 HOH HOH . C 3 HOH A 97 597 99 HOH HOH . C 3 HOH A 98 598 125 HOH HOH . C 3 HOH A 99 599 80 HOH HOH . C 3 HOH A 100 600 115 HOH HOH . C 3 HOH A 101 601 87 HOH HOH . C 3 HOH A 102 602 110 HOH HOH . C 3 HOH A 103 603 61 HOH HOH . C 3 HOH A 104 604 81 HOH HOH . C 3 HOH A 105 605 96 HOH HOH . C 3 HOH A 106 606 126 HOH HOH . C 3 HOH A 107 607 100 HOH HOH . C 3 HOH A 108 608 75 HOH HOH . C 3 HOH A 109 609 84 HOH HOH . C 3 HOH A 110 610 119 HOH HOH . C 3 HOH A 111 611 122 HOH HOH . C 3 HOH A 112 612 68 HOH HOH . C 3 HOH A 113 613 69 HOH HOH . C 3 HOH A 114 614 88 HOH HOH . C 3 HOH A 115 615 102 HOH HOH . C 3 HOH A 116 616 116 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' UD2 . . . B 2 30.304 -30.713 -13.218 1 50.97 ? C1' UD2 401 A 1 HETATM 2 C C2' UD2 . . . B 2 29.978 -31.157 -14.652 1 38.82 ? C2' UD2 401 A 1 HETATM 3 C C3' UD2 . . . B 2 30.905 -32.264 -15.086 1 38.48 ? C3' UD2 401 A 1 HETATM 4 C C4' UD2 . . . B 2 32.366 -31.907 -14.799 1 45.24 ? C4' UD2 401 A 1 HETATM 5 C C5' UD2 . . . B 2 32.59 -31.452 -13.354 1 47.95 ? C5' UD2 401 A 1 HETATM 6 C C6' UD2 . . . B 2 34.042 -31.09 -13.089 1 44.82 ? C6' UD2 401 A 1 HETATM 7 C C7' UD2 . . . B 2 27.541 -30.882 -15.229 1 49.26 ? C7' UD2 401 A 1 HETATM 8 C C8' UD2 . . . B 2 27.721 -29.477 -15.761 1 37.91 ? C8' UD2 401 A 1 HETATM 9 N N2' UD2 . . . B 2 28.606 -31.59 -14.751 1 49.88 ? N2' UD2 401 A 1 HETATM 10 O O1' UD2 . . . B 2 30.115 -31.505 -12.062 1 57.86 ? O1' UD2 401 A 1 HETATM 11 O O3' UD2 . . . B 2 30.758 -32.483 -16.458 1 46.82 ? O3' UD2 401 A 1 HETATM 12 O O4' UD2 . . . B 2 32.673 -30.863 -15.697 1 43.93 ? O4' UD2 401 A 1 HETATM 13 O O5' UD2 . . . B 2 31.681 -30.369 -13.114 1 41.09 ? O5' UD2 401 A 1 HETATM 14 O O6' UD2 . . . B 2 34.723 -30.472 -14.151 1 49.93 ? O6' UD2 401 A 1 HETATM 15 O O7' UD2 . . . B 2 26.425 -31.394 -15.272 1 57.2 ? O7' UD2 401 A 1 HETATM 16 N N1 UD2 . . . B 2 30.832 -39.748 -7.277 1 63.16 ? N1 UD2 401 A 1 HETATM 17 C C2 UD2 . . . B 2 31.097 -40.524 -6.159 1 70.98 ? C2 UD2 401 A 1 HETATM 18 N N3 UD2 . . . B 2 30.044 -41.24 -5.66 1 62.87 ? N3 UD2 401 A 1 HETATM 19 C C4 UD2 . . . B 2 28.748 -41.276 -6.167 1 70.69 ? C4 UD2 401 A 1 HETATM 20 C C5 UD2 . . . B 2 28.566 -40.452 -7.337 1 72.44 ? C5 UD2 401 A 1 HETATM 21 C C6 UD2 . . . B 2 29.584 -39.741 -7.838 1 72.38 ? C6 UD2 401 A 1 HETATM 22 O O2 UD2 . . . B 2 32.151 -40.609 -5.595 1 57.93 ? O2 UD2 401 A 1 HETATM 23 O O4 UD2 . . . B 2 27.921 -41.965 -5.609 1 62.33 ? O4 UD2 401 A 1 HETATM 24 C C1B UD2 . . . B 2 31.916 -38.943 -7.854 1 75.89 ? C1B UD2 401 A 1 HETATM 25 C C2B UD2 . . . B 2 32.633 -39.645 -9.013 1 68 ? C2B UD2 401 A 1 HETATM 26 O O2' UD2 . . . B 2 33.609 -40.542 -8.589 1 84.47 ? O2' UD2 401 A 1 HETATM 27 C C3B UD2 . . . B 2 33.25 -38.456 -9.767 1 72.44 ? C3B UD2 401 A 1 HETATM 28 C C4B UD2 . . . B 2 32.243 -37.347 -9.525 1 81.46 ? C4B UD2 401 A 1 HETATM 29 O O4B UD2 . . . B 2 31.483 -37.71 -8.364 1 75.25 ? O4B UD2 401 A 1 HETATM 30 O O3B UD2 . . . B 2 34.487 -38.058 -9.198 1 64.84 ? O3B UD2 401 A 1 HETATM 31 C C5B UD2 . . . B 2 31.319 -37.187 -10.701 1 72.42 ? C5B UD2 401 A 1 HETATM 32 O O5B UD2 . . . B 2 31.01 -35.845 -10.889 1 67.62 ? O5B UD2 401 A 1 HETATM 33 P PA UD2 . . . B 2 30.086 -35.472 -12.188 1 55.36 ? PA UD2 401 A 1 HETATM 34 O O1A UD2 . . . B 2 30.783 -35.891 -13.43 1 76.17 ? O1A UD2 401 A 1 HETATM 35 O O2A UD2 . . . B 2 28.677 -35.883 -11.84 1 71.26 ? O2A UD2 401 A 1 HETATM 36 O O3A UD2 . . . B 2 30.314 -33.86 -12.161 1 60.78 ? O3A UD2 401 A 1 HETATM 37 P PB UD2 . . . B 2 29.176 -32.806 -11.652 1 58.53 ? PB UD2 401 A 1 HETATM 38 O O1B UD2 . . . B 2 27.916 -32.93 -12.454 1 57.32 ? O1B UD2 401 A 1 HETATM 39 O O2B UD2 . . . B 2 29.162 -32.894 -10.168 1 78.41 ? O2B UD2 401 A 1 HETATM 40 H H1' UD2 . . . B 2 29.647 -30.002 -13.161 1 61.17 ? H1' UD2 401 A 1 HETATM 41 H H2' UD2 . . . B 2 30.116 -30.385 -15.223 1 46.58 ? H2' UD2 401 A 1 HETATM 42 H H3' UD2 . . . B 2 30.655 -33.02 -14.532 1 46.18 ? H3' UD2 401 A 1 HETATM 43 H H4' UD2 . . . B 2 32.89 -32.718 -14.9 1 54.29 ? H4' UD2 401 A 1 HETATM 44 H H5' UD2 . . . B 2 32.431 -32.162 -12.713 1 57.54 ? H5' UD2 401 A 1 HETATM 45 H "H6'1" UD2 . . . B 2 34.484 -31.916 -12.837 1 53.78 ? "H6'1" UD2 401 A 1 HETATM 46 H "H6'2" UD2 . . . B 2 34.038 -30.516 -12.307 1 53.78 ? "H6'2" UD2 401 A 1 HETATM 47 H "H8'1" UD2 . . . B 2 26.86 -29.086 -15.978 1 45.49 ? "H8'1" UD2 401 A 1 HETATM 48 H "H8'2" UD2 . . . B 2 28.266 -29.487 -16.563 1 45.49 ? "H8'2" UD2 401 A 1 HETATM 49 H "H8'3" UD2 . . . B 2 28.156 -28.918 -15.099 1 45.49 ? "H8'3" UD2 401 A 1 HETATM 50 H HN2' UD2 . . . B 2 28.446 -32.389 -14.476 1 59.86 ? HN2' UD2 401 A 1 HETATM 51 H HO3' UD2 . . . B 2 30.189 -33.02 -16.63 1 56.19 ? HO3' UD2 401 A 1 HETATM 52 H HO4' UD2 . . . B 2 32.472 -30.13 -15.366 1 52.72 ? HO4' UD2 401 A 1 HETATM 53 H HO6' UD2 . . . B 2 35.024 -31.017 -14.678 1 59.92 ? HO6' UD2 401 A 1 HETATM 54 H HN3 UD2 . . . B 2 30.211 -41.714 -4.962 1 75.45 ? HN3 UD2 401 A 1 HETATM 55 H H5 UD2 . . . B 2 27.733 -40.414 -7.749 1 86.93 ? H5 UD2 401 A 1 HETATM 56 H H6 UD2 . . . B 2 29.454 -39.216 -8.595 1 86.85 ? H6 UD2 401 A 1 HETATM 57 H H1B UD2 . . . B 2 32.515 -38.771 -7.111 1 91.07 ? H1B UD2 401 A 1 HETATM 58 H H2B UD2 . . . B 2 31.932 -40.074 -9.528 1 81.6 ? H2B UD2 401 A 1 HETATM 59 H HO2' UD2 . . . B 2 34.34 -40.175 -8.544 1 101.37 ? HO2' UD2 401 A 1 HETATM 60 H H3B UD2 . . . B 2 33.333 -38.665 -10.71 1 86.93 ? H3B UD2 401 A 1 HETATM 61 H H4B UD2 . . . B 2 32.714 -36.521 -9.334 1 97.75 ? H4B UD2 401 A 1 HETATM 62 H HO3A UD2 . . . B 2 34.393 -37.564 -8.542 1 77.81 ? HO3A UD2 401 A 1 HETATM 63 H "H5'1" UD2 . . . B 2 31.742 -37.552 -11.494 1 86.91 ? "H5'1" UD2 401 A 1 HETATM 64 H "H5'2" UD2 . . . B 2 30.512 -37.702 -10.547 1 86.91 ? "H5'2" UD2 401 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 26 _model_server_stats.element_count 64 #