data_8DVW # _model_server_result.job_id JqLhi6bckJqtTUytdz9Z2A _model_server_result.datetime_utc '2024-11-19 20:27:47' _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 8dvw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8DVW # _exptl.entry_id 8DVW _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 8DVW _cell.length_a 94.924 _cell.length_b 94.924 _cell.length_c 101.064 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVW _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 8DVW _atom_sites.fract_transf_matrix[1][1] 0.010535 _atom_sites.fract_transf_matrix[1][2] 0.006082 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012164 _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] 0.009895 _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 62 HOH HOH . C 3 HOH A 2 502 81 HOH HOH . C 3 HOH A 3 503 85 HOH HOH . C 3 HOH A 4 504 2 HOH HOH . C 3 HOH A 5 505 64 HOH HOH . C 3 HOH A 6 506 20 HOH HOH . C 3 HOH A 7 507 8 HOH HOH . C 3 HOH A 8 508 15 HOH HOH . C 3 HOH A 9 509 22 HOH HOH . C 3 HOH A 10 510 82 HOH HOH . C 3 HOH A 11 511 92 HOH HOH . C 3 HOH A 12 512 58 HOH HOH . C 3 HOH A 13 513 4 HOH HOH . C 3 HOH A 14 514 35 HOH HOH . C 3 HOH A 15 515 14 HOH HOH . C 3 HOH A 16 516 10 HOH HOH . C 3 HOH A 17 517 24 HOH HOH . C 3 HOH A 18 518 31 HOH HOH . C 3 HOH A 19 519 44 HOH HOH . C 3 HOH A 20 520 29 HOH HOH . C 3 HOH A 21 521 17 HOH HOH . C 3 HOH A 22 522 52 HOH HOH . C 3 HOH A 23 523 18 HOH HOH . C 3 HOH A 24 524 46 HOH HOH . C 3 HOH A 25 525 19 HOH HOH . C 3 HOH A 26 526 13 HOH HOH . C 3 HOH A 27 527 12 HOH HOH . C 3 HOH A 28 528 7 HOH HOH . C 3 HOH A 29 529 36 HOH HOH . C 3 HOH A 30 530 25 HOH HOH . C 3 HOH A 31 531 45 HOH HOH . C 3 HOH A 32 532 6 HOH HOH . C 3 HOH A 33 533 104 HOH HOH . C 3 HOH A 34 534 40 HOH HOH . C 3 HOH A 35 535 38 HOH HOH . C 3 HOH A 36 536 99 HOH HOH . C 3 HOH A 37 537 32 HOH HOH . C 3 HOH A 38 538 43 HOH HOH . C 3 HOH A 39 539 102 HOH HOH . C 3 HOH A 40 540 1 HOH HOH . C 3 HOH A 41 541 48 HOH HOH . C 3 HOH A 42 542 30 HOH HOH . C 3 HOH A 43 543 27 HOH HOH . C 3 HOH A 44 544 5 HOH HOH . C 3 HOH A 45 545 9 HOH HOH . C 3 HOH A 46 546 77 HOH HOH . C 3 HOH A 47 547 90 HOH HOH . C 3 HOH A 48 548 71 HOH HOH . C 3 HOH A 49 549 57 HOH HOH . C 3 HOH A 50 550 23 HOH HOH . C 3 HOH A 51 551 60 HOH HOH . C 3 HOH A 52 552 100 HOH HOH . C 3 HOH A 53 553 21 HOH HOH . C 3 HOH A 54 554 33 HOH HOH . C 3 HOH A 55 555 83 HOH HOH . C 3 HOH A 56 556 41 HOH HOH . C 3 HOH A 57 557 66 HOH HOH . C 3 HOH A 58 558 49 HOH HOH . C 3 HOH A 59 559 101 HOH HOH . C 3 HOH A 60 560 65 HOH HOH . C 3 HOH A 61 561 73 HOH HOH . C 3 HOH A 62 562 80 HOH HOH . C 3 HOH A 63 563 54 HOH HOH . C 3 HOH A 64 564 97 HOH HOH . C 3 HOH A 65 565 39 HOH HOH . C 3 HOH A 66 566 51 HOH HOH . C 3 HOH A 67 567 69 HOH HOH . C 3 HOH A 68 568 105 HOH HOH . C 3 HOH A 69 569 28 HOH HOH . C 3 HOH A 70 570 53 HOH HOH . C 3 HOH A 71 571 79 HOH HOH . C 3 HOH A 72 572 47 HOH HOH . C 3 HOH A 73 573 50 HOH HOH . C 3 HOH A 74 574 86 HOH HOH . C 3 HOH A 75 575 16 HOH HOH . C 3 HOH A 76 576 76 HOH HOH . C 3 HOH A 77 577 68 HOH HOH . C 3 HOH A 78 578 89 HOH HOH . C 3 HOH A 79 579 84 HOH HOH . C 3 HOH A 80 580 74 HOH HOH . C 3 HOH A 81 581 70 HOH HOH . C 3 HOH A 82 582 67 HOH HOH . C 3 HOH A 83 583 72 HOH HOH . C 3 HOH A 84 584 98 HOH HOH . C 3 HOH A 85 585 63 HOH HOH . C 3 HOH A 86 586 34 HOH HOH . C 3 HOH A 87 587 26 HOH HOH . C 3 HOH A 88 588 42 HOH HOH . C 3 HOH A 89 589 96 HOH HOH . C 3 HOH A 90 590 87 HOH HOH . C 3 HOH A 91 591 55 HOH HOH . C 3 HOH A 92 592 37 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 54.016 -10.887 3.338 1 44.12 ? C1' UD2 401 A 1 HETATM 2 C C2' UD2 . . . B 2 54.119 -10.423 1.879 1 42.93 ? C2' UD2 401 A 1 HETATM 3 C C3' UD2 . . . B 2 52.735 -10.598 1.245 1 43.36 ? C3' UD2 401 A 1 HETATM 4 C C4' UD2 . . . B 2 52.184 -12.017 1.415 1 44.36 ? C4' UD2 401 A 1 HETATM 5 C C5' UD2 . . . B 2 52.303 -12.398 2.881 1 46.01 ? C5' UD2 401 A 1 HETATM 6 C C6' UD2 . . . B 2 51.902 -13.833 3.155 1 42.98 ? C6' UD2 401 A 1 HETATM 7 C C7' UD2 . . . B 2 55.596 -8.508 1.269 1 45.23 ? C7' UD2 401 A 1 HETATM 8 C C8' UD2 . . . B 2 56.42 -9.483 0.501 1 37.49 ? C8' UD2 401 A 1 HETATM 9 N N2' UD2 . . . B 2 54.525 -9.05 1.886 1 41.85 ? N2' UD2 401 A 1 HETATM 10 O O1' UD2 . . . B 2 53.032 -10.206 4.08 1 43.33 ? O1' UD2 401 A 1 HETATM 11 O O3' UD2 . . . B 2 52.879 -10.243 -0.107 1 41.02 ? O3' UD2 401 A 1 HETATM 12 O O4' UD2 . . . B 2 52.875 -12.866 0.544 1 43.78 ? O4' UD2 401 A 1 HETATM 13 O O5' UD2 . . . B 2 53.639 -12.219 3.332 1 42.73 ? O5' UD2 401 A 1 HETATM 14 O O6' UD2 . . . B 2 52.35 -14.643 2.106 1 42.37 ? O6' UD2 401 A 1 HETATM 15 O O7' UD2 . . . B 2 55.87 -7.304 1.296 1 48.2 ? O7' UD2 401 A 1 HETATM 16 N N1 UD2 . . . B 2 46.406 -6.835 9.474 1 44.1 ? N1 UD2 401 A 1 HETATM 17 C C2 UD2 . . . B 2 45.491 -6.651 10.497 1 42.11 ? C2 UD2 401 A 1 HETATM 18 N N3 UD2 . . . B 2 45.456 -5.385 11.026 1 44.57 ? N3 UD2 401 A 1 HETATM 19 C C4 UD2 . . . B 2 46.229 -4.3 10.665 1 42.64 ? C4 UD2 401 A 1 HETATM 20 C C5 UD2 . . . B 2 47.15 -4.585 9.607 1 35.56 ? C5 UD2 401 A 1 HETATM 21 C C6 UD2 . . . B 2 47.204 -5.802 9.057 1 41.64 ? C6 UD2 401 A 1 HETATM 22 O O2 UD2 . . . B 2 44.745 -7.521 10.889 1 41.85 ? O2 UD2 401 A 1 HETATM 23 O O4 UD2 . . . B 2 46.083 -3.256 11.251 1 46.64 ? O4 UD2 401 A 1 HETATM 24 C C1B UD2 . . . B 2 46.509 -8.133 8.829 1 41.84 ? C1B UD2 401 A 1 HETATM 25 C C2B UD2 . . . B 2 45.945 -8.193 7.428 1 39.97 ? C2B UD2 401 A 1 HETATM 26 O O2' UD2 . . . B 2 44.576 -8.43 7.481 1 42.47 ? O2' UD2 401 A 1 HETATM 27 C C3B UD2 . . . B 2 46.757 -9.352 6.824 1 43.19 ? C3B UD2 401 A 1 HETATM 28 C C4B UD2 . . . B 2 48.109 -9.12 7.477 1 41.92 ? C4B UD2 401 A 1 HETATM 29 O O4B UD2 . . . B 2 47.864 -8.421 8.684 1 41.65 ? O4B UD2 401 A 1 HETATM 30 O O3B UD2 . . . B 2 46.22 -10.57 7.231 1 45.32 ? O3B UD2 401 A 1 HETATM 31 C C5B UD2 . . . B 2 48.956 -8.248 6.559 1 40.51 ? C5B UD2 401 A 1 HETATM 32 O O5B UD2 . . . B 2 49.241 -8.925 5.354 1 45.68 ? O5B UD2 401 A 1 HETATM 33 P PA UD2 . . . B 2 50.402 -8.395 4.337 1 43.11 ? PA UD2 401 A 1 HETATM 34 O O1A UD2 . . . B 2 50.414 -9.349 3.201 1 43.61 ? O1A UD2 401 A 1 HETATM 35 O O2A UD2 . . . B 2 50.249 -6.917 4.125 1 45.6 ? O2A UD2 401 A 1 HETATM 36 O O3A UD2 . . . B 2 51.659 -8.643 5.342 1 42.79 ? O3A UD2 401 A 1 HETATM 37 P PB UD2 . . . B 2 53.208 -8.772 4.871 1 46.98 ? PB UD2 401 A 1 HETATM 38 O O1B UD2 . . . B 2 53.539 -7.72 3.86 1 43.54 ? O1B UD2 401 A 1 HETATM 39 O O2B UD2 . . . B 2 54.105 -9.022 6.041 1 48.05 ? O2B UD2 401 A 1 HETATM 40 H H1' UD2 . . . B 2 54.881 -10.763 3.758 1 52.94 ? H1' UD2 401 A 1 HETATM 41 H H2' UD2 . . . B 2 54.767 -10.949 1.384 1 51.52 ? H2' UD2 401 A 1 HETATM 42 H H3' UD2 . . . B 2 52.12 -10.043 1.748 1 52.03 ? H3' UD2 401 A 1 HETATM 43 H H4' UD2 . . . B 2 51.238 -12.025 1.201 1 53.23 ? H4' UD2 401 A 1 HETATM 44 H H5' UD2 . . . B 2 51.687 -11.837 3.378 1 55.22 ? H5' UD2 401 A 1 HETATM 45 H "H6'1" UD2 . . . B 2 50.937 -13.865 3.251 1 51.57 ? "H6'1" UD2 401 A 1 HETATM 46 H "H6'2" UD2 . . . B 2 52.284 -14.097 4.006 1 51.57 ? "H6'2" UD2 401 A 1 HETATM 47 H "H8'1" UD2 . . . B 2 56.708 -10.209 1.076 1 44.99 ? "H8'1" UD2 401 A 1 HETATM 48 H "H8'2" UD2 . . . B 2 55.905 -9.856 -0.232 1 44.99 ? "H8'2" UD2 401 A 1 HETATM 49 H "H8'3" UD2 . . . B 2 57.206 -9.047 0.136 1 44.99 ? "H8'3" UD2 401 A 1 HETATM 50 H HN2' UD2 . . . B 2 54.025 -8.514 2.336 1 50.22 ? HN2' UD2 401 A 1 HETATM 51 H HO3' UD2 . . . B 2 52.349 -9.614 -0.297 1 49.23 ? HO3' UD2 401 A 1 HETATM 52 H HO4' UD2 . . . B 2 53.572 -13.144 0.926 1 52.54 ? HO4' UD2 401 A 1 HETATM 53 H HO6' UD2 . . . B 2 52.777 -15.292 2.431 1 50.85 ? HO6' UD2 401 A 1 HETATM 54 H HN3 UD2 . . . B 2 44.882 -5.265 11.654 1 53.48 ? HN3 UD2 401 A 1 HETATM 55 H H5 UD2 . . . B 2 47.718 -3.917 9.298 1 42.67 ? H5 UD2 401 A 1 HETATM 56 H H6 UD2 . . . B 2 47.8 -5.97 8.364 1 49.97 ? H6 UD2 401 A 1 HETATM 57 H H1B UD2 . . . B 2 46.036 -8.77 9.388 1 50.2 ? H1B UD2 401 A 1 HETATM 58 H H2B UD2 . . . B 2 46.165 -7.37 6.965 1 47.97 ? H2B UD2 401 A 1 HETATM 59 H HO2' UD2 . . . B 2 44.164 -7.792 7.115 1 50.97 ? HO2' UD2 401 A 1 HETATM 60 H H3B UD2 . . . B 2 46.831 -9.308 5.857 1 51.83 ? H3B UD2 401 A 1 HETATM 61 H H4B UD2 . . . B 2 48.54 -9.961 7.697 1 50.3 ? H4B UD2 401 A 1 HETATM 62 H HO3A UD2 . . . B 2 46.57 -11.183 6.779 1 54.39 ? HO3A UD2 401 A 1 HETATM 63 H "H5'1" UD2 . . . B 2 49.779 -8.01 7.014 1 48.61 ? "H5'1" UD2 401 A 1 HETATM 64 H "H5'2" UD2 . . . B 2 48.482 -7.422 6.377 1 48.61 ? "H5'2" UD2 401 A 1 # _model_server_stats.io_time_ms 88 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 391 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 64 #