data_4N3B # _model_server_result.job_id 8k9Z3wYvfVU-Dge5leyRrg _model_server_result.datetime_utc '2024-11-12 22:49:03' _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 4n3b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1501}' # _entry.id 4N3B # _exptl.entry_id 4N3B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 623.419 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' _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 4N3B _cell.length_a 98.91 _cell.length_b 98.91 _cell.length_c 364.931 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N3B _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,E _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H27 N3 O16 P2 S' _chem_comp.formula_weight 623.419 _chem_comp.id 12V _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE' # 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 C1B N1 12V sing 1 n n C2 N1 12V sing 2 n n N1 C6 12V sing 3 n n O2 C2 12V doub 4 n n C2 N3 12V sing 5 n n N3 C4 12V sing 6 n n C4 O4 12V doub 7 n n C4 C5 12V sing 8 n n C6 C5 12V doub 9 n n C5 H5 12V sing 10 n n C6 H6 12V sing 11 n n O5B PA 12V sing 12 n n O1A PA 12V doub 13 n n PA O3A 12V sing 14 n n PA O2A 12V sing 15 n n O3A PB 12V sing 16 n n O1' PB 12V sing 17 n n PB O1B 12V doub 18 n n PB O2B 12V sing 19 n n S5' C1' 12V sing 20 n n C1' C2' 12V sing 21 n n C1' O1' 12V sing 22 n n C1' H1' 12V sing 23 n n C1B O4B 12V sing 24 n n C1B C2B 12V sing 25 n n C1B H1B 12V sing 26 n n C3' C2' 12V sing 27 n n C2' N2' 12V sing 28 n n C2' H2' 12V sing 29 n n N2' C7' 12V sing 30 n n N2' HN2' 12V sing 31 n n O2' C2B 12V sing 32 n n O2' HO2' 12V sing 33 n n O2A HO2A 12V sing 34 n n C3B C2B 12V sing 35 n n C2B H2B 12V sing 36 n n O2B HO2B 12V sing 37 n n C4' C3' 12V sing 38 n n C3' O3' 12V sing 39 n n C3' H3' 12V sing 40 n n O3' HO3' 12V sing 41 n n O3B C3B 12V sing 42 n n C3B C4B 12V sing 43 n n C3B H3B 12V sing 44 n n O3B HO3B 12V sing 45 n n C5' C4' 12V sing 46 n n O4' C4' 12V sing 47 n n C4' H4' 12V sing 48 n n O4' HO4' 12V sing 49 n n C4B O4B 12V sing 50 n n C4B C5B 12V sing 51 n n C4B H4B 12V sing 52 n n C6' C5' 12V sing 53 n n C5' S5' 12V sing 54 n n C5' H5' 12V sing 55 n n O5B C5B 12V sing 56 n n C5B H5B 12V sing 57 n n C5B H5BA 12V sing 58 n n O6' C6' 12V sing 59 n n C6' H6' 12V sing 60 n n C6' "H6'A" 12V sing 61 n n O6' HO6' 12V sing 62 n n O7' C7' 12V doub 63 n n C7' C8' 12V sing 64 n n C8' H8' 12V sing 65 n n C8' "H8'A" 12V sing 66 n n C8' "H8'B" 12V sing 67 n n N3 HN3 12V sing 68 n n # _atom_sites.entry_id 4N3B _atom_sites.fract_transf_matrix[1][1] 0.01011 _atom_sites.fract_transf_matrix[1][2] 0.005837 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011674 _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] 0.00274 _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 C 3 12V A 1 1501 1501 12V 12V . D 4 HOH A 1 1601 1 HOH HOH . D 4 HOH A 2 1602 2 HOH HOH . D 4 HOH A 3 1603 3 HOH HOH . D 4 HOH A 4 1604 4 HOH HOH . D 4 HOH A 5 1605 5 HOH HOH . D 4 HOH A 6 1606 6 HOH HOH . D 4 HOH A 7 1607 7 HOH HOH . D 4 HOH A 8 1608 8 HOH HOH . D 4 HOH A 9 1609 9 HOH HOH . D 4 HOH A 10 1610 11 HOH HOH . D 4 HOH A 11 1611 12 HOH HOH . D 4 HOH A 12 1612 13 HOH HOH . D 4 HOH A 13 1613 14 HOH HOH . D 4 HOH A 14 1614 15 HOH HOH . D 4 HOH A 15 1615 16 HOH HOH . D 4 HOH A 16 1616 17 HOH HOH . D 4 HOH A 17 1617 18 HOH HOH . D 4 HOH A 18 1618 19 HOH HOH . D 4 HOH A 19 1619 20 HOH HOH . D 4 HOH A 20 1620 21 HOH HOH . D 4 HOH A 21 1621 23 HOH HOH . D 4 HOH A 22 1622 24 HOH HOH . D 4 HOH A 23 1623 25 HOH HOH . D 4 HOH A 24 1624 26 HOH HOH . D 4 HOH A 25 1625 27 HOH HOH . D 4 HOH A 26 1626 28 HOH HOH . D 4 HOH A 27 1627 29 HOH HOH . D 4 HOH A 28 1628 30 HOH HOH . D 4 HOH A 29 1629 31 HOH HOH . D 4 HOH A 30 1630 32 HOH HOH . D 4 HOH A 31 1631 33 HOH HOH . D 4 HOH A 32 1632 35 HOH HOH . D 4 HOH A 33 1633 36 HOH HOH . D 4 HOH A 34 1634 37 HOH HOH . D 4 HOH A 35 1635 38 HOH HOH . D 4 HOH A 36 1636 39 HOH HOH . D 4 HOH A 37 1637 40 HOH HOH . D 4 HOH A 38 1638 41 HOH HOH . D 4 HOH A 39 1639 42 HOH HOH . D 4 HOH A 40 1640 43 HOH HOH . D 4 HOH A 41 1641 44 HOH HOH . D 4 HOH A 42 1642 45 HOH HOH . D 4 HOH A 43 1643 46 HOH HOH . D 4 HOH A 44 1644 47 HOH HOH . D 4 HOH A 45 1645 48 HOH HOH . D 4 HOH A 46 1646 49 HOH HOH . D 4 HOH A 47 1647 50 HOH HOH . D 4 HOH A 48 1648 51 HOH HOH . D 4 HOH A 49 1649 52 HOH HOH . D 4 HOH A 50 1650 53 HOH HOH . D 4 HOH A 51 1651 54 HOH HOH . D 4 HOH A 52 1652 55 HOH HOH . D 4 HOH A 53 1653 56 HOH HOH . D 4 HOH A 54 1654 57 HOH HOH . D 4 HOH A 55 1655 58 HOH HOH . D 4 HOH A 56 1656 59 HOH HOH . D 4 HOH A 57 1657 60 HOH HOH . D 4 HOH A 58 1658 61 HOH HOH . D 4 HOH A 59 1659 62 HOH HOH . D 4 HOH A 60 1660 63 HOH HOH . D 4 HOH A 61 1661 64 HOH HOH . D 4 HOH A 62 1662 65 HOH HOH . D 4 HOH A 63 1663 66 HOH HOH . D 4 HOH A 64 1664 67 HOH HOH . D 4 HOH A 65 1665 68 HOH HOH . D 4 HOH A 66 1666 69 HOH HOH . D 4 HOH A 67 1667 70 HOH HOH . D 4 HOH A 68 1668 71 HOH HOH . D 4 HOH A 69 1669 72 HOH HOH . D 4 HOH A 70 1670 73 HOH HOH . D 4 HOH A 71 1671 74 HOH HOH . D 4 HOH A 72 1672 75 HOH HOH . D 4 HOH A 73 1673 76 HOH HOH . D 4 HOH A 74 1674 78 HOH HOH . D 4 HOH A 75 1675 79 HOH HOH . D 4 HOH A 76 1676 80 HOH HOH . D 4 HOH A 77 1677 81 HOH HOH . D 4 HOH A 78 1678 82 HOH HOH . D 4 HOH A 79 1679 83 HOH HOH . D 4 HOH A 80 1680 85 HOH HOH . D 4 HOH A 81 1681 86 HOH HOH . D 4 HOH A 82 1682 88 HOH HOH . D 4 HOH A 83 1683 89 HOH HOH . D 4 HOH A 84 1684 90 HOH HOH . D 4 HOH A 85 1685 91 HOH HOH . D 4 HOH A 86 1686 92 HOH HOH . D 4 HOH A 87 1687 93 HOH HOH . D 4 HOH A 88 1688 94 HOH HOH . D 4 HOH A 89 1689 95 HOH HOH . D 4 HOH A 90 1690 96 HOH HOH . D 4 HOH A 91 1691 97 HOH HOH . D 4 HOH A 92 1692 98 HOH HOH . D 4 HOH A 93 1693 99 HOH HOH . D 4 HOH A 94 1694 100 HOH HOH . D 4 HOH A 95 1695 101 HOH HOH . D 4 HOH A 96 1696 102 HOH HOH . D 4 HOH A 97 1697 103 HOH HOH . D 4 HOH A 98 1698 105 HOH HOH . D 4 HOH A 99 1699 107 HOH HOH . D 4 HOH A 100 1700 108 HOH HOH . D 4 HOH A 101 1701 109 HOH HOH . D 4 HOH A 102 1702 110 HOH HOH . D 4 HOH A 103 1703 111 HOH HOH . D 4 HOH A 104 1704 112 HOH HOH . D 4 HOH A 105 1705 113 HOH HOH . D 4 HOH A 106 1706 114 HOH HOH . D 4 HOH A 107 1707 115 HOH HOH . D 4 HOH A 108 1708 117 HOH HOH . D 4 HOH A 109 1709 118 HOH HOH . D 4 HOH A 110 1710 119 HOH HOH . D 4 HOH A 111 1711 120 HOH HOH . D 4 HOH A 112 1712 121 HOH HOH . D 4 HOH A 113 1713 122 HOH HOH . D 4 HOH A 114 1714 123 HOH HOH . D 4 HOH A 115 1715 124 HOH HOH . D 4 HOH A 116 1716 125 HOH HOH . D 4 HOH A 117 1717 126 HOH HOH . D 4 HOH A 118 1718 127 HOH HOH . E 4 HOH B 1 101 10 HOH HOH . E 4 HOH B 2 102 34 HOH HOH . E 4 HOH B 3 103 77 HOH HOH . E 4 HOH B 4 104 84 HOH HOH . E 4 HOH B 5 105 87 HOH HOH . E 4 HOH B 6 106 106 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 12V . . . C 3 1.212 -46.122 12.082 1 34.56 ? N1 12V 1501 A 1 HETATM 2 C C2 12V . . . C 3 2.223 -47.086 11.765 1 35.05 ? C2 12V 1501 A 1 HETATM 3 O O2 12V . . . C 3 3.356 -46.95 12.183 1 35.72 ? O2 12V 1501 A 1 HETATM 4 N N3 12V . . . C 3 1.885 -48.176 10.95 1 35.11 ? N3 12V 1501 A 1 HETATM 5 C C4 12V . . . C 3 0.643 -48.252 10.532 1 33.75 ? C4 12V 1501 A 1 HETATM 6 O O4 12V . . . C 3 0.326 -49.31 9.742 1 33.38 ? O4 12V 1501 A 1 HETATM 7 C C5 12V . . . C 3 -0.412 -47.34 10.82 1 33.23 ? C5 12V 1501 A 1 HETATM 8 C C6 12V . . . C 3 -0.072 -46.273 11.623 1 34.3 ? C6 12V 1501 A 1 HETATM 9 P PA 12V . . . C 3 -2.724 -42.119 16.309 1 35.72 ? PA 12V 1501 A 1 HETATM 10 P PB 12V . . . C 3 -3.462 -39.752 14.822 1 37.94 ? PB 12V 1501 A 1 HETATM 11 C C1' 12V . . . C 3 -2.703 -38.527 17.06 1 40.14 ? C1' 12V 1501 A 1 HETATM 12 O O1' 12V . . . C 3 -2.605 -38.502 15.749 1 38.16 ? O1' 12V 1501 A 1 HETATM 13 O O1A 12V . . . C 3 -2.574 -41.572 17.677 1 36.53 ? O1A 12V 1501 A 1 HETATM 14 C C1B 12V . . . C 3 1.539 -44.977 12.986 1 34.25 ? C1B 12V 1501 A 1 HETATM 15 O O1B 12V . . . C 3 -4.747 -40.063 15.542 1 38.76 ? O1B 12V 1501 A 1 HETATM 16 C C2' 12V . . . C 3 -3.493 -37.355 17.693 1 40.97 ? C2' 12V 1501 A 1 HETATM 17 N N2' 12V . . . C 3 -4.885 -37.41 17.311 1 42.51 ? N2' 12V 1501 A 1 HETATM 18 O O2' 12V . . . C 3 2.238 -43.039 11.725 1 34.08 ? O2' 12V 1501 A 1 HETATM 19 O O2A 12V . . . C 3 -3.696 -43.161 15.814 1 36.37 ? O2A 12V 1501 A 1 HETATM 20 C C2B 12V . . . C 3 1.189 -43.576 12.467 1 33.73 ? C2B 12V 1501 A 1 HETATM 21 O O2B 12V . . . C 3 -3.316 -39.244 13.441 1 39.4 ? O2B 12V 1501 A 1 HETATM 22 C C3' 12V . . . C 3 -2.853 -36.002 17.287 1 42.06 ? C3' 12V 1501 A 1 HETATM 23 O O3' 12V . . . C 3 -3.644 -34.978 17.83 1 42.48 ? O3' 12V 1501 A 1 HETATM 24 O O3A 12V . . . C 3 -2.597 -41.018 15.166 1 41.19 ? O3A 12V 1501 A 1 HETATM 25 C C3B 12V . . . C 3 1.014 -42.806 13.817 1 36.08 ? C3B 12V 1501 A 1 HETATM 26 O O3B 12V . . . C 3 2.3 -42.453 14.22 1 35.29 ? O3B 12V 1501 A 1 HETATM 27 C C4' 12V . . . C 3 -1.42 -35.755 17.852 1 44.13 ? C4' 12V 1501 A 1 HETATM 28 O O4' 12V . . . C 3 -1.062 -34.469 17.409 1 43.92 ? O4' 12V 1501 A 1 HETATM 29 C C4B 12V . . . C 3 0.487 -43.889 14.778 1 36.45 ? C4B 12V 1501 A 1 HETATM 30 O O4B 12V . . . C 3 0.843 -45.144 14.181 1 35.73 ? O4B 12V 1501 A 1 HETATM 31 C C5' 12V . . . C 3 -0.402 -36.751 17.291 1 43.91 ? C5' 12V 1501 A 1 HETATM 32 S S5' 12V . . . C 3 -0.934 -38.432 17.738 1 40.63 ? S5' 12V 1501 A 1 HETATM 33 C C5B 12V . . . C 3 -1.053 -43.809 14.991 1 33.17 ? C5B 12V 1501 A 1 HETATM 34 O O5B 12V . . . C 3 -1.22 -42.961 16.058 1 33.29 ? O5B 12V 1501 A 1 HETATM 35 C C6' 12V . . . C 3 0.966 -36.79 17.983 1 43.83 ? C6' 12V 1501 A 1 HETATM 36 O O6' 12V . . . C 3 0.846 -36.866 19.373 1 44.33 ? O6' 12V 1501 A 1 HETATM 37 C C7' 12V . . . C 3 -5.798 -38.082 18.087 1 43.8 ? C7' 12V 1501 A 1 HETATM 38 O O7' 12V . . . C 3 -5.473 -38.648 19.14 1 45.22 ? O7' 12V 1501 A 1 HETATM 39 C C8' 12V . . . C 3 -7.223 -38.1 17.614 1 43.37 ? C8' 12V 1501 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 39 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 643 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 39 #