data_5A01 # _model_server_result.job_id fxg3uL1BsSjKUZbMHX8stw _model_server_result.datetime_utc '2024-11-25 22:31:21' _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 5a01 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2060}' # _entry.id 5A01 # _exptl.entry_id 5A01 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 623.419 _entity.id 2 _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 3 _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 5A01 _cell.length_a 160.946 _cell.length_b 160.946 _cell.length_c 77.189 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A01 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_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 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 5A01 _atom_sites.fract_transf_matrix[1][1] 0.006213 _atom_sites.fract_transf_matrix[1][2] 0.003587 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007174 _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] 0.012955 _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 12V A 1 2060 2060 12V 12V . E 2 12V B 1 2060 2060 12V 12V . F 2 12V C 1 2060 2060 12V 12V . G 3 HOH A 1 2001 2001 HOH HOH . G 3 HOH A 2 2002 2002 HOH HOH . G 3 HOH A 3 2003 2003 HOH HOH . G 3 HOH A 4 2004 2004 HOH HOH . G 3 HOH A 5 2005 2005 HOH HOH . G 3 HOH A 6 2006 2006 HOH HOH . G 3 HOH A 7 2007 2007 HOH HOH . G 3 HOH A 8 2008 2008 HOH HOH . G 3 HOH A 9 2009 2009 HOH HOH . G 3 HOH A 10 2010 2010 HOH HOH . G 3 HOH A 11 2011 2011 HOH HOH . G 3 HOH A 12 2012 2012 HOH HOH . G 3 HOH A 13 2013 2013 HOH HOH . G 3 HOH A 14 2014 2014 HOH HOH . G 3 HOH A 15 2015 2015 HOH HOH . G 3 HOH A 16 2016 2016 HOH HOH . G 3 HOH A 17 2017 2017 HOH HOH . G 3 HOH A 18 2018 2018 HOH HOH . G 3 HOH A 19 2019 2019 HOH HOH . G 3 HOH A 20 2020 2020 HOH HOH . G 3 HOH A 21 2021 2021 HOH HOH . G 3 HOH A 22 2022 2022 HOH HOH . G 3 HOH A 23 2023 2023 HOH HOH . G 3 HOH A 24 2024 2024 HOH HOH . G 3 HOH A 25 2025 2025 HOH HOH . G 3 HOH A 26 2026 2026 HOH HOH . G 3 HOH A 27 2027 2027 HOH HOH . G 3 HOH A 28 2028 2028 HOH HOH . G 3 HOH A 29 2029 2029 HOH HOH . G 3 HOH A 30 2030 2030 HOH HOH . G 3 HOH A 31 2031 2031 HOH HOH . G 3 HOH A 32 2032 2032 HOH HOH . G 3 HOH A 33 2033 2033 HOH HOH . H 3 HOH B 1 2001 2001 HOH HOH . H 3 HOH B 2 2002 2002 HOH HOH . H 3 HOH B 3 2003 2003 HOH HOH . H 3 HOH B 4 2004 2004 HOH HOH . H 3 HOH B 5 2005 2005 HOH HOH . H 3 HOH B 6 2006 2006 HOH HOH . H 3 HOH B 7 2007 2007 HOH HOH . H 3 HOH B 8 2008 2008 HOH HOH . H 3 HOH B 9 2009 2009 HOH HOH . H 3 HOH B 10 2010 2010 HOH HOH . H 3 HOH B 11 2011 2011 HOH HOH . H 3 HOH B 12 2012 2012 HOH HOH . H 3 HOH B 13 2013 2013 HOH HOH . H 3 HOH B 14 2014 2014 HOH HOH . H 3 HOH B 15 2015 2015 HOH HOH . H 3 HOH B 16 2016 2016 HOH HOH . H 3 HOH B 17 2017 2017 HOH HOH . H 3 HOH B 18 2018 2018 HOH HOH . H 3 HOH B 19 2019 2019 HOH HOH . I 3 HOH C 1 2001 2001 HOH HOH . I 3 HOH C 2 2002 2002 HOH HOH . I 3 HOH C 3 2003 2003 HOH HOH . I 3 HOH C 4 2004 2004 HOH HOH . I 3 HOH C 5 2005 2005 HOH HOH . I 3 HOH C 6 2006 2006 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 . . . D 2 82.852 -13.009 -33.46 1 36.11 ? N1 12V 2060 A 1 HETATM 2 C C2 12V . . . D 2 83.136 -11.737 -33.811 1 37.74 ? C2 12V 2060 A 1 HETATM 3 O O2 12V . . . D 2 82.247 -10.919 -34.011 1 37.96 ? O2 12V 2060 A 1 HETATM 4 N N3 12V . . . D 2 84.455 -11.308 -33.965 1 38.76 ? N3 12V 2060 A 1 HETATM 5 C C4 12V . . . D 2 85.51 -12.2 -33.767 1 39.72 ? C4 12V 2060 A 1 HETATM 6 O O4 12V . . . D 2 86.676 -11.823 -33.919 1 40.71 ? O4 12V 2060 A 1 HETATM 7 C C5 12V . . . D 2 85.229 -13.509 -33.396 1 37.98 ? C5 12V 2060 A 1 HETATM 8 C C6 12V . . . D 2 83.905 -13.916 -33.249 1 37.5 ? C6 12V 2060 A 1 HETATM 9 P PA 12V . . . D 2 79.829 -17.295 -29.062 1 35.29 ? PA 12V 2060 A 1 HETATM 10 P PB 12V . . . D 2 79.033 -19.792 -30.043 1 31.34 ? PB 12V 2060 A 1 HETATM 11 C C1' 12V . . . D 2 76.745 -20.005 -28.784 1 31.39 ? C1' 12V 2060 A 1 HETATM 12 O O1' 12V . . . D 2 77.508 -20.137 -29.986 1 31.21 ? O1' 12V 2060 A 1 HETATM 13 O O1A 12V . . . D 2 78.831 -16.839 -28.084 1 38.17 ? O1A 12V 2060 A 1 HETATM 14 C C1B 12V . . . D 2 81.446 -13.453 -33.3 1 34.03 ? C1B 12V 2060 A 1 HETATM 15 O O1B 12V . . . D 2 79.618 -20.192 -31.364 1 32.02 ? O1B 12V 2060 A 1 HETATM 16 C C2' 12V . . . D 2 76.213 -21.376 -28.414 1 30.68 ? C2' 12V 2060 A 1 HETATM 17 N N2' 12V . . . D 2 77.326 -22.295 -28.18 1 29.41 ? N2' 12V 2060 A 1 HETATM 18 O O2' 12V . . . D 2 80.837 -14.393 -35.518 1 39.3 ? O2' 12V 2060 A 1 HETATM 19 O O2A 12V . . . D 2 81.057 -17.939 -28.574 1 39.37 ? O2A 12V 2060 A 1 HETATM 20 C C2B 12V . . . D 2 81.132 -14.686 -34.128 1 36.23 ? C2B 12V 2060 A 1 HETATM 21 O O2B 12V . . . D 2 79.573 -20.328 -28.786 1 33.68 ? O2B 12V 2060 A 1 HETATM 22 C C3' 12V . . . D 2 75.416 -21.967 -29.61 1 31.39 ? C3' 12V 2060 A 1 HETATM 23 O O3' 12V . . . D 2 75.09 -23.328 -29.362 1 31.59 ? O3' 12V 2060 A 1 HETATM 24 O O3A 12V . . . D 2 79.026 -18.196 -30.066 1 33.81 ? O3A 12V 2060 A 1 HETATM 25 C C3B 12V . . . D 2 79.879 -15.163 -33.441 1 36.96 ? C3B 12V 2060 A 1 HETATM 26 O O3B 12V . . . D 2 78.693 -14.39 -33.844 1 40.85 ? O3B 12V 2060 A 1 HETATM 27 C C4' 12V . . . D 2 74.144 -21.215 -29.962 1 32.14 ? C4' 12V 2060 A 1 HETATM 28 O O4' 12V . . . D 2 73.571 -21.908 -31.11 1 33.78 ? O4' 12V 2060 A 1 HETATM 29 C C4B 12V . . . D 2 80.203 -14.904 -31.978 1 35.18 ? C4B 12V 2060 A 1 HETATM 30 O O4B 12V . . . D 2 81.227 -13.889 -31.954 1 32.7 ? O4B 12V 2060 A 1 HETATM 31 C C5' 12V . . . D 2 74.507 -19.793 -30.367 1 33.06 ? C5' 12V 2060 A 1 HETATM 32 S S5' 12V . . . D 2 75.32 -18.961 -29.05 1 30.97 ? S5' 12V 2060 A 1 HETATM 33 C C5B 12V . . . D 2 80.687 -16.203 -31.319 1 32.88 ? C5B 12V 2060 A 1 HETATM 34 O O5B 12V . . . D 2 80.339 -16.076 -29.968 1 34.56 ? O5B 12V 2060 A 1 HETATM 35 C C6' 12V . . . D 2 73.295 -18.911 -30.642 1 34.39 ? C6' 12V 2060 A 1 HETATM 36 O O6' 12V . . . D 2 72.299 -19.218 -29.68 1 40.27 ? O6' 12V 2060 A 1 HETATM 37 C C7' 12V . . . D 2 77.609 -22.758 -26.974 1 30.69 ? C7' 12V 2060 A 1 HETATM 38 O O7' 12V . . . D 2 77.022 -22.413 -25.965 1 33.03 ? O7' 12V 2060 A 1 HETATM 39 C C8' 12V . . . D 2 78.727 -23.78 -26.89 1 31.14 ? C8' 12V 2060 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #