data_5A01 # _model_server_result.job_id ZhLbj2pd_vz-PDkiC6ISfA _model_server_result.datetime_utc '2024-11-25 22:45:43' _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":"F","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 . . . F 2 26.411 -20.986 -62.813 1 46.52 ? N1 12V 2060 C 1 HETATM 2 C C2 12V . . . F 2 27.305 -21.898 -63.215 1 47.72 ? C2 12V 2060 C 1 HETATM 3 O O2 12V . . . F 2 28.479 -21.583 -63.373 1 49.02 ? O2 12V 2060 C 1 HETATM 4 N N3 12V . . . F 2 26.909 -23.219 -63.453 1 47.5 ? N3 12V 2060 C 1 HETATM 5 C C4 12V . . . F 2 25.571 -23.584 -63.271 1 47.53 ? C4 12V 2060 C 1 HETATM 6 O O4 12V . . . F 2 25.212 -24.736 -63.483 1 48.86 ? O4 12V 2060 C 1 HETATM 7 C C5 12V . . . F 2 24.641 -22.642 -62.855 1 46.89 ? C5 12V 2060 C 1 HETATM 8 C C6 12V . . . F 2 25.065 -21.339 -62.627 1 46.49 ? C6 12V 2060 C 1 HETATM 9 P PA 12V . . . F 2 24.552 -15.897 -58.53 1 48.47 ? PA 12V 2060 C 1 HETATM 10 P PB 12V . . . F 2 22.77 -13.917 -59.444 1 45.16 ? PB 12V 2060 C 1 HETATM 11 C C1' 12V . . . F 2 24.07 -11.831 -58.228 1 41.09 ? C1' 12V 2060 C 1 HETATM 12 O O1' 12V . . . F 2 23.515 -12.428 -59.421 1 41.41 ? O1' 12V 2060 C 1 HETATM 13 O O1A 12V . . . F 2 25.41 -15.167 -57.572 1 49.91 ? O1A 12V 2060 C 1 HETATM 14 C C1B 12V . . . F 2 26.835 -19.606 -62.577 1 48.64 ? C1B 12V 2060 C 1 HETATM 15 O O1B 12V . . . F 2 22.052 -14.069 -60.734 1 46.61 ? O1B 12V 2060 C 1 HETATM 16 C C2' 12V . . . F 2 23.228 -10.617 -57.77 1 41.23 ? C2' 12V 2060 C 1 HETATM 17 N N2' 12V . . . F 2 21.881 -11.047 -57.417 1 39.84 ? N2' 12V 2060 C 1 HETATM 18 O O2' 12V . . . F 2 26.748 -18.74 -64.869 1 61.8 ? O2' 12V 2060 C 1 HETATM 19 O O2A 12V . . . F 2 23.407 -16.707 -58.052 1 51.74 ? O2A 12V 2060 C 1 HETATM 20 C C2B 12V . . . F 2 26.13 -18.679 -63.56 1 53.12 ? C2B 12V 2060 C 1 HETATM 21 O O2B 12V . . . F 2 22.025 -14.129 -58.17 1 42.81 ? O2B 12V 2060 C 1 HETATM 22 C C3' 12V . . . F 2 23.095 -9.563 -58.879 1 42.87 ? C3' 12V 2060 C 1 HETATM 23 O O3' 12V . . . F 2 22.118 -8.562 -58.518 1 42.91 ? O3' 12V 2060 C 1 HETATM 24 O O3A 12V . . . F 2 24.043 -14.876 -59.622 1 45.73 ? O3A 12V 2060 C 1 HETATM 25 C C3B 12V . . . F 2 26.307 -17.332 -62.895 1 52.29 ? C3B 12V 2060 C 1 HETATM 26 O O3B 12V . . . F 2 27.574 -16.703 -63.251 1 52.21 ? O3B 12V 2060 C 1 HETATM 27 C C4' 12V . . . F 2 24.422 -8.898 -59.215 1 42.03 ? C4' 12V 2060 C 1 HETATM 28 O O4' 12V . . . F 2 24.179 -7.979 -60.298 1 43.92 ? O4' 12V 2060 C 1 HETATM 29 C C4B 12V . . . F 2 26.337 -17.734 -61.417 1 52.04 ? C4B 12V 2060 C 1 HETATM 30 O O4B 12V . . . F 2 26.312 -19.18 -61.343 1 47.66 ? O4B 12V 2060 C 1 HETATM 31 C C5' 12V . . . F 2 25.41 -9.953 -59.694 1 41.76 ? C5' 12V 2060 C 1 HETATM 32 S S5' 12V . . . F 2 25.728 -11.206 -58.47 1 41.17 ? S5' 12V 2060 C 1 HETATM 33 C C5B 12V . . . F 2 25.091 -17.221 -60.704 1 51.13 ? C5B 12V 2060 C 1 HETATM 34 O O5B 12V . . . F 2 25.486 -16.838 -59.387 1 52.82 ? O5B 12V 2060 C 1 HETATM 35 C C6' 12V . . . F 2 26.748 -9.299 -60.023 1 42.92 ? C6' 12V 2060 C 1 HETATM 36 O O6' 12V . . . F 2 27.333 -8.826 -58.82 1 46.52 ? O6' 12V 2060 C 1 HETATM 37 C C7' 12V . . . F 2 21.416 -10.873 -56.189 1 40.95 ? C7' 12V 2060 C 1 HETATM 38 O O7' 12V . . . F 2 22.093 -10.388 -55.283 1 43.23 ? O7' 12V 2060 C 1 HETATM 39 C C8' 12V . . . F 2 19.98 -11.368 -55.953 1 38.78 ? C8' 12V 2060 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #