data_3ZQU # _model_server_result.job_id 9SMayuCFwz1A7gNef9-vng _model_server_result.datetime_utc '2024-11-07 10:35:22' _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 3zqu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1208}' # _entry.id 3ZQU # _exptl.entry_id 3ZQU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 458.36 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL _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 90 _cell.entry_id 3ZQU _cell.length_a 141.77 _cell.length_b 141.77 _cell.length_c 141.77 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZQU _symmetry.cell_setting ? _symmetry.Int_Tables_number 196 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 1,2,3,4,5,6,7,8,9,10,11,12 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 17_554 z,x+1/2,y-1/2 0 0 1 1 0 0 0 1 0 0 70.885 -70.885 3 'crystal symmetry operation' 45_455 y-1/2,z+1/2,x 0 1 0 0 0 1 1 0 0 -70.885 70.885 0 4 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 5 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 6 'crystal symmetry operation' 38_455 -x-1/2,-y+1/2,z -1 0 0 0 -1 0 0 0 1 -70.885 70.885 0 7 'crystal symmetry operation' 27_454 -x-1/2,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -70.885 0 -70.885 8 'crystal symmetry operation' 22_554 -y,z+1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 0 70.885 -70.885 9 'crystal symmetry operation' 31_454 -z-1/2,-x,y-1/2 0 0 -1 -1 0 0 0 1 0 -70.885 0 -70.885 10 'crystal symmetry operation' 44_455 -z-1/2,x+1/2,-y 0 0 -1 1 0 0 0 -1 0 -70.885 70.885 0 11 'crystal symmetry operation' 16_554 x,-y+1/2,-z-1/2 1 0 0 0 -1 0 0 0 -1 0 70.885 -70.885 12 'crystal symmetry operation' 35_454 y-1/2,-z,-x-1/2 0 1 0 0 0 -1 -1 0 0 -70.885 0 -70.885 # _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 H23 N4 O9 P' _chem_comp.formula_weight 458.36 _chem_comp.id FNR _chem_comp.mon_nstd_flag . _chem_comp.name 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE' # 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 C9A N10 FNR sing 83 n n C9A C5A FNR doub 84 n y C9A C9 FNR sing 85 n y N10 CAA FNR sing 86 n n N10 C1' FNR sing 87 n n CAA N1 FNR sing 88 n n CAA C4A FNR doub 89 n n N1 C2 FNR sing 90 n n N1 HN1 FNR sing 91 n n C2 O2 FNR doub 92 n n C2 N3 FNR sing 93 n n N3 C4 FNR sing 94 n n N3 H3 FNR sing 95 n n C4 O4 FNR doub 96 n n C4 C4A FNR sing 97 n n C4A N5 FNR sing 98 n n N5 C5A FNR sing 99 n n N5 H5 FNR sing 100 n n C5A C6 FNR sing 101 n y C6 C7 FNR doub 102 n y C6 H7 FNR sing 103 n n C7 C7M FNR sing 104 n n C7 C8 FNR sing 105 n y C7M H7M1 FNR sing 106 n n C7M H7M2 FNR sing 107 n n C7M H7M3 FNR sing 108 n n C8 C8M FNR sing 109 n n C8 C9 FNR doub 110 n y C8M H8M1 FNR sing 111 n n C8M H8M2 FNR sing 112 n n C8M H8M3 FNR sing 113 n n C9 H9 FNR sing 114 n n C1' C2' FNR sing 115 n n C1' "H1'1" FNR sing 116 n n C1' "H1'2" FNR sing 117 n n C2' O2' FNR sing 118 n n C2' C3' FNR sing 119 n n C2' H6 FNR sing 120 n n O2' H2' FNR sing 121 n n C3' O3' FNR sing 122 n n C3' C4' FNR sing 123 n n C3' H4 FNR sing 124 n n O3' H3' FNR sing 125 n n C4' O4' FNR sing 126 n n C4' C5' FNR sing 127 n n C4' H2 FNR sing 128 n n O4' H4' FNR sing 129 n n C5' O5' FNR sing 130 n n C5' "H5'1" FNR sing 131 n n C5' "H5'2" FNR sing 132 n n O5' P FNR sing 133 n n P O1P FNR sing 134 n n P O2P FNR doub 135 n n P O3P FNR sing 136 n n O1P H1 FNR sing 137 n n O3P H3P FNR sing 138 n n # _atom_sites.entry_id 3ZQU _atom_sites.fract_transf_matrix[1][1] 0.007054 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007054 _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] 0.007054 _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 FNR A 1 1208 1208 FNR FNR . C 3 SO4 A 1 1209 1209 SO4 SO4 . D 3 SO4 A 1 1210 1210 SO4 SO4 . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 HOH HOH . E 4 HOH A 51 2051 2051 HOH HOH . E 4 HOH A 52 2052 2052 HOH HOH . E 4 HOH A 53 2053 2053 HOH HOH . E 4 HOH A 54 2054 2054 HOH HOH . E 4 HOH A 55 2055 2055 HOH HOH . E 4 HOH A 56 2056 2056 HOH HOH . E 4 HOH A 57 2057 2057 HOH HOH . E 4 HOH A 58 2058 2058 HOH HOH . E 4 HOH A 59 2059 2059 HOH HOH . E 4 HOH A 60 2060 2060 HOH HOH . E 4 HOH A 61 2061 2061 HOH HOH . E 4 HOH A 62 2062 2062 HOH HOH . E 4 HOH A 63 2063 2063 HOH HOH . E 4 HOH A 64 2064 2064 HOH HOH . E 4 HOH A 65 2065 2065 HOH HOH . E 4 HOH A 66 2066 2066 HOH HOH . E 4 HOH A 67 2067 2067 HOH HOH . E 4 HOH A 68 2068 2068 HOH HOH . E 4 HOH A 69 2069 2069 HOH HOH . E 4 HOH A 70 2070 2070 HOH HOH . E 4 HOH A 71 2071 2071 HOH HOH . E 4 HOH A 72 2072 2072 HOH HOH . E 4 HOH A 73 2073 2073 HOH HOH . E 4 HOH A 74 2074 2074 HOH HOH . E 4 HOH A 75 2075 2075 HOH HOH . E 4 HOH A 76 2076 2076 HOH HOH . E 4 HOH A 77 2077 2077 HOH HOH . E 4 HOH A 78 2078 2078 HOH HOH . E 4 HOH A 79 2079 2079 HOH HOH . E 4 HOH A 80 2080 2080 HOH HOH . E 4 HOH A 81 2081 2081 HOH HOH . E 4 HOH A 82 2082 2082 HOH HOH . E 4 HOH A 83 2083 2083 HOH HOH . E 4 HOH A 84 2084 2084 HOH HOH . E 4 HOH A 85 2085 2085 HOH HOH . E 4 HOH A 86 2086 2086 HOH HOH . E 4 HOH A 87 2087 2087 HOH HOH . E 4 HOH A 88 2088 2088 HOH HOH . E 4 HOH A 89 2089 2089 HOH HOH . E 4 HOH A 90 2090 2090 HOH HOH . E 4 HOH A 91 2091 2091 HOH HOH . E 4 HOH A 92 2092 2092 HOH HOH . E 4 HOH A 93 2093 2093 HOH HOH . E 4 HOH A 94 2094 2094 HOH HOH . E 4 HOH A 95 2095 2095 HOH HOH . E 4 HOH A 96 2096 2096 HOH HOH . E 4 HOH A 97 2097 2097 HOH HOH . E 4 HOH A 98 2098 2098 HOH HOH . E 4 HOH A 99 2099 2099 HOH HOH . E 4 HOH A 100 2100 2100 HOH HOH . E 4 HOH A 101 2101 2101 HOH HOH . E 4 HOH A 102 2102 2102 HOH HOH . E 4 HOH A 103 2103 2103 HOH HOH . E 4 HOH A 104 2104 2104 HOH HOH . E 4 HOH A 105 2105 2105 HOH HOH . E 4 HOH A 106 2106 2106 HOH HOH . E 4 HOH A 107 2107 2107 HOH HOH . E 4 HOH A 108 2108 2108 HOH HOH . E 4 HOH A 109 2109 2109 HOH HOH . E 4 HOH A 110 2110 2110 HOH HOH . E 4 HOH A 111 2111 2111 HOH HOH . E 4 HOH A 112 2112 2112 HOH HOH . E 4 HOH A 113 2113 2113 HOH HOH . E 4 HOH A 114 2114 2114 HOH HOH . E 4 HOH A 115 2115 2115 HOH HOH . E 4 HOH A 116 2116 2116 HOH HOH . E 4 HOH A 117 2117 2117 HOH HOH . E 4 HOH A 118 2118 2118 HOH HOH . E 4 HOH A 119 2119 2119 HOH HOH . E 4 HOH A 120 2120 2120 HOH HOH . E 4 HOH A 121 2121 2121 HOH HOH . E 4 HOH A 122 2122 2122 HOH HOH . E 4 HOH A 123 2123 2123 HOH HOH . E 4 HOH A 124 2124 2124 HOH HOH . E 4 HOH A 125 2125 2125 HOH HOH . E 4 HOH A 126 2126 2126 HOH HOH . E 4 HOH A 127 2127 2127 HOH HOH . E 4 HOH A 128 2128 2128 HOH HOH . E 4 HOH A 129 2129 2129 HOH HOH . E 4 HOH A 130 2130 2130 HOH HOH . E 4 HOH A 131 2131 2131 HOH HOH . E 4 HOH A 132 2132 2132 HOH HOH . E 4 HOH A 133 2133 2133 HOH HOH . E 4 HOH A 134 2134 2134 HOH HOH . E 4 HOH A 135 2135 2135 HOH HOH . E 4 HOH A 136 2136 2136 HOH HOH . E 4 HOH A 137 2137 2137 HOH HOH . E 4 HOH A 138 2138 2138 HOH HOH . E 4 HOH A 139 2139 2139 HOH HOH . E 4 HOH A 140 2140 2140 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 C9A FNR . . . B 2 -5.415 28.29 -49.044 1 13.15 ? C9A FNR 1208 A 1 HETATM 2 N N10 FNR . . . B 2 -6.795 28.449 -48.695 1 13.61 ? N10 FNR 1208 A 1 HETATM 3 C CAA FNR . . . B 2 -7.033 29.089 -47.495 1 12.3 ? CAA FNR 1208 A 1 HETATM 4 N N1 FNR . . . B 2 -8.33 28.905 -46.988 1 13 ? N1 FNR 1208 A 1 HETATM 5 C C2 FNR . . . B 2 -8.61 29.534 -45.766 1 13.87 ? C2 FNR 1208 A 1 HETATM 6 O O2 FNR . . . B 2 -9.736 29.374 -45.269 1 15.56 ? O2 FNR 1208 A 1 HETATM 7 N N3 FNR . . . B 2 -7.678 30.214 -45.017 1 15 ? N3 FNR 1208 A 1 HETATM 8 C C4 FNR . . . B 2 -6.35 30.386 -45.533 1 15.14 ? C4 FNR 1208 A 1 HETATM 9 O O4 FNR . . . B 2 -5.488 30.924 -44.834 1 12.15 ? O4 FNR 1208 A 1 HETATM 10 C C4A FNR . . . B 2 -6.067 29.808 -46.778 1 13.6 ? C4A FNR 1208 A 1 HETATM 11 N N5 FNR . . . B 2 -4.78 29.919 -47.331 1 15.89 ? N5 FNR 1208 A 1 HETATM 12 C C5A FNR . . . B 2 -4.452 29.025 -48.345 1 15.41 ? C5A FNR 1208 A 1 HETATM 13 C C6 FNR . . . B 2 -3.098 28.928 -48.682 1 16.47 ? C6 FNR 1208 A 1 HETATM 14 C C7 FNR . . . B 2 -2.728 28.012 -49.658 1 17.08 ? C7 FNR 1208 A 1 HETATM 15 C C7M FNR . . . B 2 -1.207 27.915 -49.997 1 18.07 ? C7M FNR 1208 A 1 HETATM 16 C C8 FNR . . . B 2 -3.664 27.264 -50.353 1 16.4 ? C8 FNR 1208 A 1 HETATM 17 C C8M FNR . . . B 2 -3.212 26.246 -51.421 1 16.45 ? C8M FNR 1208 A 1 HETATM 18 C C9 FNR . . . B 2 -5.025 27.37 -50.027 1 15.43 ? C9 FNR 1208 A 1 HETATM 19 C C1' FNR . . . B 2 -7.94 27.932 -49.549 1 14.89 ? C1' FNR 1208 A 1 HETATM 20 C C2' FNR . . . B 2 -8.424 26.535 -49.144 1 15.65 ? C2' FNR 1208 A 1 HETATM 21 O O2' FNR . . . B 2 -7.324 25.583 -49.161 1 13.94 ? O2' FNR 1208 A 1 HETATM 22 C C3' FNR . . . B 2 -9.536 26.088 -50.099 1 14.02 ? C3' FNR 1208 A 1 HETATM 23 O O3' FNR . . . B 2 -10.686 26.965 -49.883 1 14.48 ? O3' FNR 1208 A 1 HETATM 24 C C4' FNR . . . B 2 -9.888 24.617 -49.865 1 14.9 ? C4' FNR 1208 A 1 HETATM 25 O O4' FNR . . . B 2 -11.055 24.379 -50.622 1 16.41 ? O4' FNR 1208 A 1 HETATM 26 C C5' FNR . . . B 2 -10.054 24.187 -48.404 1 15.41 ? C5' FNR 1208 A 1 HETATM 27 O O5' FNR . . . B 2 -10.346 22.787 -48.432 1 13.71 ? O5' FNR 1208 A 1 HETATM 28 P P FNR . . . B 2 -10.217 21.917 -47.214 1 12.3 ? P FNR 1208 A 1 HETATM 29 O O1P FNR . . . B 2 -10.878 20.531 -47.628 1 14.93 ? O1P FNR 1208 A 1 HETATM 30 O O2P FNR . . . B 2 -11.154 22.584 -46.116 1 14.54 ? O2P FNR 1208 A 1 HETATM 31 O O3P FNR . . . B 2 -8.83 21.802 -46.794 1 12.87 ? O3P FNR 1208 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #