data_2YPC # _model_server_result.job_id -fLIwz87pVYqhfxp0wuaew _model_server_result.datetime_utc '2024-11-25 05:49:43' _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 2ypc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1379}' # _entry.id 2YPC # _exptl.entry_id 2YPC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 345.272 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanyl-2-sulfanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol' _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 94.89 _cell.angle_gamma 90 _cell.entry_id 2YPC _cell.length_a 40.28 _cell.length_b 47.49 _cell.length_c 53.76 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YPC _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 'C10 H12 N5 O5 P S' _chem_comp.formula_weight 345.272 _chem_comp.id QQX _chem_comp.mon_nstd_flag . _chem_comp.name '[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanyl-2-sulfanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-2',3'-CYCLOPHOSPHOROTHIOATE" # 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 OP3 P QQX sing 277 n n S1P P QQX doub 278 n n O5' C5' QQX sing 279 n n C5' C4' QQX sing 280 n n C4' O4' QQX sing 281 n n C4' C3' QQX sing 282 n n O4' C1' QQX sing 283 n n C3' O3' QQX sing 284 n n C3' C2' QQX sing 285 n n O3' P QQX sing 286 n n C2' O2' QQX sing 287 n n C2' C1' QQX sing 288 n n O2' P QQX sing 289 n n C1' N9 QQX sing 290 n n N9 C8 QQX sing 291 n y N9 C4 QQX sing 292 n y C8 N7 QQX doub 293 n y N7 C5 QQX sing 294 n y C5 C6 QQX doub 295 n y C5 C4 QQX sing 296 n y N3 C4 QQX doub 297 n y C6 N6 QQX sing 298 n n C6 N1 QQX sing 299 n y N1 C2 QQX doub 300 n y C2 N3 QQX sing 301 n y OP3 HP3 QQX sing 302 n n O5' H5' QQX sing 303 n n C5' "H5'1" QQX sing 304 n n C5' "H5'2" QQX sing 305 n n C4' H4' QQX sing 306 n n C3' H3' QQX sing 307 n n C1' H1' QQX sing 308 n n C2' H2' QQX sing 309 n n C8 H8 QQX sing 310 n n N6 H61N QQX sing 311 n n N6 H62N QQX sing 312 n n C2 H2 QQX sing 313 n n # _atom_sites.entry_id 2YPC _atom_sites.fract_transf_matrix[1][1] 0.024826 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002124 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021057 _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] 0.018669 _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 QQX A 1 1379 1379 QQX QQX . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 HOH HOH . C 3 HOH A 42 2042 2042 HOH HOH . C 3 HOH A 43 2043 2043 HOH HOH . C 3 HOH A 44 2044 2044 HOH HOH . C 3 HOH A 45 2045 2045 HOH HOH . C 3 HOH A 46 2046 2046 HOH HOH . C 3 HOH A 47 2047 2047 HOH HOH . C 3 HOH A 48 2048 2048 HOH HOH . C 3 HOH A 49 2049 2049 HOH HOH . C 3 HOH A 50 2050 2050 HOH HOH . C 3 HOH A 51 2051 2051 HOH HOH . C 3 HOH A 52 2052 2052 HOH HOH . C 3 HOH A 53 2053 2053 HOH HOH . C 3 HOH A 54 2054 2054 HOH HOH . C 3 HOH A 55 2055 2055 HOH HOH . C 3 HOH A 56 2056 2056 HOH HOH . C 3 HOH A 57 2057 2057 HOH HOH . C 3 HOH A 58 2058 2058 HOH HOH . C 3 HOH A 59 2059 2059 HOH HOH . C 3 HOH A 60 2060 2060 HOH HOH . C 3 HOH A 61 2061 2061 HOH HOH . C 3 HOH A 62 2062 2062 HOH HOH . C 3 HOH A 63 2063 2063 HOH HOH . C 3 HOH A 64 2064 2064 HOH HOH . C 3 HOH A 65 2065 2065 HOH HOH . C 3 HOH A 66 2066 2066 HOH HOH . C 3 HOH A 67 2067 2067 HOH HOH . C 3 HOH A 68 2068 2068 HOH HOH . C 3 HOH A 69 2069 2069 HOH HOH . C 3 HOH A 70 2070 2070 HOH HOH . C 3 HOH A 71 2071 2071 HOH HOH . C 3 HOH A 72 2072 2072 HOH HOH . C 3 HOH A 73 2073 2073 HOH HOH . C 3 HOH A 74 2074 2074 HOH HOH . C 3 HOH A 75 2075 2075 HOH HOH . C 3 HOH A 76 2076 2076 HOH HOH . C 3 HOH A 77 2077 2077 HOH HOH . C 3 HOH A 78 2078 2078 HOH HOH . C 3 HOH A 79 2079 2079 HOH HOH . C 3 HOH A 80 2080 2080 HOH HOH . C 3 HOH A 81 2081 2081 HOH HOH . C 3 HOH A 82 2082 2082 HOH HOH . C 3 HOH A 83 2083 2083 HOH HOH . C 3 HOH A 84 2084 2084 HOH HOH . C 3 HOH A 85 2085 2085 HOH HOH . C 3 HOH A 86 2086 2086 HOH HOH . C 3 HOH A 87 2087 2087 HOH HOH . C 3 HOH A 88 2088 2088 HOH HOH . C 3 HOH A 89 2089 2089 HOH HOH . C 3 HOH A 90 2090 2090 HOH HOH . C 3 HOH A 91 2091 2091 HOH HOH . C 3 HOH A 92 2092 2092 HOH HOH . C 3 HOH A 93 2093 2093 HOH HOH . C 3 HOH A 94 2094 2094 HOH HOH . C 3 HOH A 95 2095 2095 HOH HOH . C 3 HOH A 96 2096 2096 HOH HOH . C 3 HOH A 97 2097 2097 HOH HOH . C 3 HOH A 98 2098 2098 HOH HOH . C 3 HOH A 99 2099 2099 HOH HOH . C 3 HOH A 100 2100 2100 HOH HOH . C 3 HOH A 101 2101 2101 HOH HOH . C 3 HOH A 102 2102 2102 HOH HOH . C 3 HOH A 103 2103 2103 HOH HOH . C 3 HOH A 104 2104 2104 HOH HOH . C 3 HOH A 105 2105 2105 HOH HOH . C 3 HOH A 106 2106 2106 HOH HOH . C 3 HOH A 107 2107 2107 HOH HOH . C 3 HOH A 108 2108 2108 HOH HOH . C 3 HOH A 109 2109 2109 HOH HOH . C 3 HOH A 110 2110 2110 HOH HOH . C 3 HOH A 111 2111 2111 HOH HOH . C 3 HOH A 112 2112 2112 HOH HOH . C 3 HOH A 113 2113 2113 HOH HOH . C 3 HOH A 114 2114 2114 HOH HOH . C 3 HOH A 115 2115 2115 HOH HOH . C 3 HOH A 116 2116 2116 HOH HOH . C 3 HOH A 117 2117 2117 HOH HOH . C 3 HOH A 118 2118 2118 HOH HOH . C 3 HOH A 119 2119 2119 HOH HOH . C 3 HOH A 120 2120 2120 HOH HOH . C 3 HOH A 121 2121 2121 HOH HOH . C 3 HOH A 122 2122 2122 HOH HOH . C 3 HOH A 123 2123 2123 HOH HOH . C 3 HOH A 124 2124 2124 HOH HOH . C 3 HOH A 125 2125 2125 HOH HOH . C 3 HOH A 126 2126 2126 HOH HOH . C 3 HOH A 127 2127 2127 HOH HOH . C 3 HOH A 128 2128 2128 HOH HOH . C 3 HOH A 129 2129 2129 HOH HOH . C 3 HOH A 130 2130 2130 HOH HOH . C 3 HOH A 131 2131 2131 HOH HOH . C 3 HOH A 132 2132 2132 HOH HOH . C 3 HOH A 133 2133 2133 HOH HOH . C 3 HOH A 134 2134 2134 HOH HOH . C 3 HOH A 135 2135 2135 HOH HOH . C 3 HOH A 136 2136 2136 HOH HOH . C 3 HOH A 137 2137 2137 HOH HOH . C 3 HOH A 138 2138 2138 HOH HOH . C 3 HOH A 139 2139 2139 HOH HOH . C 3 HOH A 140 2140 2140 HOH HOH . C 3 HOH A 141 2141 2141 HOH HOH . C 3 HOH A 142 2142 2142 HOH HOH . C 3 HOH A 143 2143 2143 HOH HOH . C 3 HOH A 144 2144 2144 HOH HOH . C 3 HOH A 145 2145 2145 HOH HOH . C 3 HOH A 146 2146 2146 HOH HOH . C 3 HOH A 147 2147 2147 HOH HOH . C 3 HOH A 148 2148 2148 HOH HOH . C 3 HOH A 149 2149 2149 HOH HOH . C 3 HOH A 150 2150 2150 HOH HOH . C 3 HOH A 151 2151 2151 HOH HOH . C 3 HOH A 152 2152 2152 HOH HOH . C 3 HOH A 153 2153 2153 HOH HOH . C 3 HOH A 154 2154 2154 HOH HOH . C 3 HOH A 155 2155 2155 HOH HOH . C 3 HOH A 156 2156 2156 HOH HOH . C 3 HOH A 157 2157 2157 HOH HOH . C 3 HOH A 158 2158 2158 HOH HOH . C 3 HOH A 159 2159 2159 HOH HOH . C 3 HOH A 160 2160 2160 HOH HOH . C 3 HOH A 161 2161 2161 HOH HOH . C 3 HOH A 162 2162 2162 HOH HOH . C 3 HOH A 163 2163 2163 HOH HOH . C 3 HOH A 164 2164 2164 HOH HOH . C 3 HOH A 165 2165 2165 HOH HOH . C 3 HOH A 166 2166 2166 HOH HOH . C 3 HOH A 167 2167 2167 HOH HOH . C 3 HOH A 168 2168 2168 HOH HOH . C 3 HOH A 169 2169 2169 HOH HOH . C 3 HOH A 170 2170 2170 HOH HOH . C 3 HOH A 171 2171 2171 HOH HOH . C 3 HOH A 172 2172 2172 HOH HOH . C 3 HOH A 173 2173 2173 HOH HOH . C 3 HOH A 174 2174 2174 HOH HOH . C 3 HOH A 175 2175 2175 HOH HOH . C 3 HOH A 176 2176 2176 HOH HOH . C 3 HOH A 177 2177 2177 HOH HOH . C 3 HOH A 178 2178 2178 HOH HOH . C 3 HOH A 179 2179 2179 HOH HOH . C 3 HOH A 180 2180 2180 HOH HOH . C 3 HOH A 181 2181 2181 HOH HOH . C 3 HOH A 182 2182 2182 HOH HOH . C 3 HOH A 183 2183 2183 HOH HOH . C 3 HOH A 184 2184 2184 HOH HOH . C 3 HOH A 185 2185 2185 HOH HOH . C 3 HOH A 186 2186 2186 HOH HOH . C 3 HOH A 187 2187 2187 HOH HOH . C 3 HOH A 188 2188 2188 HOH HOH . C 3 HOH A 189 2189 2189 HOH HOH . C 3 HOH A 190 2190 2190 HOH HOH . C 3 HOH A 191 2191 2191 HOH HOH . C 3 HOH A 192 2192 2192 HOH HOH . C 3 HOH A 193 2193 2193 HOH HOH . C 3 HOH A 194 2194 2194 HOH HOH . C 3 HOH A 195 2195 2195 HOH HOH . C 3 HOH A 196 2196 2196 HOH HOH . C 3 HOH A 197 2197 2197 HOH HOH . C 3 HOH A 198 2198 2198 HOH HOH . C 3 HOH A 199 2199 2199 HOH HOH . C 3 HOH A 200 2200 2200 HOH HOH . C 3 HOH A 201 2201 2201 HOH HOH . C 3 HOH A 202 2202 2202 HOH HOH . C 3 HOH A 203 2203 2203 HOH HOH . C 3 HOH A 204 2204 2204 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 O OP3 QQX . . . B 2 4.007 -1.093 21.47 0.7 15.97 ? OP3 QQX 1379 A 1 HETATM 2 S S1P QQX . . . B 2 1.351 -1.913 21.804 0.7 26.27 ? S1P QQX 1379 A 1 HETATM 3 O O5' QQX . . . B 2 4.485 -3.196 27.31 0.7 18.64 ? O5' QQX 1379 A 1 HETATM 4 C C5' QQX . . . B 2 4.122 -1.859 27.181 0.7 23.08 ? C5' QQX 1379 A 1 HETATM 5 C C4' QQX . . . B 2 4.325 -1.351 25.79 0.7 15.44 ? C4' QQX 1379 A 1 HETATM 6 O O4' QQX . . . B 2 5.619 -1.611 25.365 0.7 25.37 ? O4' QQX 1379 A 1 HETATM 7 C C3' QQX . . . B 2 3.439 -1.985 24.813 0.7 9.33 ? C3' QQX 1379 A 1 HETATM 8 O O3' QQX . . . B 2 3.106 -1.12 23.828 0.7 13.62 ? O3' QQX 1379 A 1 HETATM 9 C C2' QQX . . . B 2 4.243 -3.069 24.177 0.7 13.49 ? C2' QQX 1379 A 1 HETATM 10 O O2' QQX . . . B 2 3.729 -3.209 22.908 0.7 12.86 ? O2' QQX 1379 A 1 HETATM 11 C C1' QQX . . . B 2 5.615 -2.519 24.29 0.7 18.51 ? C1' QQX 1379 A 1 HETATM 12 N N9 QQX . . . B 2 6.661 -3.488 24.542 0.7 16.55 ? N9 QQX 1379 A 1 HETATM 13 C C8 QQX . . . B 2 6.696 -4.454 25.559 0.7 11.28 ? C8 QQX 1379 A 1 HETATM 14 N N7 QQX . . . B 2 7.828 -5.209 25.541 0.7 13.62 ? N7 QQX 1379 A 1 HETATM 15 C C5 QQX . . . B 2 8.606 -4.733 24.47 0.7 15.3 ? C5 QQX 1379 A 1 HETATM 16 C C6 QQX . . . B 2 9.877 -5.086 23.941 0.7 14.91 ? C6 QQX 1379 A 1 HETATM 17 N N6 QQX . . . B 2 10.649 -6.142 24.517 0.7 20.7 ? N6 QQX 1379 A 1 HETATM 18 N N1 QQX . . . B 2 10.297 -4.366 22.881 0.7 23.54 ? N1 QQX 1379 A 1 HETATM 19 C C2 QQX . . . B 2 9.607 -3.38 22.337 0.7 20.18 ? C2 QQX 1379 A 1 HETATM 20 C C4 QQX . . . B 2 7.873 -3.646 23.854 0.7 15.17 ? C4 QQX 1379 A 1 HETATM 21 N N3 QQX . . . B 2 8.423 -3.027 22.799 0.7 23.35 ? N3 QQX 1379 A 1 HETATM 22 P P QQX . . . B 2 3.14 -1.843 22.495 0.7 13.01 ? P QQX 1379 A 1 HETATM 23 H HP3 QQX . . . B 2 4.836 -1.399 21.505 0.7 19.16 ? HP3 QQX 1379 A 1 HETATM 24 H H5' QQX . . . B 2 4.179 -3.51 28.065 0.7 22.37 ? H5' QQX 1379 A 1 HETATM 25 H "H5'1" QQX . . . B 2 3.187 -1.763 27.417 0.7 27.69 ? "H5'1" QQX 1379 A 1 HETATM 26 H "H5'2" QQX . . . B 2 4.658 -1.325 27.793 0.7 27.69 ? "H5'2" QQX 1379 A 1 HETATM 27 H H4' QQX . . . B 2 4.171 -0.396 25.78 0.7 18.53 ? H4' QQX 1379 A 1 HETATM 28 H H3' QQX . . . B 2 2.657 -2.365 25.24 0.7 11.2 ? H3' QQX 1379 A 1 HETATM 29 H H1' QQX . . . B 2 5.809 -2.025 23.477 0.7 22.21 ? H1' QQX 1379 A 1 HETATM 30 H H2' QQX . . . B 2 4.147 -3.9 24.673 0.7 16.19 ? H2' QQX 1379 A 1 HETATM 31 H H8 QQX . . . B 2 5.981 -4.58 26.199 0.7 13.53 ? H8 QQX 1379 A 1 HETATM 32 H H2 QQX . . . B 2 9.981 -2.904 21.559 0.7 24.21 ? H2 QQX 1379 A 1 HETATM 33 H HN62 QQX . . . B 2 11.558 -6.153 24.416 0.7 24.84 ? HN62 QQX 1379 A 1 HETATM 34 H HN61 QQX . . . B 2 10.231 -6.812 24.989 0.7 24.84 ? HN61 QQX 1379 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #