data_2ZYW # _model_server_result.job_id l070fb3PVc4I9eHNIE7Pwg _model_server_result.datetime_utc '2024-11-05 23:28:55' _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 2zyw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 2ZYW # _exptl.entry_id 2ZYW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-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 105.25 _cell.angle_gamma 90 _cell.entry_id 2ZYW _cell.length_a 155.313 _cell.length_b 67.838 _cell.length_c 42.867 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZYW _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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,D,E,F,G,H _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 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 2ZYW _atom_sites.fract_transf_matrix[1][1] 0.006439 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001755 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014741 _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] 0.024179 _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 A3P X 1 501 501 A3P A3P . C 3 NPO X 1 601 601 NPO NPO . D 3 NPO X 1 602 602 NPO NPO . E 4 GOL X 1 1001 1001 GOL GOL . F 4 GOL X 1 1002 1002 GOL GOL . G 4 GOL X 1 1003 1003 GOL GOL . H 5 HOH X 1 2001 2001 HOH HOH . H 5 HOH X 2 2002 2002 HOH HOH . H 5 HOH X 3 2003 2003 HOH HOH . H 5 HOH X 4 2004 2004 HOH HOH . H 5 HOH X 5 2005 2005 HOH HOH . H 5 HOH X 6 2006 2006 HOH HOH . H 5 HOH X 7 2007 2007 HOH HOH . H 5 HOH X 8 2008 2008 HOH HOH . H 5 HOH X 9 2009 2009 HOH HOH . H 5 HOH X 10 2010 2010 HOH HOH . H 5 HOH X 11 2011 2011 HOH HOH . H 5 HOH X 12 2012 2012 HOH HOH . H 5 HOH X 13 2013 2013 HOH HOH . H 5 HOH X 14 2014 2014 HOH HOH . H 5 HOH X 15 2015 2015 HOH HOH . H 5 HOH X 16 2016 2016 HOH HOH . H 5 HOH X 17 2017 2017 HOH HOH . H 5 HOH X 18 2018 2018 HOH HOH . H 5 HOH X 19 2019 2019 HOH HOH . H 5 HOH X 20 2020 2020 HOH HOH . H 5 HOH X 21 2021 2021 HOH HOH . H 5 HOH X 22 2022 2022 HOH HOH . H 5 HOH X 23 2023 2023 HOH HOH . H 5 HOH X 24 2024 2024 HOH HOH . H 5 HOH X 25 2025 2025 HOH HOH . H 5 HOH X 26 2026 2026 HOH HOH . H 5 HOH X 27 2027 2027 HOH HOH . H 5 HOH X 28 2028 2028 HOH HOH . H 5 HOH X 29 2029 2029 HOH HOH . H 5 HOH X 30 2030 2030 HOH HOH . H 5 HOH X 31 2031 2031 HOH HOH . H 5 HOH X 32 2032 2032 HOH HOH . H 5 HOH X 33 2033 2033 HOH HOH . H 5 HOH X 34 2034 2034 HOH HOH . H 5 HOH X 35 2035 2035 HOH HOH . H 5 HOH X 36 2036 2036 HOH HOH . H 5 HOH X 37 2037 2037 HOH HOH . H 5 HOH X 38 2038 2038 HOH HOH . H 5 HOH X 39 2039 2039 HOH HOH . H 5 HOH X 40 2040 2040 HOH HOH . H 5 HOH X 41 2041 2041 HOH HOH . H 5 HOH X 42 2042 2042 HOH HOH . H 5 HOH X 43 2043 2043 HOH HOH . H 5 HOH X 44 2044 2044 HOH HOH . H 5 HOH X 45 2045 2045 HOH HOH . H 5 HOH X 46 2046 2046 HOH HOH . H 5 HOH X 47 2047 2047 HOH HOH . H 5 HOH X 48 2048 2048 HOH HOH . H 5 HOH X 49 2050 2050 HOH HOH . H 5 HOH X 50 2051 2051 HOH HOH . H 5 HOH X 51 2052 2052 HOH HOH . H 5 HOH X 52 2053 2053 HOH HOH . H 5 HOH X 53 2054 2054 HOH HOH . H 5 HOH X 54 2055 2055 HOH HOH . H 5 HOH X 55 2056 2056 HOH HOH . H 5 HOH X 56 2057 2057 HOH HOH . H 5 HOH X 57 2058 2058 HOH HOH . H 5 HOH X 58 2059 2059 HOH HOH . H 5 HOH X 59 2060 2060 HOH HOH . H 5 HOH X 60 2061 2061 HOH HOH . H 5 HOH X 61 2062 2062 HOH HOH . H 5 HOH X 62 2063 2063 HOH HOH . H 5 HOH X 63 2064 2064 HOH HOH . H 5 HOH X 64 2065 2065 HOH HOH . H 5 HOH X 65 2066 2066 HOH HOH . H 5 HOH X 66 2067 2067 HOH HOH . H 5 HOH X 67 2068 2068 HOH HOH . H 5 HOH X 68 2070 2070 HOH HOH . H 5 HOH X 69 2071 2071 HOH HOH . H 5 HOH X 70 2072 2072 HOH HOH . H 5 HOH X 71 2073 2073 HOH HOH . H 5 HOH X 72 2074 2074 HOH HOH . H 5 HOH X 73 2075 2075 HOH HOH . H 5 HOH X 74 2076 2076 HOH HOH . H 5 HOH X 75 2078 2078 HOH HOH . H 5 HOH X 76 2079 2079 HOH HOH . H 5 HOH X 77 2080 2080 HOH HOH . H 5 HOH X 78 2081 2081 HOH HOH . H 5 HOH X 79 2082 2082 HOH HOH . H 5 HOH X 80 2083 2083 HOH HOH . H 5 HOH X 81 2084 2084 HOH HOH . H 5 HOH X 82 2085 2085 HOH HOH . H 5 HOH X 83 2086 2086 HOH HOH . H 5 HOH X 84 2087 2087 HOH HOH . H 5 HOH X 85 2088 2088 HOH HOH . H 5 HOH X 86 2089 2089 HOH HOH . H 5 HOH X 87 2090 2090 HOH HOH . H 5 HOH X 88 2091 2091 HOH HOH . H 5 HOH X 89 2092 2092 HOH HOH . H 5 HOH X 90 2093 2093 HOH HOH . H 5 HOH X 91 2094 2094 HOH HOH . H 5 HOH X 92 2095 2095 HOH HOH . H 5 HOH X 93 2096 2096 HOH HOH . H 5 HOH X 94 2097 2097 HOH HOH . H 5 HOH X 95 2098 2098 HOH HOH . H 5 HOH X 96 2099 2099 HOH HOH . H 5 HOH X 97 2100 2100 HOH HOH . H 5 HOH X 98 2101 2101 HOH HOH . H 5 HOH X 99 2102 2102 HOH HOH . H 5 HOH X 100 2103 2103 HOH HOH . H 5 HOH X 101 2104 2104 HOH HOH . H 5 HOH X 102 2105 2105 HOH HOH . H 5 HOH X 103 2106 2106 HOH HOH . H 5 HOH X 104 2107 2107 HOH HOH . H 5 HOH X 105 2108 2108 HOH HOH . H 5 HOH X 106 2109 2109 HOH HOH . H 5 HOH X 107 2110 2110 HOH HOH . H 5 HOH X 108 2111 2111 HOH HOH . H 5 HOH X 109 2112 2112 HOH HOH . H 5 HOH X 110 2113 2113 HOH HOH . H 5 HOH X 111 2114 2114 HOH HOH . H 5 HOH X 112 2115 2115 HOH HOH . H 5 HOH X 113 2116 2116 HOH HOH . H 5 HOH X 114 2117 2117 HOH HOH . H 5 HOH X 115 2118 2118 HOH HOH . H 5 HOH X 116 2120 2120 HOH HOH . H 5 HOH X 117 2121 2121 HOH HOH . H 5 HOH X 118 2122 2122 HOH HOH . H 5 HOH X 119 2126 2126 HOH HOH . H 5 HOH X 120 2127 2127 HOH HOH . H 5 HOH X 121 2128 2128 HOH HOH . H 5 HOH X 122 2129 2129 HOH HOH . H 5 HOH X 123 2130 2130 HOH HOH . H 5 HOH X 124 2131 2131 HOH HOH . H 5 HOH X 125 2132 2132 HOH HOH . H 5 HOH X 126 2135 2135 HOH HOH . H 5 HOH X 127 2136 2136 HOH HOH . H 5 HOH X 128 2137 2137 HOH HOH . H 5 HOH X 129 2138 2138 HOH HOH . H 5 HOH X 130 2139 2139 HOH HOH . H 5 HOH X 131 2141 2141 HOH HOH . H 5 HOH X 132 2142 2142 HOH HOH . H 5 HOH X 133 2143 2143 HOH HOH . H 5 HOH X 134 2144 2144 HOH HOH . H 5 HOH X 135 2146 2146 HOH HOH . H 5 HOH X 136 2147 2147 HOH HOH . H 5 HOH X 137 2148 2148 HOH HOH . H 5 HOH X 138 2149 2149 HOH HOH . H 5 HOH X 139 2150 2150 HOH HOH . H 5 HOH X 140 2151 2151 HOH HOH . H 5 HOH X 141 2152 2152 HOH HOH . H 5 HOH X 142 2153 2153 HOH HOH . H 5 HOH X 143 2154 2154 HOH HOH . H 5 HOH X 144 2155 2155 HOH HOH . H 5 HOH X 145 2156 2156 HOH HOH . H 5 HOH X 146 2157 2157 HOH HOH . H 5 HOH X 147 2158 2158 HOH HOH . H 5 HOH X 148 2159 2159 HOH HOH . H 5 HOH X 149 2160 2160 HOH HOH . H 5 HOH X 150 2161 2161 HOH HOH . H 5 HOH X 151 2162 2162 HOH HOH . H 5 HOH X 152 2163 2163 HOH HOH . H 5 HOH X 153 2164 2164 HOH HOH . H 5 HOH X 154 2165 2165 HOH HOH . H 5 HOH X 155 2166 2166 HOH HOH . H 5 HOH X 156 2167 2167 HOH HOH . H 5 HOH X 157 2168 2168 HOH HOH . H 5 HOH X 158 2169 2169 HOH HOH . H 5 HOH X 159 2170 2170 HOH HOH . H 5 HOH X 160 2171 2171 HOH HOH . H 5 HOH X 161 2172 2172 HOH HOH . H 5 HOH X 162 2173 2173 HOH HOH . H 5 HOH X 163 2175 2175 HOH HOH . H 5 HOH X 164 2176 2176 HOH HOH . H 5 HOH X 165 2177 2177 HOH HOH . H 5 HOH X 166 2178 2178 HOH HOH . H 5 HOH X 167 2179 2179 HOH HOH . H 5 HOH X 168 2180 2180 HOH HOH . H 5 HOH X 169 2181 2181 HOH HOH . H 5 HOH X 170 2182 2182 HOH HOH . H 5 HOH X 171 2183 2183 HOH HOH . H 5 HOH X 172 2184 2184 HOH HOH . H 5 HOH X 173 2185 2185 HOH HOH . H 5 HOH X 174 2186 2186 HOH HOH . H 5 HOH X 175 2187 2187 HOH HOH . H 5 HOH X 176 2188 2188 HOH HOH . H 5 HOH X 177 2189 2189 HOH HOH . H 5 HOH X 178 2190 2190 HOH HOH . H 5 HOH X 179 2191 2191 HOH HOH . H 5 HOH X 180 2192 2192 HOH HOH . H 5 HOH X 181 2193 2193 HOH HOH . H 5 HOH X 182 2194 2194 HOH HOH . H 5 HOH X 183 2195 2195 HOH HOH . H 5 HOH X 184 2202 2202 HOH HOH . H 5 HOH X 185 2204 2204 HOH HOH . H 5 HOH X 186 2205 2205 HOH HOH . H 5 HOH X 187 2206 2206 HOH HOH . H 5 HOH X 188 2210 2210 HOH HOH . H 5 HOH X 189 2211 2211 HOH HOH . H 5 HOH X 190 2212 2212 HOH HOH . H 5 HOH X 191 2214 2214 HOH HOH . H 5 HOH X 192 2215 2215 HOH HOH . H 5 HOH X 193 2216 2216 HOH HOH . H 5 HOH X 194 2217 2217 HOH HOH . H 5 HOH X 195 2218 2218 HOH HOH . H 5 HOH X 196 2219 2219 HOH HOH . H 5 HOH X 197 2220 2220 HOH HOH . H 5 HOH X 198 2221 2221 HOH HOH . H 5 HOH X 199 2222 2222 HOH HOH . H 5 HOH X 200 2226 2226 HOH HOH . H 5 HOH X 201 2229 2229 HOH HOH . H 5 HOH X 202 2231 2231 HOH HOH . H 5 HOH X 203 2233 2233 HOH HOH . H 5 HOH X 204 2234 2234 HOH HOH . H 5 HOH X 205 2238 2238 HOH HOH . H 5 HOH X 206 2239 2239 HOH HOH . H 5 HOH X 207 2240 2240 HOH HOH . H 5 HOH X 208 2241 2241 HOH HOH . H 5 HOH X 209 2243 2243 HOH HOH . H 5 HOH X 210 2247 2247 HOH HOH . H 5 HOH X 211 2248 2248 HOH HOH . H 5 HOH X 212 2249 2249 HOH HOH . H 5 HOH X 213 2250 2250 HOH HOH . H 5 HOH X 214 2255 2255 HOH HOH . H 5 HOH X 215 2257 2257 HOH HOH . H 5 HOH X 216 2258 2258 HOH HOH . H 5 HOH X 217 2259 2259 HOH HOH . H 5 HOH X 218 2260 2260 HOH HOH . H 5 HOH X 219 2261 2261 HOH HOH . H 5 HOH X 220 2262 2262 HOH HOH . H 5 HOH X 221 2265 2265 HOH HOH . H 5 HOH X 222 2266 2266 HOH HOH . H 5 HOH X 223 2270 2270 HOH HOH . H 5 HOH X 224 2272 2272 HOH HOH . H 5 HOH X 225 2273 2273 HOH HOH . H 5 HOH X 226 2274 2274 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 P P1 A3P . . . B 2 -23.238 -35.168 21.434 1 17.39 ? P1 A3P 501 X 1 HETATM 2 O O1P A3P . . . B 2 -22.308 -34.003 21.204 1 18.45 ? O1P A3P 501 X 1 HETATM 3 O O2P A3P . . . B 2 -22.901 -36.438 20.702 1 17.54 ? O2P A3P 501 X 1 HETATM 4 O O3P A3P . . . B 2 -23.563 -35.394 22.895 1 18.12 ? O3P A3P 501 X 1 HETATM 5 P P2 A3P . . . B 2 -28.959 -35.685 16.475 1 17.99 ? P2 A3P 501 X 1 HETATM 6 O O4P A3P . . . B 2 -28.33 -36.992 16.038 1 18.75 ? O4P A3P 501 X 1 HETATM 7 O O5P A3P . . . B 2 -29.057 -34.645 15.387 1 17.55 ? O5P A3P 501 X 1 HETATM 8 O O6P A3P . . . B 2 -30.215 -35.827 17.29 1 17.87 ? O6P A3P 501 X 1 HETATM 9 O O5' A3P . . . B 2 -27.92 -35.02 17.507 1 16.74 ? O5' A3P 501 X 1 HETATM 10 C C5' A3P . . . B 2 -27.388 -35.763 18.596 1 16.47 ? C5' A3P 501 X 1 HETATM 11 C C4' A3P . . . B 2 -26.593 -34.789 19.46 1 17.39 ? C4' A3P 501 X 1 HETATM 12 O O4' A3P . . . B 2 -27.495 -33.925 20.16 1 17.59 ? O4' A3P 501 X 1 HETATM 13 C C3' A3P . . . B 2 -25.762 -35.5 20.528 1 17.28 ? C3' A3P 501 X 1 HETATM 14 O O3' A3P . . . B 2 -24.647 -34.648 20.806 1 17.18 ? O3' A3P 501 X 1 HETATM 15 C C2' A3P . . . B 2 -26.736 -35.509 21.69 1 18.2 ? C2' A3P 501 X 1 HETATM 16 O O2' A3P . . . B 2 -26.139 -35.757 22.969 1 18.98 ? O2' A3P 501 X 1 HETATM 17 C C1' A3P . . . B 2 -27.321 -34.108 21.566 1 18.17 ? C1' A3P 501 X 1 HETATM 18 N N9 A3P . . . B 2 -28.601 -33.947 22.287 1 18.71 ? N9 A3P 501 X 1 HETATM 19 C C8 A3P . . . B 2 -29.682 -34.749 22.222 1 18.84 ? C8 A3P 501 X 1 HETATM 20 N N7 A3P . . . B 2 -30.675 -34.283 23.018 1 18.49 ? N7 A3P 501 X 1 HETATM 21 C C5 A3P . . . B 2 -30.214 -33.156 23.599 1 18.33 ? C5 A3P 501 X 1 HETATM 22 C C6 A3P . . . B 2 -30.728 -32.161 24.562 1 18.57 ? C6 A3P 501 X 1 HETATM 23 N N6 A3P . . . B 2 -31.979 -32.291 25.06 1 18.38 ? N6 A3P 501 X 1 HETATM 24 N N1 A3P . . . B 2 -29.916 -31.124 24.916 1 18 ? N1 A3P 501 X 1 HETATM 25 C C2 A3P . . . B 2 -28.669 -30.991 24.427 1 18.94 ? C2 A3P 501 X 1 HETATM 26 N N3 A3P . . . B 2 -28.133 -31.861 23.546 1 18.36 ? N3 A3P 501 X 1 HETATM 27 C C4 A3P . . . B 2 -28.849 -32.939 23.113 1 18.02 ? C4 A3P 501 X 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 27 #