data_3DAF # _model_server_result.job_id kCAKYwxmrdGHCjiX3mRwxQ _model_server_result.datetime_utc '2024-11-26 12:00:37' _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 3daf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 3DAF # _exptl.entry_id 3DAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 26.017 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CYANIDE ION' _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 3DAF _cell.length_a 97.14 _cell.length_b 97.14 _cell.length_c 166.03 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DAF _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 176 A CYS 176 1_555 C FE FE2 . A FE2 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc2 D C CYN . A CYN 401 1_555 C FE FE2 . A FE2 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? metalc ? metalc3 G N1 FEG . A FEG 501 1_555 C FE FE2 . A FE2 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 E C CMO . A CMO 502 1_555 C FE FE2 . A FE2 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.791 ? metalc ? metalc5 C FE FE2 . A FE2 503 1_555 F C CMO . A CMO 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.787 ? metalc ? metalc6 C FE FE2 . A FE2 503 1_555 H O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? # _chem_comp.formula 'C N -1' _chem_comp.formula_weight 26.017 _chem_comp.id CYN _chem_comp.mon_nstd_flag . _chem_comp.name 'CYANIDE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _chem_comp_bond.atom_id_1 C _chem_comp_bond.atom_id_2 N _chem_comp_bond.comp_id CYN _chem_comp_bond.value_order trip _chem_comp_bond.pdbx_ordinal 71 _chem_comp_bond.pdbx_stereo_config n _chem_comp_bond.pdbx_aromatic_flag n # _atom_sites.entry_id 3DAF _atom_sites.fract_transf_matrix[1][1] 0.010294 _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] 0.010294 _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] 0.006023 _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 PO4 A 1 2022 2022 PO4 PO4 . C 3 FE2 A 1 503 503 FE2 FE2 . D 4 CYN A 1 401 401 CYN CYN . E 5 CMO A 1 502 502 CMO CMO . F 5 CMO A 1 504 504 CMO CMO . G 6 FEG A 1 501 501 FEG FEG . H 7 HOH A 1 505 505 HOH HOH . H 7 HOH A 2 2023 2023 HOH HOH . H 7 HOH A 3 2024 2024 HOH HOH . H 7 HOH A 4 2025 2025 HOH HOH . H 7 HOH A 5 2026 2026 HOH HOH . H 7 HOH A 6 2027 2027 HOH HOH . H 7 HOH A 7 2028 2028 HOH HOH . H 7 HOH A 8 2029 2029 HOH HOH . H 7 HOH A 9 2030 2030 HOH HOH . H 7 HOH A 10 2031 2031 HOH HOH . H 7 HOH A 11 2032 2032 HOH HOH . H 7 HOH A 12 2033 2033 HOH HOH . H 7 HOH A 13 2034 2034 HOH HOH . H 7 HOH A 14 2035 2035 HOH HOH . H 7 HOH A 15 2036 2036 HOH HOH . H 7 HOH A 16 2037 2037 HOH HOH . H 7 HOH A 17 2038 2038 HOH HOH . H 7 HOH A 18 2039 2039 HOH HOH . H 7 HOH A 19 2040 2040 HOH HOH . H 7 HOH A 20 2041 2041 HOH HOH . H 7 HOH A 21 2042 2042 HOH HOH . H 7 HOH A 22 2043 2043 HOH HOH . H 7 HOH A 23 2044 2044 HOH HOH . H 7 HOH A 24 2045 2045 HOH HOH . H 7 HOH A 25 2046 2046 HOH HOH . H 7 HOH A 26 2047 2047 HOH HOH . H 7 HOH A 27 2048 2048 HOH HOH . H 7 HOH A 28 2049 2049 HOH HOH . H 7 HOH A 29 2050 2050 HOH HOH . H 7 HOH A 30 2051 2051 HOH HOH . H 7 HOH A 31 2052 2052 HOH HOH . H 7 HOH A 32 2053 2053 HOH HOH . H 7 HOH A 33 2054 2054 HOH HOH . H 7 HOH A 34 2055 2055 HOH HOH . H 7 HOH A 35 2056 2056 HOH HOH . H 7 HOH A 36 2057 2057 HOH HOH . H 7 HOH A 37 2058 2058 HOH HOH . H 7 HOH A 38 2059 2059 HOH HOH . H 7 HOH A 39 2060 2060 HOH HOH . H 7 HOH A 40 2061 2061 HOH HOH . H 7 HOH A 41 2062 2062 HOH HOH . H 7 HOH A 42 2063 2063 HOH HOH . H 7 HOH A 43 2064 2064 HOH HOH . H 7 HOH A 44 2065 2065 HOH HOH . H 7 HOH A 45 2066 2066 HOH HOH . H 7 HOH A 46 2067 2067 HOH HOH . H 7 HOH A 47 2068 2068 HOH HOH . H 7 HOH A 48 2069 2069 HOH HOH . H 7 HOH A 49 2070 2070 HOH HOH . H 7 HOH A 50 2071 2071 HOH HOH . H 7 HOH A 51 2072 2072 HOH HOH . H 7 HOH A 52 2073 2073 HOH HOH . H 7 HOH A 53 2074 2074 HOH HOH . H 7 HOH A 54 2075 2075 HOH HOH . H 7 HOH A 55 2076 2076 HOH HOH . H 7 HOH A 56 2077 2077 HOH HOH . H 7 HOH A 57 2078 2078 HOH HOH . H 7 HOH A 58 2079 2079 HOH HOH . H 7 HOH A 59 2080 2080 HOH HOH . H 7 HOH A 60 2081 2081 HOH HOH . H 7 HOH A 61 2082 2082 HOH HOH . H 7 HOH A 62 2083 2083 HOH HOH . H 7 HOH A 63 2084 2084 HOH HOH . H 7 HOH A 64 2085 2085 HOH HOH . H 7 HOH A 65 2086 2086 HOH HOH . H 7 HOH A 66 2087 2087 HOH HOH . H 7 HOH A 67 2088 2088 HOH HOH . H 7 HOH A 68 2089 2089 HOH HOH . H 7 HOH A 69 2090 2090 HOH HOH . H 7 HOH A 70 2091 2091 HOH HOH . H 7 HOH A 71 2092 2092 HOH HOH . H 7 HOH A 72 2093 2093 HOH HOH . H 7 HOH A 73 2094 2094 HOH HOH . H 7 HOH A 74 2095 2095 HOH HOH . H 7 HOH A 75 2096 2096 HOH HOH . H 7 HOH A 76 2097 2097 HOH HOH . H 7 HOH A 77 2098 2098 HOH HOH . H 7 HOH A 78 2099 2099 HOH HOH . H 7 HOH A 79 2100 2100 HOH HOH . H 7 HOH A 80 2101 2101 HOH HOH . H 7 HOH A 81 2102 2102 HOH HOH . H 7 HOH A 82 2103 2103 HOH HOH . H 7 HOH A 83 2104 2104 HOH HOH . H 7 HOH A 84 2105 2105 HOH HOH . H 7 HOH A 85 2106 2106 HOH HOH . H 7 HOH A 86 2107 2107 HOH HOH . H 7 HOH A 87 2108 2108 HOH HOH . H 7 HOH A 88 2109 2109 HOH HOH . H 7 HOH A 89 2110 2110 HOH HOH . H 7 HOH A 90 2111 2111 HOH HOH . H 7 HOH A 91 2112 2112 HOH HOH . H 7 HOH A 92 2113 2113 HOH HOH . H 7 HOH A 93 2114 2114 HOH HOH . H 7 HOH A 94 2115 2115 HOH HOH . H 7 HOH A 95 2116 2116 HOH HOH . H 7 HOH A 96 2117 2117 HOH HOH . H 7 HOH A 97 2118 2118 HOH HOH . H 7 HOH A 98 2119 2119 HOH HOH . H 7 HOH A 99 2120 2120 HOH HOH . H 7 HOH A 100 2121 2121 HOH HOH . H 7 HOH A 101 2122 2122 HOH HOH . H 7 HOH A 102 2123 2123 HOH HOH . H 7 HOH A 103 2124 2124 HOH HOH . H 7 HOH A 104 2125 2125 HOH HOH . H 7 HOH A 105 2126 2126 HOH HOH . H 7 HOH A 106 2127 2127 HOH HOH . H 7 HOH A 107 2128 2128 HOH HOH . H 7 HOH A 108 2129 2129 HOH HOH . H 7 HOH A 109 2130 2130 HOH HOH . H 7 HOH A 110 2131 2131 HOH HOH . H 7 HOH A 111 2132 2132 HOH HOH . H 7 HOH A 112 2133 2133 HOH HOH . H 7 HOH A 113 2134 2134 HOH HOH . H 7 HOH A 114 2135 2135 HOH HOH . H 7 HOH A 115 2136 2136 HOH HOH . H 7 HOH A 116 2137 2137 HOH HOH . H 7 HOH A 117 2138 2138 HOH HOH . H 7 HOH A 118 2139 2139 HOH HOH . H 7 HOH A 119 2140 2140 HOH HOH . H 7 HOH A 120 2141 2141 HOH HOH . H 7 HOH A 121 2142 2142 HOH HOH . H 7 HOH A 122 2143 2143 HOH HOH . H 7 HOH A 123 2144 2144 HOH HOH . H 7 HOH A 124 2145 2145 HOH HOH . H 7 HOH A 125 2146 2146 HOH HOH . H 7 HOH A 126 2147 2147 HOH HOH . H 7 HOH A 127 2148 2148 HOH HOH . H 7 HOH A 128 2149 2149 HOH HOH . H 7 HOH A 129 2150 2150 HOH HOH . H 7 HOH A 130 2151 2151 HOH HOH . H 7 HOH A 131 2152 2152 HOH HOH . H 7 HOH A 132 2153 2153 HOH HOH . H 7 HOH A 133 2154 2154 HOH HOH . H 7 HOH A 134 2155 2155 HOH HOH . H 7 HOH A 135 2156 2156 HOH HOH . H 7 HOH A 136 2157 2157 HOH HOH . H 7 HOH A 137 2158 2158 HOH HOH . H 7 HOH A 138 2159 2159 HOH HOH . H 7 HOH A 139 2160 2160 HOH HOH . H 7 HOH A 140 2161 2161 HOH HOH . H 7 HOH A 141 2162 2162 HOH HOH . H 7 HOH A 142 2163 2163 HOH HOH . H 7 HOH A 143 2164 2164 HOH HOH . H 7 HOH A 144 2165 2165 HOH HOH . H 7 HOH A 145 2166 2166 HOH HOH . H 7 HOH A 146 2167 2167 HOH HOH . H 7 HOH A 147 2168 2168 HOH HOH . H 7 HOH A 148 2169 2169 HOH HOH . H 7 HOH A 149 2170 2170 HOH HOH . H 7 HOH A 150 2171 2171 HOH HOH . H 7 HOH A 151 2172 2172 HOH HOH . H 7 HOH A 152 2173 2173 HOH HOH . H 7 HOH A 153 2174 2174 HOH HOH . H 7 HOH A 154 2175 2175 HOH HOH . H 7 HOH A 155 2176 2176 HOH HOH . H 7 HOH A 156 2177 2177 HOH HOH . H 7 HOH A 157 2178 2178 HOH HOH . H 7 HOH A 158 2179 2179 HOH HOH . H 7 HOH A 159 2180 2180 HOH HOH . H 7 HOH A 160 2181 2181 HOH HOH . H 7 HOH A 161 2182 2182 HOH HOH . H 7 HOH A 162 2183 2183 HOH HOH . H 7 HOH A 163 2184 2184 HOH HOH . H 7 HOH A 164 2185 2185 HOH HOH . H 7 HOH A 165 2186 2186 HOH HOH . H 7 HOH A 166 2187 2187 HOH HOH . H 7 HOH A 167 2188 2188 HOH HOH . H 7 HOH A 168 2189 2189 HOH HOH . H 7 HOH A 169 2190 2190 HOH HOH . H 7 HOH A 170 2191 2191 HOH HOH . H 7 HOH A 171 2192 2192 HOH HOH . H 7 HOH A 172 2193 2193 HOH HOH . H 7 HOH A 173 2194 2194 HOH HOH . H 7 HOH A 174 2195 2195 HOH HOH . H 7 HOH A 175 2196 2196 HOH HOH . H 7 HOH A 176 2197 2197 HOH HOH . H 7 HOH A 177 2198 2198 HOH HOH . H 7 HOH A 178 2199 2199 HOH HOH . H 7 HOH A 179 2200 2200 HOH HOH . H 7 HOH A 180 2201 2201 HOH HOH . H 7 HOH A 181 2202 2202 HOH HOH . H 7 HOH A 182 2203 2203 HOH HOH . H 7 HOH A 183 2204 2204 HOH HOH . H 7 HOH A 184 2205 2205 HOH HOH . H 7 HOH A 185 2206 2206 HOH HOH . H 7 HOH A 186 2207 2207 HOH HOH . H 7 HOH A 187 2208 2208 HOH HOH . H 7 HOH A 188 2209 2209 HOH HOH . H 7 HOH A 189 2210 2210 HOH HOH . H 7 HOH A 190 2211 2211 HOH HOH . H 7 HOH A 191 2212 2212 HOH HOH . H 7 HOH A 192 2213 2213 HOH HOH . H 7 HOH A 193 2214 2214 HOH HOH . H 7 HOH A 194 2215 2215 HOH HOH . H 7 HOH A 195 2216 2216 HOH HOH . H 7 HOH A 196 2217 2217 HOH HOH . H 7 HOH A 197 2218 2218 HOH HOH . H 7 HOH A 198 2219 2219 HOH HOH . H 7 HOH A 199 2220 2220 HOH HOH . H 7 HOH A 200 2221 2221 HOH HOH . H 7 HOH A 201 2222 2222 HOH HOH . H 7 HOH A 202 2223 2223 HOH HOH . H 7 HOH A 203 2224 2224 HOH HOH . H 7 HOH A 204 2225 2225 HOH HOH . H 7 HOH A 205 2226 2226 HOH HOH . H 7 HOH A 206 2227 2227 HOH HOH . H 7 HOH A 207 2228 2228 HOH HOH . H 7 HOH A 208 2229 2229 HOH HOH . H 7 HOH A 209 2230 2230 HOH HOH . H 7 HOH A 210 2231 2231 HOH HOH . H 7 HOH A 211 2232 2232 HOH HOH . H 7 HOH A 212 2233 2233 HOH HOH . H 7 HOH A 213 2234 2234 HOH HOH . H 7 HOH A 214 2235 2235 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 C CYN . . . D 4 18.178 8.564 23.827 0.9 33.62 ? C CYN 401 A 1 HETATM 2 N N CYN . . . D 4 17.109 8.189 23.73 0.9 36.21 ? N CYN 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 2 #