data_1YD2 # _model_server_result.job_id v5mJvpArj9jWuRq3hj-eIw _model_server_result.datetime_utc '2024-10-19 12:40:20' _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 1yd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2004}' # _entry.id 1YD2 # _exptl.entry_id 1YD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 5 _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 1YD2 _cell.length_a 55.817 _cell.length_b 55.817 _cell.length_c 111.352 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N 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 OE1 GLU 60 A GLU 60 1_555 E MN MN . A MN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc2 A OE2 GLU 76 A GLU 76 1_555 B MN MN . A MN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc3 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc4 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc6 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2036 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc7 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2037 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc8 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc9 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc10 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc11 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc12 E MN MN . A MN 2005 1_555 H O HOH . A HOH 2069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YD2 _atom_sites.fract_transf_matrix[1][1] 0.017916 _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] 0.017916 _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] 0.008981 _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 MN A 1 2001 1 MN MN . C 2 MN A 1 2002 2 MN MN . D 2 MN A 1 2004 4 MN MN . E 2 MN A 1 2005 5 MN MN . F 2 MN A 1 2006 6 MN MN . G 3 GOL A 1 1001 1 GOL GOL . H 4 HOH A 1 2007 1 HOH HOH . H 4 HOH A 2 2008 2 HOH HOH . H 4 HOH A 3 2009 3 HOH HOH . H 4 HOH A 4 2010 4 HOH HOH . H 4 HOH A 5 2011 5 HOH HOH . H 4 HOH A 6 2012 6 HOH HOH . H 4 HOH A 7 2013 7 HOH HOH . H 4 HOH A 8 2014 8 HOH HOH . H 4 HOH A 9 2015 9 HOH HOH . H 4 HOH A 10 2016 10 HOH HOH . H 4 HOH A 11 2017 11 HOH HOH . H 4 HOH A 12 2018 12 HOH HOH . H 4 HOH A 13 2019 13 HOH HOH . H 4 HOH A 14 2020 14 HOH HOH . H 4 HOH A 15 2021 15 HOH HOH . H 4 HOH A 16 2022 16 HOH HOH . H 4 HOH A 17 2023 17 HOH HOH . H 4 HOH A 18 2024 18 HOH HOH . H 4 HOH A 19 2025 19 HOH HOH . H 4 HOH A 20 2026 20 HOH HOH . H 4 HOH A 21 2027 21 HOH HOH . H 4 HOH A 22 2028 22 HOH HOH . H 4 HOH A 23 2029 23 HOH HOH . H 4 HOH A 24 2030 24 HOH HOH . H 4 HOH A 25 2031 25 HOH HOH . H 4 HOH A 26 2032 26 HOH HOH . H 4 HOH A 27 2033 27 HOH HOH . H 4 HOH A 28 2034 28 HOH HOH . H 4 HOH A 29 2035 29 HOH HOH . H 4 HOH A 30 2036 30 HOH HOH . H 4 HOH A 31 2037 31 HOH HOH . H 4 HOH A 32 2038 32 HOH HOH . H 4 HOH A 33 2039 33 HOH HOH . H 4 HOH A 34 2040 34 HOH HOH . H 4 HOH A 35 2041 35 HOH HOH . H 4 HOH A 36 2042 36 HOH HOH . H 4 HOH A 37 2043 37 HOH HOH . H 4 HOH A 38 2044 38 HOH HOH . H 4 HOH A 39 2045 39 HOH HOH . H 4 HOH A 40 2046 40 HOH HOH . H 4 HOH A 41 2047 41 HOH HOH . H 4 HOH A 42 2048 42 HOH HOH . H 4 HOH A 43 2049 43 HOH HOH . H 4 HOH A 44 2050 44 HOH HOH . H 4 HOH A 45 2051 45 HOH HOH . H 4 HOH A 46 2052 46 HOH HOH . H 4 HOH A 47 2053 47 HOH HOH . H 4 HOH A 48 2054 48 HOH HOH . H 4 HOH A 49 2055 49 HOH HOH . H 4 HOH A 50 2056 50 HOH HOH . H 4 HOH A 51 2057 51 HOH HOH . H 4 HOH A 52 2058 52 HOH HOH . H 4 HOH A 53 2059 53 HOH HOH . H 4 HOH A 54 2060 54 HOH HOH . H 4 HOH A 55 2061 55 HOH HOH . H 4 HOH A 56 2062 56 HOH HOH . H 4 HOH A 57 2063 57 HOH HOH . H 4 HOH A 58 2064 58 HOH HOH . H 4 HOH A 59 2065 59 HOH HOH . H 4 HOH A 60 2066 61 HOH HOH . H 4 HOH A 61 2067 62 HOH HOH . H 4 HOH A 62 2068 64 HOH HOH . H 4 HOH A 63 2069 65 HOH HOH . H 4 HOH A 64 2070 66 HOH HOH . H 4 HOH A 65 2071 67 HOH HOH . H 4 HOH A 66 2072 68 HOH HOH . H 4 HOH A 67 2073 69 HOH HOH . H 4 HOH A 68 2074 70 HOH HOH . H 4 HOH A 69 2075 71 HOH HOH . H 4 HOH A 70 2076 72 HOH HOH . H 4 HOH A 71 2077 73 HOH HOH . H 4 HOH A 72 2078 74 HOH HOH . H 4 HOH A 73 2079 75 HOH HOH . H 4 HOH A 74 2080 76 HOH HOH . H 4 HOH A 75 2081 77 HOH HOH . H 4 HOH A 76 2082 78 HOH HOH . H 4 HOH A 77 2083 79 HOH HOH . H 4 HOH A 78 2084 80 HOH HOH . H 4 HOH A 79 2085 81 HOH HOH . H 4 HOH A 80 2086 82 HOH HOH . H 4 HOH A 81 2087 83 HOH HOH . H 4 HOH A 82 2088 84 HOH HOH . H 4 HOH A 83 2089 85 HOH HOH . H 4 HOH A 84 2090 86 HOH HOH . H 4 HOH A 85 2091 87 HOH HOH . H 4 HOH A 86 2092 88 HOH HOH . H 4 HOH A 87 2093 89 HOH HOH . H 4 HOH A 88 2094 90 HOH HOH . H 4 HOH A 89 2095 91 HOH HOH . H 4 HOH A 90 2096 92 HOH HOH . H 4 HOH A 91 2097 93 HOH HOH . H 4 HOH A 92 2098 94 HOH HOH . H 4 HOH A 93 2099 95 HOH HOH . H 4 HOH A 94 2100 96 HOH HOH . H 4 HOH A 95 2101 97 HOH HOH . H 4 HOH A 96 2102 98 HOH HOH . H 4 HOH A 97 2103 99 HOH HOH . H 4 HOH A 98 2104 100 HOH HOH . H 4 HOH A 99 2105 101 HOH HOH . H 4 HOH A 100 2106 103 HOH HOH . H 4 HOH A 101 2107 104 HOH HOH . H 4 HOH A 102 2108 105 HOH HOH . H 4 HOH A 103 2109 106 HOH HOH . H 4 HOH A 104 2110 107 HOH HOH . H 4 HOH A 105 2111 108 HOH HOH . H 4 HOH A 106 2112 109 HOH HOH . H 4 HOH A 107 2113 110 HOH HOH . H 4 HOH A 108 2114 111 HOH HOH . H 4 HOH A 109 2115 112 HOH HOH . H 4 HOH A 110 2116 113 HOH HOH . H 4 HOH A 111 2117 114 HOH HOH . H 4 HOH A 112 2118 115 HOH HOH . H 4 HOH A 113 2119 116 HOH HOH . H 4 HOH A 114 2120 117 HOH HOH . H 4 HOH A 115 2121 118 HOH HOH . H 4 HOH A 116 2122 119 HOH HOH . H 4 HOH A 117 2123 120 HOH HOH . H 4 HOH A 118 2124 121 HOH HOH . H 4 HOH A 119 2125 122 HOH HOH . H 4 HOH A 120 2126 123 HOH HOH . H 4 HOH A 121 2127 124 HOH HOH . H 4 HOH A 122 2128 125 HOH HOH . H 4 HOH A 123 2129 126 HOH HOH . H 4 HOH A 124 2130 127 HOH HOH . H 4 HOH A 125 2131 128 HOH HOH . H 4 HOH A 126 2132 129 HOH HOH . H 4 HOH A 127 2133 130 HOH HOH . H 4 HOH A 128 2134 131 HOH HOH . H 4 HOH A 129 2135 132 HOH HOH . H 4 HOH A 130 2136 133 HOH HOH . H 4 HOH A 131 2137 134 HOH HOH . H 4 HOH A 132 2138 135 HOH HOH . H 4 HOH A 133 2139 136 HOH HOH . H 4 HOH A 134 2140 137 HOH HOH . H 4 HOH A 135 2141 138 HOH HOH . H 4 HOH A 136 2142 139 HOH HOH . H 4 HOH A 137 2143 140 HOH HOH . H 4 HOH A 138 2144 141 HOH HOH . H 4 HOH A 139 2145 142 HOH HOH . H 4 HOH A 140 2146 143 HOH HOH . H 4 HOH A 141 2147 144 HOH HOH . H 4 HOH A 142 2148 145 HOH HOH . H 4 HOH A 143 2149 146 HOH HOH . H 4 HOH A 144 2150 147 HOH HOH . H 4 HOH A 145 2151 148 HOH HOH . H 4 HOH A 146 2152 149 HOH HOH . H 4 HOH A 147 2153 150 HOH HOH . H 4 HOH A 148 2154 151 HOH HOH . H 4 HOH A 149 2155 152 HOH HOH . H 4 HOH A 150 2156 153 HOH HOH . H 4 HOH A 151 2157 154 HOH HOH . H 4 HOH A 152 2158 155 HOH HOH . H 4 HOH A 153 2159 156 HOH HOH . H 4 HOH A 154 2160 157 HOH HOH . H 4 HOH A 155 2161 158 HOH HOH . H 4 HOH A 156 2162 159 HOH HOH . H 4 HOH A 157 2163 160 HOH HOH . H 4 HOH A 158 2164 161 HOH HOH . H 4 HOH A 159 2165 162 HOH HOH . H 4 HOH A 160 2166 163 HOH HOH . H 4 HOH A 161 2167 164 HOH HOH . H 4 HOH A 162 2168 165 HOH HOH . H 4 HOH A 163 2169 166 HOH HOH . H 4 HOH A 164 2170 167 HOH HOH . H 4 HOH A 165 2171 168 HOH HOH . H 4 HOH A 166 2172 169 HOH HOH . H 4 HOH A 167 2173 170 HOH HOH . H 4 HOH A 168 2174 171 HOH HOH . H 4 HOH A 169 2175 172 HOH HOH . H 4 HOH A 170 2176 173 HOH HOH . H 4 HOH A 171 2177 174 HOH HOH . H 4 HOH A 172 2178 175 HOH HOH . H 4 HOH A 173 2179 176 HOH HOH . H 4 HOH A 174 2180 177 HOH HOH . H 4 HOH A 175 2181 178 HOH HOH . H 4 HOH A 176 2182 179 HOH HOH . H 4 HOH A 177 2183 180 HOH HOH . H 4 HOH A 178 2184 183 HOH HOH . H 4 HOH A 179 2185 184 HOH HOH . H 4 HOH A 180 2186 185 HOH HOH . H 4 HOH A 181 2187 186 HOH HOH . H 4 HOH A 182 2188 189 HOH HOH . H 4 HOH A 183 2189 191 HOH HOH . H 4 HOH A 184 2190 192 HOH HOH . H 4 HOH A 185 2191 193 HOH HOH . H 4 HOH A 186 2192 194 HOH HOH . H 4 HOH A 187 2193 196 HOH HOH . H 4 HOH A 188 2194 197 HOH HOH . H 4 HOH A 189 2195 198 HOH HOH . H 4 HOH A 190 2196 199 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 2 _atom_site.Cartn_x 50.61 _atom_site.Cartn_y 40.925 _atom_site.Cartn_z 50.109 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 48.78 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 2004 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #