data_1YD3 # _model_server_result.job_id raNiZJALTLtiKtcO4IWSNA _model_server_result.datetime_utc '2024-10-19 12:25:11' _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 1yd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2002}' # _entry.id 1YD3 # _exptl.entry_id 1YD3 _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 1YD3 _cell.length_a 56.094 _cell.length_b 56.094 _cell.length_c 111.491 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YD3 _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 49 A GLU 49 1_555 D MN MN . A MN 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc2 A OE1 GLU 60 A GLU 60 1_555 E MN MN . A MN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc3 A OE2 GLU 76 A GLU 76 1_555 B MN MN . A MN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc4 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2035 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2045 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc6 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2092 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc7 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc8 B MN MN . A MN 2001 1_555 H O HOH . A HOH 2179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc9 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc10 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc11 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc12 D MN MN . A MN 2004 1_555 H O HOH . A HOH 2156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc13 E MN MN . A MN 2005 1_555 H O HOH . A HOH 2132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc14 E MN MN . A MN 2005 1_555 H O HOH . A HOH 2174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? # _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 1YD3 _atom_sites.fract_transf_matrix[1][1] 0.017827 _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] 0.017827 _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] 0.008969 _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 44 HOH HOH . H 4 HOH A 44 2050 46 HOH HOH . H 4 HOH A 45 2051 47 HOH HOH . H 4 HOH A 46 2052 48 HOH HOH . H 4 HOH A 47 2053 49 HOH HOH . H 4 HOH A 48 2054 50 HOH HOH . H 4 HOH A 49 2055 51 HOH HOH . H 4 HOH A 50 2056 52 HOH HOH . H 4 HOH A 51 2057 54 HOH HOH . H 4 HOH A 52 2058 55 HOH HOH . H 4 HOH A 53 2059 56 HOH HOH . H 4 HOH A 54 2060 57 HOH HOH . H 4 HOH A 55 2061 58 HOH HOH . H 4 HOH A 56 2062 59 HOH HOH . H 4 HOH A 57 2063 60 HOH HOH . H 4 HOH A 58 2064 61 HOH HOH . H 4 HOH A 59 2065 62 HOH HOH . H 4 HOH A 60 2066 63 HOH HOH . H 4 HOH A 61 2067 64 HOH HOH . H 4 HOH A 62 2068 65 HOH HOH . H 4 HOH A 63 2069 66 HOH HOH . H 4 HOH A 64 2070 67 HOH HOH . H 4 HOH A 65 2071 68 HOH HOH . H 4 HOH A 66 2072 69 HOH HOH . H 4 HOH A 67 2073 70 HOH HOH . H 4 HOH A 68 2074 71 HOH HOH . H 4 HOH A 69 2075 72 HOH HOH . H 4 HOH A 70 2076 73 HOH HOH . H 4 HOH A 71 2077 74 HOH HOH . H 4 HOH A 72 2078 75 HOH HOH . H 4 HOH A 73 2079 76 HOH HOH . H 4 HOH A 74 2080 77 HOH HOH . H 4 HOH A 75 2081 78 HOH HOH . H 4 HOH A 76 2082 79 HOH HOH . H 4 HOH A 77 2083 80 HOH HOH . H 4 HOH A 78 2084 81 HOH HOH . H 4 HOH A 79 2085 82 HOH HOH . H 4 HOH A 80 2086 83 HOH HOH . H 4 HOH A 81 2087 84 HOH HOH . H 4 HOH A 82 2088 85 HOH HOH . H 4 HOH A 83 2089 86 HOH HOH . H 4 HOH A 84 2090 87 HOH HOH . H 4 HOH A 85 2091 88 HOH HOH . H 4 HOH A 86 2092 89 HOH HOH . H 4 HOH A 87 2093 90 HOH HOH . H 4 HOH A 88 2094 91 HOH HOH . H 4 HOH A 89 2095 92 HOH HOH . H 4 HOH A 90 2096 93 HOH HOH . H 4 HOH A 91 2097 94 HOH HOH . H 4 HOH A 92 2098 95 HOH HOH . H 4 HOH A 93 2099 96 HOH HOH . H 4 HOH A 94 2100 97 HOH HOH . H 4 HOH A 95 2101 98 HOH HOH . H 4 HOH A 96 2102 99 HOH HOH . H 4 HOH A 97 2103 100 HOH HOH . H 4 HOH A 98 2104 101 HOH HOH . H 4 HOH A 99 2105 102 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 106 HOH HOH . H 4 HOH A 103 2109 107 HOH HOH . H 4 HOH A 104 2110 109 HOH HOH . H 4 HOH A 105 2111 110 HOH HOH . H 4 HOH A 106 2112 111 HOH HOH . H 4 HOH A 107 2113 112 HOH HOH . H 4 HOH A 108 2114 113 HOH HOH . H 4 HOH A 109 2115 115 HOH HOH . H 4 HOH A 110 2116 117 HOH HOH . H 4 HOH A 111 2117 118 HOH HOH . H 4 HOH A 112 2118 119 HOH HOH . H 4 HOH A 113 2119 120 HOH HOH . H 4 HOH A 114 2120 121 HOH HOH . H 4 HOH A 115 2121 122 HOH HOH . H 4 HOH A 116 2122 123 HOH HOH . H 4 HOH A 117 2123 124 HOH HOH . H 4 HOH A 118 2124 125 HOH HOH . H 4 HOH A 119 2125 126 HOH HOH . H 4 HOH A 120 2126 127 HOH HOH . H 4 HOH A 121 2127 128 HOH HOH . H 4 HOH A 122 2128 129 HOH HOH . H 4 HOH A 123 2129 131 HOH HOH . H 4 HOH A 124 2130 132 HOH HOH . H 4 HOH A 125 2131 133 HOH HOH . H 4 HOH A 126 2132 134 HOH HOH . H 4 HOH A 127 2133 135 HOH HOH . H 4 HOH A 128 2134 139 HOH HOH . H 4 HOH A 129 2135 140 HOH HOH . H 4 HOH A 130 2136 142 HOH HOH . H 4 HOH A 131 2137 145 HOH HOH . H 4 HOH A 132 2138 146 HOH HOH . H 4 HOH A 133 2139 147 HOH HOH . H 4 HOH A 134 2140 148 HOH HOH . H 4 HOH A 135 2141 149 HOH HOH . H 4 HOH A 136 2142 150 HOH HOH . H 4 HOH A 137 2143 152 HOH HOH . H 4 HOH A 138 2144 153 HOH HOH . H 4 HOH A 139 2145 155 HOH HOH . H 4 HOH A 140 2146 160 HOH HOH . H 4 HOH A 141 2147 162 HOH HOH . H 4 HOH A 142 2148 164 HOH HOH . H 4 HOH A 143 2149 166 HOH HOH . H 4 HOH A 144 2150 167 HOH HOH . H 4 HOH A 145 2151 171 HOH HOH . H 4 HOH A 146 2152 174 HOH HOH . H 4 HOH A 147 2153 175 HOH HOH . H 4 HOH A 148 2154 179 HOH HOH . H 4 HOH A 149 2155 180 HOH HOH . H 4 HOH A 150 2156 181 HOH HOH . H 4 HOH A 151 2157 183 HOH HOH . H 4 HOH A 152 2158 184 HOH HOH . H 4 HOH A 153 2159 186 HOH HOH . H 4 HOH A 154 2160 187 HOH HOH . H 4 HOH A 155 2161 188 HOH HOH . H 4 HOH A 156 2162 189 HOH HOH . H 4 HOH A 157 2163 191 HOH HOH . H 4 HOH A 158 2164 192 HOH HOH . H 4 HOH A 159 2165 193 HOH HOH . H 4 HOH A 160 2166 194 HOH HOH . H 4 HOH A 161 2167 195 HOH HOH . H 4 HOH A 162 2168 196 HOH HOH . H 4 HOH A 163 2169 199 HOH HOH . H 4 HOH A 164 2170 200 HOH HOH . H 4 HOH A 165 2171 203 HOH HOH . H 4 HOH A 166 2172 204 HOH HOH . H 4 HOH A 167 2173 205 HOH HOH . H 4 HOH A 168 2174 207 HOH HOH . H 4 HOH A 169 2175 209 HOH HOH . H 4 HOH A 170 2176 211 HOH HOH . H 4 HOH A 171 2177 214 HOH HOH . H 4 HOH A 172 2178 216 HOH HOH . H 4 HOH A 173 2179 217 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 C _atom_site.label_entity_id 2 _atom_site.Cartn_x 35.069 _atom_site.Cartn_y 20.105 _atom_site.Cartn_z 50.665 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.39 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 2002 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #