data_3RFQ # _model_server_result.job_id 4-gEuETJDwq-vPvRcaBfTw _model_server_result.datetime_utc '2025-03-12 20:19:33' _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 3rfq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":181}' # _entry.id 3RFQ # _exptl.entry_id 3RFQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 2 _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 3RFQ _cell.length_a 125.64 _cell.length_b 137.64 _cell.length_c 73.96 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RFQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I _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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 36.98 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D 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 OG SER 129 A SER 124 1_555 D NA NA . A NA 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc2 A OD1 ASP 165 A ASP 160 1_555 D NA NA . A NA 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc3 D NA NA . A NA 181 1_555 G O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc4 D NA NA . A NA 181 1_555 G O HOH . A HOH 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc5 D NA NA . A NA 181 1_555 G O HOH . A HOH 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc6 C OG SER 129 C SER 124 1_555 F NA NA . C NA 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc7 C OD1 ASP 165 C ASP 160 1_555 F NA NA . C NA 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc8 F NA NA . C NA 181 1_555 I O HOH . C HOH 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc9 F NA NA . C NA 181 1_555 I O HOH . C HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3RFQ _atom_sites.fract_transf_matrix[1][1] 0.007959 _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] 0.007265 _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] 0.013521 _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 D 2 NA A 1 181 1 NA NA . E 3 B3P A 1 182 3 B3P B3P . F 2 NA C 1 181 2 NA NA . G 4 HOH A 1 183 183 HOH HOH . G 4 HOH A 2 184 184 HOH HOH . G 4 HOH A 3 185 1 HOH HOH . G 4 HOH A 4 186 2 HOH HOH . G 4 HOH A 5 187 187 HOH HOH . G 4 HOH A 6 188 188 HOH HOH . G 4 HOH A 7 189 4 HOH HOH . G 4 HOH A 8 190 6 HOH HOH . G 4 HOH A 9 191 8 HOH HOH . G 4 HOH A 10 192 14 HOH HOH . G 4 HOH A 11 193 19 HOH HOH . G 4 HOH A 12 194 24 HOH HOH . G 4 HOH A 13 195 31 HOH HOH . G 4 HOH A 14 196 41 HOH HOH . G 4 HOH A 15 197 42 HOH HOH . G 4 HOH A 16 198 44 HOH HOH . G 4 HOH A 17 199 47 HOH HOH . G 4 HOH A 18 200 49 HOH HOH . G 4 HOH A 19 201 52 HOH HOH . G 4 HOH A 20 202 54 HOH HOH . G 4 HOH A 21 203 56 HOH HOH . G 4 HOH A 22 204 58 HOH HOH . G 4 HOH A 23 205 60 HOH HOH . G 4 HOH A 24 206 61 HOH HOH . G 4 HOH A 25 207 63 HOH HOH . G 4 HOH A 26 208 64 HOH HOH . G 4 HOH A 27 209 74 HOH HOH . G 4 HOH A 28 210 76 HOH HOH . G 4 HOH A 29 211 79 HOH HOH . G 4 HOH A 30 212 81 HOH HOH . G 4 HOH A 31 213 82 HOH HOH . G 4 HOH A 32 214 86 HOH HOH . G 4 HOH A 33 215 89 HOH HOH . G 4 HOH A 34 216 90 HOH HOH . G 4 HOH A 35 217 93 HOH HOH . G 4 HOH A 36 218 103 HOH HOH . G 4 HOH A 37 219 107 HOH HOH . G 4 HOH A 38 220 108 HOH HOH . G 4 HOH A 39 221 111 HOH HOH . G 4 HOH A 40 222 112 HOH HOH . G 4 HOH A 41 223 114 HOH HOH . G 4 HOH A 42 224 117 HOH HOH . G 4 HOH A 43 225 120 HOH HOH . G 4 HOH A 44 226 226 HOH HOH . G 4 HOH A 45 227 122 HOH HOH . G 4 HOH A 46 228 127 HOH HOH . G 4 HOH A 47 229 129 HOH HOH . G 4 HOH A 48 230 133 HOH HOH . G 4 HOH A 49 231 134 HOH HOH . G 4 HOH A 50 232 135 HOH HOH . G 4 HOH A 51 233 136 HOH HOH . G 4 HOH A 52 234 137 HOH HOH . G 4 HOH A 53 235 144 HOH HOH . G 4 HOH A 54 236 146 HOH HOH . G 4 HOH A 55 237 147 HOH HOH . G 4 HOH A 56 238 148 HOH HOH . G 4 HOH A 57 239 149 HOH HOH . G 4 HOH A 58 240 150 HOH HOH . G 4 HOH A 59 241 151 HOH HOH . G 4 HOH A 60 242 152 HOH HOH . G 4 HOH A 61 243 153 HOH HOH . G 4 HOH A 62 244 154 HOH HOH . G 4 HOH A 63 245 155 HOH HOH . G 4 HOH A 64 246 156 HOH HOH . G 4 HOH A 65 247 157 HOH HOH . G 4 HOH A 66 248 158 HOH HOH . G 4 HOH A 67 249 159 HOH HOH . G 4 HOH A 68 250 160 HOH HOH . G 4 HOH A 69 251 161 HOH HOH . G 4 HOH A 70 252 162 HOH HOH . G 4 HOH A 71 253 164 HOH HOH . G 4 HOH A 72 254 166 HOH HOH . G 4 HOH A 73 255 181 HOH HOH . G 4 HOH A 74 256 182 HOH HOH . G 4 HOH A 75 271 271 HOH HOH . G 4 HOH A 76 272 272 HOH HOH . G 4 HOH A 77 273 273 HOH HOH . G 4 HOH A 78 274 274 HOH HOH . G 4 HOH A 79 283 283 HOH HOH . G 4 HOH A 80 284 284 HOH HOH . G 4 HOH A 81 285 285 HOH HOH . G 4 HOH A 82 286 286 HOH HOH . G 4 HOH A 83 287 287 HOH HOH . H 4 HOH B 1 181 9 HOH HOH . H 4 HOH B 2 182 11 HOH HOH . H 4 HOH B 3 183 13 HOH HOH . H 4 HOH B 4 184 15 HOH HOH . H 4 HOH B 5 185 185 HOH HOH . H 4 HOH B 6 186 20 HOH HOH . H 4 HOH B 7 187 21 HOH HOH . H 4 HOH B 8 188 22 HOH HOH . H 4 HOH B 9 189 23 HOH HOH . H 4 HOH B 10 190 190 HOH HOH . H 4 HOH B 11 191 191 HOH HOH . H 4 HOH B 12 192 192 HOH HOH . H 4 HOH B 13 193 193 HOH HOH . H 4 HOH B 14 194 194 HOH HOH . H 4 HOH B 15 195 195 HOH HOH . H 4 HOH B 16 196 196 HOH HOH . H 4 HOH B 17 197 197 HOH HOH . H 4 HOH B 18 198 198 HOH HOH . H 4 HOH B 19 199 199 HOH HOH . H 4 HOH B 20 200 200 HOH HOH . H 4 HOH B 21 201 201 HOH HOH . H 4 HOH B 22 202 202 HOH HOH . H 4 HOH B 23 203 203 HOH HOH . H 4 HOH B 24 204 204 HOH HOH . H 4 HOH B 25 205 205 HOH HOH . H 4 HOH B 26 206 206 HOH HOH . H 4 HOH B 27 207 207 HOH HOH . H 4 HOH B 28 208 208 HOH HOH . H 4 HOH B 29 209 209 HOH HOH . H 4 HOH B 30 210 210 HOH HOH . H 4 HOH B 31 211 211 HOH HOH . H 4 HOH B 32 212 212 HOH HOH . H 4 HOH B 33 213 213 HOH HOH . H 4 HOH B 34 214 214 HOH HOH . H 4 HOH B 35 215 215 HOH HOH . H 4 HOH B 36 216 216 HOH HOH . H 4 HOH B 37 217 217 HOH HOH . H 4 HOH B 38 218 218 HOH HOH . H 4 HOH B 39 219 219 HOH HOH . H 4 HOH B 40 220 220 HOH HOH . H 4 HOH B 41 221 221 HOH HOH . H 4 HOH B 42 222 222 HOH HOH . H 4 HOH B 43 223 223 HOH HOH . H 4 HOH B 44 224 224 HOH HOH . H 4 HOH B 45 225 225 HOH HOH . H 4 HOH B 46 226 25 HOH HOH . H 4 HOH B 47 227 26 HOH HOH . H 4 HOH B 48 228 27 HOH HOH . H 4 HOH B 49 229 29 HOH HOH . H 4 HOH B 50 230 30 HOH HOH . H 4 HOH B 51 231 35 HOH HOH . H 4 HOH B 52 232 38 HOH HOH . H 4 HOH B 53 233 40 HOH HOH . H 4 HOH B 54 234 43 HOH HOH . H 4 HOH B 55 235 45 HOH HOH . H 4 HOH B 56 236 46 HOH HOH . H 4 HOH B 57 237 51 HOH HOH . H 4 HOH B 58 238 55 HOH HOH . H 4 HOH B 59 239 57 HOH HOH . H 4 HOH B 60 240 59 HOH HOH . H 4 HOH B 61 241 68 HOH HOH . H 4 HOH B 62 242 69 HOH HOH . H 4 HOH B 63 243 70 HOH HOH . H 4 HOH B 64 244 71 HOH HOH . H 4 HOH B 65 245 72 HOH HOH . H 4 HOH B 66 246 73 HOH HOH . H 4 HOH B 67 247 75 HOH HOH . H 4 HOH B 68 248 84 HOH HOH . H 4 HOH B 69 249 87 HOH HOH . H 4 HOH B 70 250 88 HOH HOH . H 4 HOH B 71 251 91 HOH HOH . H 4 HOH B 72 252 92 HOH HOH . H 4 HOH B 73 253 95 HOH HOH . H 4 HOH B 74 254 97 HOH HOH . H 4 HOH B 75 255 100 HOH HOH . H 4 HOH B 76 256 101 HOH HOH . H 4 HOH B 77 257 102 HOH HOH . H 4 HOH B 78 258 104 HOH HOH . H 4 HOH B 79 259 109 HOH HOH . H 4 HOH B 80 260 113 HOH HOH . H 4 HOH B 81 261 121 HOH HOH . H 4 HOH B 82 262 124 HOH HOH . H 4 HOH B 83 263 126 HOH HOH . H 4 HOH B 84 264 128 HOH HOH . H 4 HOH B 85 265 138 HOH HOH . H 4 HOH B 86 266 139 HOH HOH . H 4 HOH B 87 267 140 HOH HOH . H 4 HOH B 88 268 145 HOH HOH . H 4 HOH B 89 269 269 HOH HOH . H 4 HOH B 90 270 270 HOH HOH . H 4 HOH B 91 271 165 HOH HOH . H 4 HOH B 92 272 167 HOH HOH . H 4 HOH B 93 275 275 HOH HOH . H 4 HOH B 94 276 276 HOH HOH . I 4 HOH C 1 182 3 HOH HOH . I 4 HOH C 2 183 5 HOH HOH . I 4 HOH C 3 184 7 HOH HOH . I 4 HOH C 4 185 10 HOH HOH . I 4 HOH C 5 186 186 HOH HOH . I 4 HOH C 6 187 12 HOH HOH . I 4 HOH C 7 188 16 HOH HOH . I 4 HOH C 8 189 189 HOH HOH . I 4 HOH C 9 190 17 HOH HOH . I 4 HOH C 10 191 18 HOH HOH . I 4 HOH C 11 192 28 HOH HOH . I 4 HOH C 12 193 32 HOH HOH . I 4 HOH C 13 194 33 HOH HOH . I 4 HOH C 14 195 34 HOH HOH . I 4 HOH C 15 196 36 HOH HOH . I 4 HOH C 16 197 37 HOH HOH . I 4 HOH C 17 198 39 HOH HOH . I 4 HOH C 18 199 48 HOH HOH . I 4 HOH C 19 200 50 HOH HOH . I 4 HOH C 20 201 53 HOH HOH . I 4 HOH C 21 202 62 HOH HOH . I 4 HOH C 22 203 65 HOH HOH . I 4 HOH C 23 204 66 HOH HOH . I 4 HOH C 24 205 67 HOH HOH . I 4 HOH C 25 206 77 HOH HOH . I 4 HOH C 26 207 78 HOH HOH . I 4 HOH C 27 208 80 HOH HOH . I 4 HOH C 28 209 83 HOH HOH . I 4 HOH C 29 210 85 HOH HOH . I 4 HOH C 30 211 94 HOH HOH . I 4 HOH C 31 212 96 HOH HOH . I 4 HOH C 32 213 98 HOH HOH . I 4 HOH C 33 214 99 HOH HOH . I 4 HOH C 34 215 105 HOH HOH . I 4 HOH C 35 216 106 HOH HOH . I 4 HOH C 36 217 110 HOH HOH . I 4 HOH C 37 218 115 HOH HOH . I 4 HOH C 38 219 116 HOH HOH . I 4 HOH C 39 220 118 HOH HOH . I 4 HOH C 40 221 119 HOH HOH . I 4 HOH C 41 222 123 HOH HOH . I 4 HOH C 42 223 125 HOH HOH . I 4 HOH C 43 224 130 HOH HOH . I 4 HOH C 44 225 131 HOH HOH . I 4 HOH C 45 226 132 HOH HOH . I 4 HOH C 46 227 227 HOH HOH . I 4 HOH C 47 228 228 HOH HOH . I 4 HOH C 48 229 229 HOH HOH . I 4 HOH C 49 230 230 HOH HOH . I 4 HOH C 50 231 231 HOH HOH . I 4 HOH C 51 232 232 HOH HOH . I 4 HOH C 52 233 233 HOH HOH . I 4 HOH C 53 234 234 HOH HOH . I 4 HOH C 54 235 235 HOH HOH . I 4 HOH C 55 236 236 HOH HOH . I 4 HOH C 56 237 237 HOH HOH . I 4 HOH C 57 238 238 HOH HOH . I 4 HOH C 58 239 239 HOH HOH . I 4 HOH C 59 240 240 HOH HOH . I 4 HOH C 60 241 241 HOH HOH . I 4 HOH C 61 242 242 HOH HOH . I 4 HOH C 62 243 243 HOH HOH . I 4 HOH C 63 244 244 HOH HOH . I 4 HOH C 64 245 245 HOH HOH . I 4 HOH C 65 246 246 HOH HOH . I 4 HOH C 66 247 247 HOH HOH . I 4 HOH C 67 248 248 HOH HOH . I 4 HOH C 68 249 249 HOH HOH . I 4 HOH C 69 250 250 HOH HOH . I 4 HOH C 70 251 251 HOH HOH . I 4 HOH C 71 252 252 HOH HOH . I 4 HOH C 72 253 253 HOH HOH . I 4 HOH C 73 254 254 HOH HOH . I 4 HOH C 74 255 255 HOH HOH . I 4 HOH C 75 256 256 HOH HOH . I 4 HOH C 76 257 257 HOH HOH . I 4 HOH C 77 258 258 HOH HOH . I 4 HOH C 78 259 259 HOH HOH . I 4 HOH C 79 260 260 HOH HOH . I 4 HOH C 80 261 261 HOH HOH . I 4 HOH C 81 262 262 HOH HOH . I 4 HOH C 82 263 263 HOH HOH . I 4 HOH C 83 264 264 HOH HOH . I 4 HOH C 84 265 265 HOH HOH . I 4 HOH C 85 266 266 HOH HOH . I 4 HOH C 86 267 267 HOH HOH . I 4 HOH C 87 268 268 HOH HOH . I 4 HOH C 88 269 141 HOH HOH . I 4 HOH C 89 270 142 HOH HOH . I 4 HOH C 90 271 143 HOH HOH . I 4 HOH C 91 272 163 HOH HOH . I 4 HOH C 92 273 168 HOH HOH . I 4 HOH C 93 274 169 HOH HOH . I 4 HOH C 94 275 170 HOH HOH . I 4 HOH C 95 276 171 HOH HOH . I 4 HOH C 96 277 277 HOH HOH . I 4 HOH C 97 278 278 HOH HOH . I 4 HOH C 98 279 279 HOH HOH . I 4 HOH C 99 280 280 HOH HOH . I 4 HOH C 100 281 281 HOH HOH . I 4 HOH C 101 282 282 HOH HOH . I 4 HOH C 102 283 172 HOH HOH . I 4 HOH C 103 284 173 HOH HOH . I 4 HOH C 104 285 174 HOH HOH . I 4 HOH C 105 286 175 HOH HOH . I 4 HOH C 106 287 176 HOH HOH . I 4 HOH C 107 288 177 HOH HOH . I 4 HOH C 108 289 178 HOH HOH . I 4 HOH C 109 290 179 HOH HOH . I 4 HOH C 110 291 180 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _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 -1.876 _atom_site.Cartn_y -35.324 _atom_site.Cartn_z 9.488 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 24.81 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 181 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #