data_3GP4 # _model_server_result.job_id gpyvtsHRDUkl4VcRSYQmog _model_server_result.datetime_utc '2024-12-21 13:03:49' _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 3gp4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":159}' # _entry.id 3GP4 # _exptl.entry_id 3GP4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 120 _cell.entry_id 3GP4 _cell.length_a 80.647 _cell.length_b 80.647 _cell.length_c 127.126 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GP4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 1,2,3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 80.647 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 40.3235 69.842351 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 B O SER 2 B SER 18 1_555 E NA NA . B NA 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc2 E NA NA . B NA 159 1_555 H O HOH . B HOH 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc3 E NA NA . B NA 159 1_555 H O HOH . B HOH 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc4 E NA NA . B NA 159 1_555 H O HOH . B HOH 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? # _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 3GP4 _atom_sites.fract_transf_matrix[1][1] 0.0124 _atom_sites.fract_transf_matrix[1][2] 0.007159 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014318 _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] 0.007866 _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 C 2 GOL A 1 2 2 GOL GOL . D 2 GOL B 1 1 1 GOL GOL . E 3 NA B 1 159 1 NA NA . F 4 MED B 1 513 513 MED MED . G 5 HOH A 1 4 4 HOH HOH . G 5 HOH A 2 7 7 HOH HOH . G 5 HOH A 3 8 8 HOH HOH . G 5 HOH A 4 9 9 HOH HOH . G 5 HOH A 5 11 11 HOH HOH . G 5 HOH A 6 16 16 HOH HOH . G 5 HOH A 7 159 159 HOH HOH . G 5 HOH A 8 160 160 HOH HOH . G 5 HOH A 9 161 161 HOH HOH . G 5 HOH A 10 162 162 HOH HOH . G 5 HOH A 11 163 2 HOH HOH . G 5 HOH A 12 164 164 HOH HOH . G 5 HOH A 13 165 17 HOH HOH . G 5 HOH A 14 166 18 HOH HOH . G 5 HOH A 15 167 20 HOH HOH . G 5 HOH A 16 168 168 HOH HOH . G 5 HOH A 17 169 169 HOH HOH . G 5 HOH A 18 170 22 HOH HOH . G 5 HOH A 19 171 23 HOH HOH . G 5 HOH A 20 172 27 HOH HOH . G 5 HOH A 21 173 28 HOH HOH . G 5 HOH A 22 174 33 HOH HOH . G 5 HOH A 23 175 175 HOH HOH . G 5 HOH A 24 176 176 HOH HOH . G 5 HOH A 25 177 177 HOH HOH . G 5 HOH A 26 178 178 HOH HOH . G 5 HOH A 27 179 34 HOH HOH . G 5 HOH A 28 180 36 HOH HOH . G 5 HOH A 29 181 38 HOH HOH . G 5 HOH A 30 182 182 HOH HOH . G 5 HOH A 31 183 183 HOH HOH . G 5 HOH A 32 184 184 HOH HOH . G 5 HOH A 33 185 185 HOH HOH . G 5 HOH A 34 186 186 HOH HOH . G 5 HOH A 35 187 40 HOH HOH . G 5 HOH A 36 188 188 HOH HOH . G 5 HOH A 37 189 189 HOH HOH . G 5 HOH A 38 190 190 HOH HOH . G 5 HOH A 39 191 191 HOH HOH . G 5 HOH A 40 192 41 HOH HOH . G 5 HOH A 41 193 193 HOH HOH . G 5 HOH A 42 194 46 HOH HOH . G 5 HOH A 43 195 195 HOH HOH . G 5 HOH A 44 196 47 HOH HOH . G 5 HOH A 45 197 54 HOH HOH . G 5 HOH A 46 198 198 HOH HOH . G 5 HOH A 47 199 58 HOH HOH . G 5 HOH A 48 200 200 HOH HOH . G 5 HOH A 49 201 59 HOH HOH . G 5 HOH A 50 202 60 HOH HOH . G 5 HOH A 51 203 203 HOH HOH . G 5 HOH A 52 204 61 HOH HOH . G 5 HOH A 53 205 205 HOH HOH . G 5 HOH A 54 206 62 HOH HOH . G 5 HOH A 55 207 63 HOH HOH . G 5 HOH A 56 208 208 HOH HOH . G 5 HOH A 57 209 209 HOH HOH . G 5 HOH A 58 210 64 HOH HOH . G 5 HOH A 59 211 68 HOH HOH . G 5 HOH A 60 212 70 HOH HOH . G 5 HOH A 61 213 213 HOH HOH . G 5 HOH A 62 214 73 HOH HOH . G 5 HOH A 63 215 74 HOH HOH . G 5 HOH A 64 216 216 HOH HOH . G 5 HOH A 65 217 75 HOH HOH . G 5 HOH A 66 218 80 HOH HOH . G 5 HOH A 67 219 219 HOH HOH . G 5 HOH A 68 220 81 HOH HOH . G 5 HOH A 69 221 221 HOH HOH . G 5 HOH A 70 222 82 HOH HOH . G 5 HOH A 71 223 84 HOH HOH . G 5 HOH A 72 224 224 HOH HOH . G 5 HOH A 73 225 85 HOH HOH . G 5 HOH A 74 226 86 HOH HOH . G 5 HOH A 75 227 87 HOH HOH . G 5 HOH A 76 228 90 HOH HOH . G 5 HOH A 77 229 229 HOH HOH . G 5 HOH A 78 230 230 HOH HOH . G 5 HOH A 79 231 92 HOH HOH . G 5 HOH A 80 232 98 HOH HOH . G 5 HOH A 81 233 99 HOH HOH . G 5 HOH A 82 234 104 HOH HOH . G 5 HOH A 83 235 105 HOH HOH . G 5 HOH A 84 236 236 HOH HOH . G 5 HOH A 85 237 106 HOH HOH . G 5 HOH A 86 238 238 HOH HOH . G 5 HOH A 87 239 107 HOH HOH . G 5 HOH A 88 240 240 HOH HOH . G 5 HOH A 89 241 109 HOH HOH . G 5 HOH A 90 242 242 HOH HOH . G 5 HOH A 91 243 110 HOH HOH . G 5 HOH A 92 244 244 HOH HOH . G 5 HOH A 93 245 112 HOH HOH . G 5 HOH A 94 246 246 HOH HOH . G 5 HOH A 95 247 115 HOH HOH . G 5 HOH A 96 248 116 HOH HOH . G 5 HOH A 97 249 117 HOH HOH . G 5 HOH A 98 250 119 HOH HOH . G 5 HOH A 99 251 121 HOH HOH . G 5 HOH A 100 252 126 HOH HOH . G 5 HOH A 101 253 127 HOH HOH . G 5 HOH A 102 254 130 HOH HOH . G 5 HOH A 103 255 132 HOH HOH . G 5 HOH A 104 256 136 HOH HOH . G 5 HOH A 105 257 139 HOH HOH . G 5 HOH A 106 258 140 HOH HOH . G 5 HOH A 107 259 142 HOH HOH . G 5 HOH A 108 260 146 HOH HOH . G 5 HOH A 109 261 147 HOH HOH . G 5 HOH A 110 262 148 HOH HOH . G 5 HOH A 111 263 150 HOH HOH . G 5 HOH A 112 264 155 HOH HOH . G 5 HOH A 113 265 156 HOH HOH . G 5 HOH A 114 266 158 HOH HOH . H 5 HOH B 1 3 3 HOH HOH . H 5 HOH B 2 5 5 HOH HOH . H 5 HOH B 3 6 6 HOH HOH . H 5 HOH B 4 10 10 HOH HOH . H 5 HOH B 5 12 12 HOH HOH . H 5 HOH B 6 13 13 HOH HOH . H 5 HOH B 7 14 14 HOH HOH . H 5 HOH B 8 15 15 HOH HOH . H 5 HOH B 9 160 1 HOH HOH . H 5 HOH B 10 161 19 HOH HOH . H 5 HOH B 11 162 21 HOH HOH . H 5 HOH B 12 163 163 HOH HOH . H 5 HOH B 13 164 24 HOH HOH . H 5 HOH B 14 165 165 HOH HOH . H 5 HOH B 15 166 166 HOH HOH . H 5 HOH B 16 167 167 HOH HOH . H 5 HOH B 17 168 25 HOH HOH . H 5 HOH B 18 169 26 HOH HOH . H 5 HOH B 19 170 170 HOH HOH . H 5 HOH B 20 171 171 HOH HOH . H 5 HOH B 21 172 172 HOH HOH . H 5 HOH B 22 173 173 HOH HOH . H 5 HOH B 23 174 174 HOH HOH . H 5 HOH B 24 175 29 HOH HOH . H 5 HOH B 25 176 30 HOH HOH . H 5 HOH B 26 177 31 HOH HOH . H 5 HOH B 27 178 32 HOH HOH . H 5 HOH B 28 179 179 HOH HOH . H 5 HOH B 29 180 180 HOH HOH . H 5 HOH B 30 181 181 HOH HOH . H 5 HOH B 31 182 35 HOH HOH . H 5 HOH B 32 183 37 HOH HOH . H 5 HOH B 33 184 39 HOH HOH . H 5 HOH B 34 185 42 HOH HOH . H 5 HOH B 35 186 43 HOH HOH . H 5 HOH B 36 187 187 HOH HOH . H 5 HOH B 37 188 44 HOH HOH . H 5 HOH B 38 189 48 HOH HOH . H 5 HOH B 39 190 49 HOH HOH . H 5 HOH B 40 191 50 HOH HOH . H 5 HOH B 41 192 192 HOH HOH . H 5 HOH B 42 193 51 HOH HOH . H 5 HOH B 43 194 194 HOH HOH . H 5 HOH B 44 195 52 HOH HOH . H 5 HOH B 45 196 196 HOH HOH . H 5 HOH B 46 197 197 HOH HOH . H 5 HOH B 47 198 53 HOH HOH . H 5 HOH B 48 199 199 HOH HOH . H 5 HOH B 49 200 55 HOH HOH . H 5 HOH B 50 201 201 HOH HOH . H 5 HOH B 51 202 202 HOH HOH . H 5 HOH B 52 203 56 HOH HOH . H 5 HOH B 53 204 204 HOH HOH . H 5 HOH B 54 205 57 HOH HOH . H 5 HOH B 55 206 206 HOH HOH . H 5 HOH B 56 207 207 HOH HOH . H 5 HOH B 57 208 65 HOH HOH . H 5 HOH B 58 209 66 HOH HOH . H 5 HOH B 59 210 210 HOH HOH . H 5 HOH B 60 211 211 HOH HOH . H 5 HOH B 61 212 212 HOH HOH . H 5 HOH B 62 213 67 HOH HOH . H 5 HOH B 63 214 214 HOH HOH . H 5 HOH B 64 215 215 HOH HOH . H 5 HOH B 65 216 69 HOH HOH . H 5 HOH B 66 217 217 HOH HOH . H 5 HOH B 67 218 218 HOH HOH . H 5 HOH B 68 219 71 HOH HOH . H 5 HOH B 69 220 220 HOH HOH . H 5 HOH B 70 221 72 HOH HOH . H 5 HOH B 71 222 222 HOH HOH . H 5 HOH B 72 223 223 HOH HOH . H 5 HOH B 73 224 76 HOH HOH . H 5 HOH B 74 225 225 HOH HOH . H 5 HOH B 75 226 226 HOH HOH . H 5 HOH B 76 227 227 HOH HOH . H 5 HOH B 77 228 228 HOH HOH . H 5 HOH B 78 229 77 HOH HOH . H 5 HOH B 79 230 78 HOH HOH . H 5 HOH B 80 231 231 HOH HOH . H 5 HOH B 81 232 232 HOH HOH . H 5 HOH B 82 233 233 HOH HOH . H 5 HOH B 83 234 79 HOH HOH . H 5 HOH B 84 235 235 HOH HOH . H 5 HOH B 85 236 83 HOH HOH . H 5 HOH B 86 237 237 HOH HOH . H 5 HOH B 87 238 88 HOH HOH . H 5 HOH B 88 239 239 HOH HOH . H 5 HOH B 89 240 89 HOH HOH . H 5 HOH B 90 241 241 HOH HOH . H 5 HOH B 91 242 91 HOH HOH . H 5 HOH B 92 243 243 HOH HOH . H 5 HOH B 93 244 93 HOH HOH . H 5 HOH B 94 245 245 HOH HOH . H 5 HOH B 95 246 94 HOH HOH . H 5 HOH B 96 247 247 HOH HOH . H 5 HOH B 97 248 248 HOH HOH . H 5 HOH B 98 249 249 HOH HOH . H 5 HOH B 99 250 95 HOH HOH . H 5 HOH B 100 251 96 HOH HOH . H 5 HOH B 101 252 97 HOH HOH . H 5 HOH B 102 253 100 HOH HOH . H 5 HOH B 103 254 101 HOH HOH . H 5 HOH B 104 255 102 HOH HOH . H 5 HOH B 105 256 103 HOH HOH . H 5 HOH B 106 257 108 HOH HOH . H 5 HOH B 107 258 111 HOH HOH . H 5 HOH B 108 259 113 HOH HOH . H 5 HOH B 109 260 114 HOH HOH . H 5 HOH B 110 261 118 HOH HOH . H 5 HOH B 111 262 120 HOH HOH . H 5 HOH B 112 263 122 HOH HOH . H 5 HOH B 113 264 123 HOH HOH . H 5 HOH B 114 265 124 HOH HOH . H 5 HOH B 115 266 125 HOH HOH . H 5 HOH B 116 267 128 HOH HOH . H 5 HOH B 117 268 129 HOH HOH . H 5 HOH B 118 269 131 HOH HOH . H 5 HOH B 119 270 133 HOH HOH . H 5 HOH B 120 271 134 HOH HOH . H 5 HOH B 121 272 135 HOH HOH . H 5 HOH B 122 273 137 HOH HOH . H 5 HOH B 123 274 138 HOH HOH . H 5 HOH B 124 275 141 HOH HOH . H 5 HOH B 125 276 143 HOH HOH . H 5 HOH B 126 277 144 HOH HOH . H 5 HOH B 127 278 145 HOH HOH . H 5 HOH B 128 279 149 HOH HOH . H 5 HOH B 129 280 151 HOH HOH . H 5 HOH B 130 281 152 HOH HOH . H 5 HOH B 131 282 153 HOH HOH . H 5 HOH B 132 283 154 HOH HOH . H 5 HOH B 133 284 157 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 E _atom_site.label_entity_id 3 _atom_site.Cartn_x 11.752 _atom_site.Cartn_y 20.806 _atom_site.Cartn_z 49.134 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 34.7 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 159 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #