data_3CMD # _model_server_result.job_id cZ-MDpJoF5HmRQeBitiFGA _model_server_result.datetime_utc '2024-10-20 03:28:57' _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 3cmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":190}' # _entry.id 3CMD # _exptl.entry_id 3CMD _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 8 _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 3CMD _cell.length_a 149.47 _cell.length_b 149.47 _cell.length_c 143.329 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CMD _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E,F,G,H,Q 1 1 B,I,J,K,L,M,N,O,P,R 2 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 ? 3 D N N ? 3 E N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O 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 45 A GLU 36 1_555 E NA NA . A NA 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc2 A SG CYS 123 A CYS 114 1_555 C FE FE . A FE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc3 A NE2 HIS 166 A HIS 157 1_555 C FE FE . A FE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc4 A NE2 HIS 170 A HIS 161 1_555 C FE FE . A FE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc5 D NA NA . A NA 189 1_555 Q O HOH . A HOH 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc6 E NA NA . A NA 190 1_555 Q O HOH . A HOH 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc7 B O HIS 110 B HIS 101 1_555 O NA NA . B NA 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc8 B SG CYS 123 B CYS 114 1_555 I FE FE . B FE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc9 B NE2 HIS 166 B HIS 157 1_555 I FE FE . B FE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc10 B NE2 HIS 170 B HIS 161 1_555 I FE FE . B FE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _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 3CMD _atom_sites.fract_transf_matrix[1][1] 0.00669 _atom_sites.fract_transf_matrix[1][2] 0.003863 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007725 _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] 0.006977 _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 FE A 1 188 1 FE FE . D 3 NA A 1 189 1 NA NA . E 3 NA A 1 190 8 NA NA . F 4 MLI A 1 191 1 MLI MLI . G 4 MLI A 1 192 3 MLI MLI . H 4 MLI A 1 193 4 MLI MLI . I 2 FE B 1 188 2 FE FE . J 3 NA B 1 189 2 NA NA . K 3 NA B 1 190 3 NA NA . L 3 NA B 1 191 4 NA NA . M 3 NA B 1 192 5 NA NA . N 3 NA B 1 193 6 NA NA . O 3 NA B 1 194 7 NA NA . P 4 MLI B 1 195 2 MLI MLI . Q 5 HOH A 1 194 2 HOH HOH . Q 5 HOH A 2 195 9 HOH HOH . Q 5 HOH A 3 196 10 HOH HOH . Q 5 HOH A 4 197 11 HOH HOH . Q 5 HOH A 5 198 12 HOH HOH . Q 5 HOH A 6 199 18 HOH HOH . Q 5 HOH A 7 200 19 HOH HOH . Q 5 HOH A 8 201 20 HOH HOH . Q 5 HOH A 9 202 23 HOH HOH . Q 5 HOH A 10 203 24 HOH HOH . Q 5 HOH A 11 204 26 HOH HOH . Q 5 HOH A 12 205 33 HOH HOH . Q 5 HOH A 13 206 34 HOH HOH . Q 5 HOH A 14 207 35 HOH HOH . Q 5 HOH A 15 208 36 HOH HOH . Q 5 HOH A 16 209 39 HOH HOH . Q 5 HOH A 17 210 40 HOH HOH . Q 5 HOH A 18 211 43 HOH HOH . Q 5 HOH A 19 212 45 HOH HOH . Q 5 HOH A 20 213 47 HOH HOH . Q 5 HOH A 21 214 50 HOH HOH . Q 5 HOH A 22 215 51 HOH HOH . Q 5 HOH A 23 216 53 HOH HOH . Q 5 HOH A 24 217 54 HOH HOH . Q 5 HOH A 25 218 55 HOH HOH . Q 5 HOH A 26 219 59 HOH HOH . Q 5 HOH A 27 220 60 HOH HOH . Q 5 HOH A 28 221 61 HOH HOH . Q 5 HOH A 29 222 62 HOH HOH . Q 5 HOH A 30 223 64 HOH HOH . Q 5 HOH A 31 224 68 HOH HOH . Q 5 HOH A 32 225 71 HOH HOH . Q 5 HOH A 33 226 72 HOH HOH . Q 5 HOH A 34 227 74 HOH HOH . Q 5 HOH A 35 228 75 HOH HOH . Q 5 HOH A 36 229 81 HOH HOH . Q 5 HOH A 37 230 82 HOH HOH . Q 5 HOH A 38 231 84 HOH HOH . Q 5 HOH A 39 232 86 HOH HOH . Q 5 HOH A 40 233 88 HOH HOH . Q 5 HOH A 41 234 92 HOH HOH . Q 5 HOH A 42 235 93 HOH HOH . Q 5 HOH A 43 236 94 HOH HOH . Q 5 HOH A 44 237 95 HOH HOH . Q 5 HOH A 45 238 100 HOH HOH . Q 5 HOH A 46 239 101 HOH HOH . Q 5 HOH A 47 240 105 HOH HOH . Q 5 HOH A 48 241 108 HOH HOH . Q 5 HOH A 49 242 109 HOH HOH . Q 5 HOH A 50 243 112 HOH HOH . Q 5 HOH A 51 244 114 HOH HOH . Q 5 HOH A 52 245 115 HOH HOH . Q 5 HOH A 53 246 116 HOH HOH . Q 5 HOH A 54 247 117 HOH HOH . Q 5 HOH A 55 248 118 HOH HOH . Q 5 HOH A 56 249 120 HOH HOH . Q 5 HOH A 57 250 121 HOH HOH . Q 5 HOH A 58 251 122 HOH HOH . Q 5 HOH A 59 252 123 HOH HOH . Q 5 HOH A 60 253 125 HOH HOH . Q 5 HOH A 61 254 128 HOH HOH . Q 5 HOH A 62 255 133 HOH HOH . Q 5 HOH A 63 256 134 HOH HOH . Q 5 HOH A 64 257 136 HOH HOH . Q 5 HOH A 65 258 138 HOH HOH . Q 5 HOH A 66 259 139 HOH HOH . Q 5 HOH A 67 260 140 HOH HOH . Q 5 HOH A 68 261 143 HOH HOH . Q 5 HOH A 69 262 144 HOH HOH . Q 5 HOH A 70 263 149 HOH HOH . Q 5 HOH A 71 264 150 HOH HOH . Q 5 HOH A 72 265 152 HOH HOH . Q 5 HOH A 73 266 154 HOH HOH . Q 5 HOH A 74 267 155 HOH HOH . Q 5 HOH A 75 268 156 HOH HOH . Q 5 HOH A 76 269 159 HOH HOH . Q 5 HOH A 77 270 160 HOH HOH . Q 5 HOH A 78 271 164 HOH HOH . Q 5 HOH A 79 272 165 HOH HOH . Q 5 HOH A 80 273 166 HOH HOH . Q 5 HOH A 81 274 167 HOH HOH . Q 5 HOH A 82 275 168 HOH HOH . Q 5 HOH A 83 276 169 HOH HOH . Q 5 HOH A 84 277 170 HOH HOH . Q 5 HOH A 85 278 173 HOH HOH . Q 5 HOH A 86 279 174 HOH HOH . Q 5 HOH A 87 280 175 HOH HOH . Q 5 HOH A 88 281 177 HOH HOH . Q 5 HOH A 89 282 178 HOH HOH . Q 5 HOH A 90 283 179 HOH HOH . Q 5 HOH A 91 284 181 HOH HOH . Q 5 HOH A 92 285 186 HOH HOH . Q 5 HOH A 93 286 188 HOH HOH . Q 5 HOH A 94 287 189 HOH HOH . Q 5 HOH A 95 288 193 HOH HOH . Q 5 HOH A 96 289 194 HOH HOH . Q 5 HOH A 97 290 195 HOH HOH . Q 5 HOH A 98 291 196 HOH HOH . Q 5 HOH A 99 292 197 HOH HOH . Q 5 HOH A 100 293 198 HOH HOH . Q 5 HOH A 101 294 199 HOH HOH . Q 5 HOH A 102 295 210 HOH HOH . Q 5 HOH A 103 296 211 HOH HOH . Q 5 HOH A 104 297 212 HOH HOH . Q 5 HOH A 105 298 213 HOH HOH . R 5 HOH B 1 196 5 HOH HOH . R 5 HOH B 2 197 8 HOH HOH . R 5 HOH B 3 198 13 HOH HOH . R 5 HOH B 4 199 14 HOH HOH . R 5 HOH B 5 200 15 HOH HOH . R 5 HOH B 6 201 16 HOH HOH . R 5 HOH B 7 202 17 HOH HOH . R 5 HOH B 8 203 21 HOH HOH . R 5 HOH B 9 204 22 HOH HOH . R 5 HOH B 10 205 25 HOH HOH . R 5 HOH B 11 206 27 HOH HOH . R 5 HOH B 12 207 28 HOH HOH . R 5 HOH B 13 208 29 HOH HOH . R 5 HOH B 14 209 30 HOH HOH . R 5 HOH B 15 210 31 HOH HOH . R 5 HOH B 16 211 32 HOH HOH . R 5 HOH B 17 212 37 HOH HOH . R 5 HOH B 18 213 38 HOH HOH . R 5 HOH B 19 214 41 HOH HOH . R 5 HOH B 20 215 42 HOH HOH . R 5 HOH B 21 216 44 HOH HOH . R 5 HOH B 22 217 46 HOH HOH . R 5 HOH B 23 218 48 HOH HOH . R 5 HOH B 24 219 49 HOH HOH . R 5 HOH B 25 220 52 HOH HOH . R 5 HOH B 26 221 56 HOH HOH . R 5 HOH B 27 222 57 HOH HOH . R 5 HOH B 28 223 58 HOH HOH . R 5 HOH B 29 224 63 HOH HOH . R 5 HOH B 30 225 65 HOH HOH . R 5 HOH B 31 226 66 HOH HOH . R 5 HOH B 32 227 67 HOH HOH . R 5 HOH B 33 228 69 HOH HOH . R 5 HOH B 34 229 70 HOH HOH . R 5 HOH B 35 230 73 HOH HOH . R 5 HOH B 36 231 76 HOH HOH . R 5 HOH B 37 232 77 HOH HOH . R 5 HOH B 38 233 78 HOH HOH . R 5 HOH B 39 234 79 HOH HOH . R 5 HOH B 40 235 80 HOH HOH . R 5 HOH B 41 236 83 HOH HOH . R 5 HOH B 42 237 85 HOH HOH . R 5 HOH B 43 238 87 HOH HOH . R 5 HOH B 44 239 89 HOH HOH . R 5 HOH B 45 240 90 HOH HOH . R 5 HOH B 46 241 91 HOH HOH . R 5 HOH B 47 242 96 HOH HOH . R 5 HOH B 48 243 97 HOH HOH . R 5 HOH B 49 244 98 HOH HOH . R 5 HOH B 50 245 99 HOH HOH . R 5 HOH B 51 246 102 HOH HOH . R 5 HOH B 52 247 103 HOH HOH . R 5 HOH B 53 248 104 HOH HOH . R 5 HOH B 54 249 106 HOH HOH . R 5 HOH B 55 250 107 HOH HOH . R 5 HOH B 56 251 110 HOH HOH . R 5 HOH B 57 252 111 HOH HOH . R 5 HOH B 58 253 113 HOH HOH . R 5 HOH B 59 254 119 HOH HOH . R 5 HOH B 60 255 124 HOH HOH . R 5 HOH B 61 256 126 HOH HOH . R 5 HOH B 62 257 127 HOH HOH . R 5 HOH B 63 258 129 HOH HOH . R 5 HOH B 64 259 130 HOH HOH . R 5 HOH B 65 260 131 HOH HOH . R 5 HOH B 66 261 132 HOH HOH . R 5 HOH B 67 262 135 HOH HOH . R 5 HOH B 68 263 137 HOH HOH . R 5 HOH B 69 264 141 HOH HOH . R 5 HOH B 70 265 142 HOH HOH . R 5 HOH B 71 266 145 HOH HOH . R 5 HOH B 72 267 146 HOH HOH . R 5 HOH B 73 268 147 HOH HOH . R 5 HOH B 74 269 148 HOH HOH . R 5 HOH B 75 270 151 HOH HOH . R 5 HOH B 76 271 153 HOH HOH . R 5 HOH B 77 272 157 HOH HOH . R 5 HOH B 78 273 158 HOH HOH . R 5 HOH B 79 274 161 HOH HOH . R 5 HOH B 80 275 162 HOH HOH . R 5 HOH B 81 276 163 HOH HOH . R 5 HOH B 82 277 171 HOH HOH . R 5 HOH B 83 278 172 HOH HOH . R 5 HOH B 84 279 176 HOH HOH . R 5 HOH B 85 280 180 HOH HOH . R 5 HOH B 86 281 182 HOH HOH . R 5 HOH B 87 282 183 HOH HOH . R 5 HOH B 88 283 184 HOH HOH . R 5 HOH B 89 284 185 HOH HOH . R 5 HOH B 90 285 214 HOH HOH . R 5 HOH B 91 286 215 HOH HOH . R 5 HOH B 92 287 216 HOH HOH . R 5 HOH B 93 288 217 HOH HOH . R 5 HOH B 94 289 218 HOH HOH . R 5 HOH B 95 290 220 HOH HOH . R 5 HOH B 96 291 221 HOH HOH . R 5 HOH B 97 292 222 HOH HOH . R 5 HOH B 98 293 223 HOH HOH . R 5 HOH B 99 294 224 HOH HOH . R 5 HOH B 100 295 225 HOH HOH . R 5 HOH B 101 296 226 HOH HOH . R 5 HOH B 102 297 227 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 18.142 _atom_site.Cartn_y 50.936 _atom_site.Cartn_z 85.413 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 22.44 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 190 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 45 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #