data_5YDB
#
_model_server_result.job_id            TtjA71DaPy47ufBJawM-jw 
_model_server_result.datetime_utc      '2024-12-02 04:52:15' 
_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          5ydb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":201}' 
#
_entry.id    5YDB 
#
_exptl.entry_id    5YDB 
_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    4 
_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            5YDB 
_cell.length_a            139.117 
_cell.length_b            139.117 
_cell.length_c            79.587 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YDB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,I,J,K,L,M,N,O,P 
_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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K N N 
#
_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                     5YDB 
_atom_sites.fract_transf_matrix[1][1]    0.007188 
_atom_sites.fract_transf_matrix[1][2]    0.00415 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.0083 
_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]    0.012565 
_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
E 2 NA A 1 201 4 NA NA . 
F 3 DQA A 1 202 2 DQA DQA . 
G 2 NA B 1 201 3 NA NA . 
H 3 DQA B 1 202 1 DQA DQA . 
I 2 NA C 1 201 2 NA NA . 
J 3 DQA C 1 202 3 DQA DQA . 
K 2 NA D 1 201 1 NA NA . 
L 3 DQA D 1 202 4 DQA DQA . 
M 4 HOH A 1 301 118 HOH HOH . 
M 4 HOH A 2 302 110 HOH HOH . 
M 4 HOH A 3 303 59 HOH HOH . 
M 4 HOH A 4 304 283 HOH HOH . 
M 4 HOH A 5 305 167 HOH HOH . 
M 4 HOH A 6 306 18 HOH HOH . 
M 4 HOH A 7 307 248 HOH HOH . 
M 4 HOH A 8 308 180 HOH HOH . 
M 4 HOH A 9 309 279 HOH HOH . 
M 4 HOH A 10 310 16 HOH HOH . 
M 4 HOH A 11 311 295 HOH HOH . 
M 4 HOH A 12 312 280 HOH HOH . 
M 4 HOH A 13 313 120 HOH HOH . 
M 4 HOH A 14 314 301 HOH HOH . 
M 4 HOH A 15 315 119 HOH HOH . 
M 4 HOH A 16 316 146 HOH HOH . 
M 4 HOH A 17 317 284 HOH HOH . 
M 4 HOH A 18 318 1 HOH HOH . 
M 4 HOH A 19 319 306 HOH HOH . 
M 4 HOH A 20 320 175 HOH HOH . 
M 4 HOH A 21 321 4 HOH HOH . 
M 4 HOH A 22 322 91 HOH HOH . 
M 4 HOH A 23 323 166 HOH HOH . 
M 4 HOH A 24 324 281 HOH HOH . 
M 4 HOH A 25 325 303 HOH HOH . 
M 4 HOH A 26 326 111 HOH HOH . 
M 4 HOH A 27 327 176 HOH HOH . 
M 4 HOH A 28 328 292 HOH HOH . 
M 4 HOH A 29 329 286 HOH HOH . 
M 4 HOH A 30 330 285 HOH HOH . 
M 4 HOH A 31 331 151 HOH HOH . 
M 4 HOH A 32 332 149 HOH HOH . 
M 4 HOH A 33 333 95 HOH HOH . 
M 4 HOH A 34 334 304 HOH HOH . 
M 4 HOH A 35 335 278 HOH HOH . 
M 4 HOH A 36 336 179 HOH HOH . 
M 4 HOH A 37 337 165 HOH HOH . 
M 4 HOH A 38 338 276 HOH HOH . 
M 4 HOH A 39 339 60 HOH HOH . 
M 4 HOH A 40 340 147 HOH HOH . 
M 4 HOH A 41 341 282 HOH HOH . 
M 4 HOH A 42 342 173 HOH HOH . 
M 4 HOH A 43 343 115 HOH HOH . 
M 4 HOH A 44 344 168 HOH HOH . 
M 4 HOH A 45 345 109 HOH HOH . 
M 4 HOH A 46 346 177 HOH HOH . 
M 4 HOH A 47 347 170 HOH HOH . 
M 4 HOH A 48 348 184 HOH HOH . 
M 4 HOH A 49 349 171 HOH HOH . 
M 4 HOH A 50 350 92 HOH HOH . 
M 4 HOH A 51 351 145 HOH HOH . 
M 4 HOH A 52 352 319 HOH HOH . 
M 4 HOH A 53 353 181 HOH HOH . 
M 4 HOH A 54 354 169 HOH HOH . 
M 4 HOH A 55 355 287 HOH HOH . 
M 4 HOH A 56 356 189 HOH HOH . 
M 4 HOH A 57 357 74 HOH HOH . 
M 4 HOH A 58 358 172 HOH HOH . 
M 4 HOH A 59 359 174 HOH HOH . 
N 4 HOH B 1 301 108 HOH HOH . 
N 4 HOH B 2 302 139 HOH HOH . 
N 4 HOH B 3 303 155 HOH HOH . 
N 4 HOH B 4 304 193 HOH HOH . 
N 4 HOH B 5 305 183 HOH HOH . 
N 4 HOH B 6 306 240 HOH HOH . 
N 4 HOH B 7 307 229 HOH HOH . 
N 4 HOH B 8 308 140 HOH HOH . 
N 4 HOH B 9 309 249 HOH HOH . 
N 4 HOH B 10 310 244 HOH HOH . 
N 4 HOH B 11 311 178 HOH HOH . 
N 4 HOH B 12 312 37 HOH HOH . 
N 4 HOH B 13 313 219 HOH HOH . 
N 4 HOH B 14 314 247 HOH HOH . 
N 4 HOH B 15 315 243 HOH HOH . 
N 4 HOH B 16 316 84 HOH HOH . 
N 4 HOH B 17 317 307 HOH HOH . 
N 4 HOH B 18 318 299 HOH HOH . 
N 4 HOH B 19 319 135 HOH HOH . 
N 4 HOH B 20 320 232 HOH HOH . 
N 4 HOH B 21 321 131 HOH HOH . 
N 4 HOH B 22 322 35 HOH HOH . 
N 4 HOH B 23 323 99 HOH HOH . 
N 4 HOH B 24 324 152 HOH HOH . 
N 4 HOH B 25 325 159 HOH HOH . 
N 4 HOH B 26 326 130 HOH HOH . 
N 4 HOH B 27 327 136 HOH HOH . 
N 4 HOH B 28 328 134 HOH HOH . 
N 4 HOH B 29 329 297 HOH HOH . 
N 4 HOH B 30 330 154 HOH HOH . 
N 4 HOH B 31 331 153 HOH HOH . 
N 4 HOH B 32 332 308 HOH HOH . 
N 4 HOH B 33 333 250 HOH HOH . 
N 4 HOH B 34 334 289 HOH HOH . 
N 4 HOH B 35 335 320 HOH HOH . 
N 4 HOH B 36 336 98 HOH HOH . 
N 4 HOH B 37 337 33 HOH HOH . 
N 4 HOH B 38 338 231 HOH HOH . 
N 4 HOH B 39 339 290 HOH HOH . 
N 4 HOH B 40 340 242 HOH HOH . 
N 4 HOH B 41 341 239 HOH HOH . 
N 4 HOH B 42 342 312 HOH HOH . 
N 4 HOH B 43 343 241 HOH HOH . 
N 4 HOH B 44 344 309 HOH HOH . 
N 4 HOH B 45 345 85 HOH HOH . 
N 4 HOH B 46 346 237 HOH HOH . 
N 4 HOH B 47 347 230 HOH HOH . 
O 4 HOH C 1 301 106 HOH HOH . 
O 4 HOH C 2 302 187 HOH HOH . 
O 4 HOH C 3 303 105 HOH HOH . 
O 4 HOH C 4 304 103 HOH HOH . 
O 4 HOH C 5 305 256 HOH HOH . 
O 4 HOH C 6 306 158 HOH HOH . 
O 4 HOH C 7 307 190 HOH HOH . 
O 4 HOH C 8 308 199 HOH HOH . 
O 4 HOH C 9 309 191 HOH HOH . 
O 4 HOH C 10 310 195 HOH HOH . 
O 4 HOH C 11 311 194 HOH HOH . 
O 4 HOH C 12 312 43 HOH HOH . 
O 4 HOH C 13 313 186 HOH HOH . 
O 4 HOH C 14 314 262 HOH HOH . 
O 4 HOH C 15 315 254 HOH HOH . 
O 4 HOH C 16 316 265 HOH HOH . 
O 4 HOH C 17 317 160 HOH HOH . 
O 4 HOH C 18 318 204 HOH HOH . 
O 4 HOH C 19 319 245 HOH HOH . 
O 4 HOH C 20 320 253 HOH HOH . 
O 4 HOH C 21 321 133 HOH HOH . 
O 4 HOH C 22 322 104 HOH HOH . 
O 4 HOH C 23 323 197 HOH HOH . 
O 4 HOH C 24 324 203 HOH HOH . 
O 4 HOH C 25 325 267 HOH HOH . 
O 4 HOH C 26 326 44 HOH HOH . 
O 4 HOH C 27 327 201 HOH HOH . 
O 4 HOH C 28 328 100 HOH HOH . 
O 4 HOH C 29 329 263 HOH HOH . 
O 4 HOH C 30 330 251 HOH HOH . 
O 4 HOH C 31 331 264 HOH HOH . 
O 4 HOH C 32 332 36 HOH HOH . 
O 4 HOH C 33 333 156 HOH HOH . 
O 4 HOH C 34 334 101 HOH HOH . 
O 4 HOH C 35 335 137 HOH HOH . 
O 4 HOH C 36 336 198 HOH HOH . 
O 4 HOH C 37 337 157 HOH HOH . 
O 4 HOH C 38 338 255 HOH HOH . 
O 4 HOH C 39 339 259 HOH HOH . 
O 4 HOH C 40 340 277 HOH HOH . 
O 4 HOH C 41 341 188 HOH HOH . 
O 4 HOH C 42 342 257 HOH HOH . 
O 4 HOH C 43 343 164 HOH HOH . 
O 4 HOH C 44 344 102 HOH HOH . 
O 4 HOH C 45 345 185 HOH HOH . 
O 4 HOH C 46 346 258 HOH HOH . 
O 4 HOH C 47 347 202 HOH HOH . 
O 4 HOH C 48 348 310 HOH HOH . 
P 4 HOH D 1 301 42 HOH HOH . 
P 4 HOH D 2 302 271 HOH HOH . 
P 4 HOH D 3 303 52 HOH HOH . 
P 4 HOH D 4 304 210 HOH HOH . 
P 4 HOH D 5 305 40 HOH HOH . 
P 4 HOH D 6 306 314 HOH HOH . 
P 4 HOH D 7 307 273 HOH HOH . 
P 4 HOH D 8 308 208 HOH HOH . 
P 4 HOH D 9 309 196 HOH HOH . 
P 4 HOH D 10 310 223 HOH HOH . 
P 4 HOH D 11 311 51 HOH HOH . 
P 4 HOH D 12 312 212 HOH HOH . 
P 4 HOH D 13 313 300 HOH HOH . 
P 4 HOH D 14 314 47 HOH HOH . 
P 4 HOH D 15 315 45 HOH HOH . 
P 4 HOH D 16 316 107 HOH HOH . 
P 4 HOH D 17 317 268 HOH HOH . 
P 4 HOH D 18 318 38 HOH HOH . 
P 4 HOH D 19 319 226 HOH HOH . 
P 4 HOH D 20 320 48 HOH HOH . 
P 4 HOH D 21 321 274 HOH HOH . 
P 4 HOH D 22 322 46 HOH HOH . 
P 4 HOH D 23 323 220 HOH HOH . 
P 4 HOH D 24 324 222 HOH HOH . 
P 4 HOH D 25 325 227 HOH HOH . 
P 4 HOH D 26 326 53 HOH HOH . 
P 4 HOH D 27 327 221 HOH HOH . 
P 4 HOH D 28 328 132 HOH HOH . 
P 4 HOH D 29 329 216 HOH HOH . 
P 4 HOH D 30 330 214 HOH HOH . 
P 4 HOH D 31 331 217 HOH HOH . 
P 4 HOH D 32 332 49 HOH HOH . 
P 4 HOH D 33 333 39 HOH HOH . 
P 4 HOH D 34 334 207 HOH HOH . 
P 4 HOH D 35 335 54 HOH HOH . 
P 4 HOH D 36 336 269 HOH HOH . 
P 4 HOH D 37 337 215 HOH HOH . 
P 4 HOH D 38 338 266 HOH HOH . 
P 4 HOH D 39 339 313 HOH HOH . 
P 4 HOH D 40 340 228 HOH HOH . 
P 4 HOH D 41 341 209 HOH HOH . 
P 4 HOH D 42 342 311 HOH HOH . 
P 4 HOH D 43 343 213 HOH HOH . 
P 4 HOH D 44 344 275 HOH HOH . 
P 4 HOH D 45 345 218 HOH HOH . 
P 4 HOH D 46 346 200 HOH HOH . 
P 4 HOH D 47 347 225 HOH HOH . 
P 4 HOH D 48 348 211 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         G 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               -19.005 
_atom_site.Cartn_y               -6.747 
_atom_site.Cartn_z               -41.928 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        40.58 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           201 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           260 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#