data_8D38 # _model_server_result.job_id LjUde_YR8ZjNvLGSzAushg _model_server_result.datetime_utc '2024-10-19 13:18:59' _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 8d38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 8D38 # _exptl.entry_id 8D38 _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 8D38 _cell.length_a 102.963 _cell.length_b 102.963 _cell.length_c 167.763 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D38 _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 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 _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # 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 E 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 O SER 51 A SER 2 1_555 D NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc2 A OG SER 51 A SER 2 1_555 D NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc3 A O ILE 54 A ILE 5 1_555 D NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc4 A OH TYR 129 A TYR 80 1_555 D NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc5 D NA NA . A NA 301 1_555 F O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc6 B O SER 51 B SER 2 1_555 E NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc7 B OG SER 51 B SER 2 1_555 E NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc8 B O ILE 54 B ILE 5 1_555 E NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc9 B OH TYR 129 B TYR 80 1_555 E NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc10 E NA NA . B NA 301 1_555 G O HOH . B HOH 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? # _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 8D38 _atom_sites.fract_transf_matrix[1][1] 0.009712 _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] 0.009712 _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] 0.005961 _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 1 301 2 NA NA . E 2 NA B 1 301 1 NA NA . F 3 HOH A 1 401 253 HOH HOH . F 3 HOH A 2 402 206 HOH HOH . F 3 HOH A 3 403 269 HOH HOH . F 3 HOH A 4 404 149 HOH HOH . F 3 HOH A 5 405 79 HOH HOH . F 3 HOH A 6 406 26 HOH HOH . F 3 HOH A 7 407 133 HOH HOH . F 3 HOH A 8 408 93 HOH HOH . F 3 HOH A 9 409 142 HOH HOH . F 3 HOH A 10 410 40 HOH HOH . F 3 HOH A 11 411 254 HOH HOH . F 3 HOH A 12 412 263 HOH HOH . F 3 HOH A 13 413 8 HOH HOH . F 3 HOH A 14 414 195 HOH HOH . F 3 HOH A 15 415 48 HOH HOH . F 3 HOH A 16 416 55 HOH HOH . F 3 HOH A 17 417 32 HOH HOH . F 3 HOH A 18 418 151 HOH HOH . F 3 HOH A 19 419 35 HOH HOH . F 3 HOH A 20 420 175 HOH HOH . F 3 HOH A 21 421 162 HOH HOH . F 3 HOH A 22 422 123 HOH HOH . F 3 HOH A 23 423 121 HOH HOH . F 3 HOH A 24 424 245 HOH HOH . F 3 HOH A 25 425 12 HOH HOH . F 3 HOH A 26 426 134 HOH HOH . F 3 HOH A 27 427 180 HOH HOH . F 3 HOH A 28 428 46 HOH HOH . F 3 HOH A 29 429 100 HOH HOH . F 3 HOH A 30 430 166 HOH HOH . F 3 HOH A 31 431 113 HOH HOH . F 3 HOH A 32 432 22 HOH HOH . F 3 HOH A 33 433 218 HOH HOH . F 3 HOH A 34 434 74 HOH HOH . F 3 HOH A 35 435 27 HOH HOH . F 3 HOH A 36 436 171 HOH HOH . F 3 HOH A 37 437 94 HOH HOH . F 3 HOH A 38 438 111 HOH HOH . F 3 HOH A 39 439 47 HOH HOH . F 3 HOH A 40 440 177 HOH HOH . F 3 HOH A 41 441 260 HOH HOH . F 3 HOH A 42 442 28 HOH HOH . F 3 HOH A 43 443 196 HOH HOH . F 3 HOH A 44 444 234 HOH HOH . F 3 HOH A 45 445 62 HOH HOH . F 3 HOH A 46 446 11 HOH HOH . F 3 HOH A 47 447 88 HOH HOH . F 3 HOH A 48 448 52 HOH HOH . F 3 HOH A 49 449 44 HOH HOH . F 3 HOH A 50 450 69 HOH HOH . F 3 HOH A 51 451 81 HOH HOH . F 3 HOH A 52 452 154 HOH HOH . F 3 HOH A 53 453 266 HOH HOH . F 3 HOH A 54 454 152 HOH HOH . F 3 HOH A 55 455 14 HOH HOH . F 3 HOH A 56 456 208 HOH HOH . F 3 HOH A 57 457 2 HOH HOH . F 3 HOH A 58 458 58 HOH HOH . F 3 HOH A 59 459 108 HOH HOH . F 3 HOH A 60 460 17 HOH HOH . F 3 HOH A 61 461 186 HOH HOH . F 3 HOH A 62 462 9 HOH HOH . F 3 HOH A 63 463 211 HOH HOH . F 3 HOH A 64 464 16 HOH HOH . F 3 HOH A 65 465 201 HOH HOH . F 3 HOH A 66 466 33 HOH HOH . F 3 HOH A 67 467 197 HOH HOH . F 3 HOH A 68 468 68 HOH HOH . F 3 HOH A 69 469 1 HOH HOH . F 3 HOH A 70 470 50 HOH HOH . F 3 HOH A 71 471 181 HOH HOH . F 3 HOH A 72 472 5 HOH HOH . F 3 HOH A 73 473 36 HOH HOH . F 3 HOH A 74 474 205 HOH HOH . F 3 HOH A 75 475 21 HOH HOH . F 3 HOH A 76 476 235 HOH HOH . F 3 HOH A 77 477 146 HOH HOH . F 3 HOH A 78 478 252 HOH HOH . F 3 HOH A 79 479 228 HOH HOH . F 3 HOH A 80 480 262 HOH HOH . F 3 HOH A 81 481 165 HOH HOH . F 3 HOH A 82 482 215 HOH HOH . F 3 HOH A 83 483 238 HOH HOH . F 3 HOH A 84 484 106 HOH HOH . F 3 HOH A 85 485 57 HOH HOH . F 3 HOH A 86 486 10 HOH HOH . F 3 HOH A 87 487 159 HOH HOH . F 3 HOH A 88 488 96 HOH HOH . F 3 HOH A 89 489 145 HOH HOH . F 3 HOH A 90 490 246 HOH HOH . F 3 HOH A 91 491 184 HOH HOH . F 3 HOH A 92 492 117 HOH HOH . F 3 HOH A 93 493 168 HOH HOH . F 3 HOH A 94 494 191 HOH HOH . F 3 HOH A 95 495 167 HOH HOH . F 3 HOH A 96 496 174 HOH HOH . F 3 HOH A 97 497 255 HOH HOH . F 3 HOH A 98 498 3 HOH HOH . F 3 HOH A 99 499 244 HOH HOH . F 3 HOH A 100 500 200 HOH HOH . F 3 HOH A 101 501 265 HOH HOH . F 3 HOH A 102 502 241 HOH HOH . F 3 HOH A 103 503 128 HOH HOH . F 3 HOH A 104 504 75 HOH HOH . F 3 HOH A 105 505 160 HOH HOH . F 3 HOH A 106 506 115 HOH HOH . F 3 HOH A 107 507 150 HOH HOH . F 3 HOH A 108 508 125 HOH HOH . F 3 HOH A 109 509 138 HOH HOH . F 3 HOH A 110 510 156 HOH HOH . F 3 HOH A 111 511 137 HOH HOH . F 3 HOH A 112 512 71 HOH HOH . G 3 HOH B 1 401 135 HOH HOH . G 3 HOH B 2 402 248 HOH HOH . G 3 HOH B 3 403 153 HOH HOH . G 3 HOH B 4 404 4 HOH HOH . G 3 HOH B 5 405 63 HOH HOH . G 3 HOH B 6 406 91 HOH HOH . G 3 HOH B 7 407 163 HOH HOH . G 3 HOH B 8 408 127 HOH HOH . G 3 HOH B 9 409 38 HOH HOH . G 3 HOH B 10 410 76 HOH HOH . G 3 HOH B 11 411 199 HOH HOH . G 3 HOH B 12 412 56 HOH HOH . G 3 HOH B 13 413 89 HOH HOH . G 3 HOH B 14 414 49 HOH HOH . G 3 HOH B 15 415 54 HOH HOH . G 3 HOH B 16 416 95 HOH HOH . G 3 HOH B 17 417 98 HOH HOH . G 3 HOH B 18 418 225 HOH HOH . G 3 HOH B 19 419 90 HOH HOH . G 3 HOH B 20 420 23 HOH HOH . G 3 HOH B 21 421 188 HOH HOH . G 3 HOH B 22 422 176 HOH HOH . G 3 HOH B 23 423 34 HOH HOH . G 3 HOH B 24 424 70 HOH HOH . G 3 HOH B 25 425 243 HOH HOH . G 3 HOH B 26 426 65 HOH HOH . G 3 HOH B 27 427 257 HOH HOH . G 3 HOH B 28 428 267 HOH HOH . G 3 HOH B 29 429 247 HOH HOH . G 3 HOH B 30 430 271 HOH HOH . G 3 HOH B 31 431 82 HOH HOH . G 3 HOH B 32 432 83 HOH HOH . G 3 HOH B 33 433 131 HOH HOH . G 3 HOH B 34 434 86 HOH HOH . G 3 HOH B 35 435 73 HOH HOH . G 3 HOH B 36 436 43 HOH HOH . G 3 HOH B 37 437 80 HOH HOH . G 3 HOH B 38 438 216 HOH HOH . G 3 HOH B 39 439 209 HOH HOH . G 3 HOH B 40 440 24 HOH HOH . G 3 HOH B 41 441 66 HOH HOH . G 3 HOH B 42 442 190 HOH HOH . G 3 HOH B 43 443 219 HOH HOH . G 3 HOH B 44 444 187 HOH HOH . G 3 HOH B 45 445 136 HOH HOH . G 3 HOH B 46 446 193 HOH HOH . G 3 HOH B 47 447 59 HOH HOH . G 3 HOH B 48 448 130 HOH HOH . G 3 HOH B 49 449 194 HOH HOH . G 3 HOH B 50 450 7 HOH HOH . G 3 HOH B 51 451 189 HOH HOH . G 3 HOH B 52 452 258 HOH HOH . G 3 HOH B 53 453 25 HOH HOH . G 3 HOH B 54 454 92 HOH HOH . G 3 HOH B 55 455 120 HOH HOH . G 3 HOH B 56 456 41 HOH HOH . G 3 HOH B 57 457 122 HOH HOH . G 3 HOH B 58 458 240 HOH HOH . G 3 HOH B 59 459 77 HOH HOH . G 3 HOH B 60 460 178 HOH HOH . G 3 HOH B 61 461 19 HOH HOH . G 3 HOH B 62 462 60 HOH HOH . G 3 HOH B 63 463 210 HOH HOH . G 3 HOH B 64 464 222 HOH HOH . G 3 HOH B 65 465 119 HOH HOH . G 3 HOH B 66 466 39 HOH HOH . G 3 HOH B 67 467 67 HOH HOH . G 3 HOH B 68 468 29 HOH HOH . G 3 HOH B 69 469 53 HOH HOH . G 3 HOH B 70 470 183 HOH HOH . G 3 HOH B 71 471 155 HOH HOH . G 3 HOH B 72 472 18 HOH HOH . G 3 HOH B 73 473 231 HOH HOH . G 3 HOH B 74 474 182 HOH HOH . G 3 HOH B 75 475 126 HOH HOH . G 3 HOH B 76 476 242 HOH HOH . G 3 HOH B 77 477 204 HOH HOH . G 3 HOH B 78 478 230 HOH HOH . G 3 HOH B 79 479 251 HOH HOH . G 3 HOH B 80 480 224 HOH HOH . G 3 HOH B 81 481 233 HOH HOH . G 3 HOH B 82 482 61 HOH HOH . G 3 HOH B 83 483 192 HOH HOH . G 3 HOH B 84 484 272 HOH HOH . G 3 HOH B 85 485 275 HOH HOH . G 3 HOH B 86 486 261 HOH HOH . G 3 HOH B 87 487 102 HOH HOH . G 3 HOH B 88 488 270 HOH HOH . G 3 HOH B 89 489 157 HOH HOH . G 3 HOH B 90 490 274 HOH HOH . G 3 HOH B 91 491 118 HOH HOH . G 3 HOH B 92 492 273 HOH HOH . H 3 HOH C 1 301 107 HOH HOH . H 3 HOH C 2 302 103 HOH HOH . H 3 HOH C 3 303 237 HOH HOH . H 3 HOH C 4 304 87 HOH HOH . H 3 HOH C 5 305 97 HOH HOH . H 3 HOH C 6 306 51 HOH HOH . H 3 HOH C 7 307 148 HOH HOH . H 3 HOH C 8 308 172 HOH HOH . H 3 HOH C 9 309 116 HOH HOH . H 3 HOH C 10 310 37 HOH HOH . H 3 HOH C 11 311 268 HOH HOH . H 3 HOH C 12 312 78 HOH HOH . H 3 HOH C 13 313 13 HOH HOH . H 3 HOH C 14 314 85 HOH HOH . H 3 HOH C 15 315 109 HOH HOH . H 3 HOH C 16 316 64 HOH HOH . H 3 HOH C 17 317 170 HOH HOH . H 3 HOH C 18 318 143 HOH HOH . H 3 HOH C 19 319 112 HOH HOH . H 3 HOH C 20 320 110 HOH HOH . H 3 HOH C 21 321 99 HOH HOH . H 3 HOH C 22 322 104 HOH HOH . H 3 HOH C 23 323 220 HOH HOH . H 3 HOH C 24 324 45 HOH HOH . H 3 HOH C 25 325 221 HOH HOH . H 3 HOH C 26 326 239 HOH HOH . H 3 HOH C 27 327 42 HOH HOH . H 3 HOH C 28 328 227 HOH HOH . H 3 HOH C 29 329 31 HOH HOH . H 3 HOH C 30 330 140 HOH HOH . H 3 HOH C 31 331 129 HOH HOH . H 3 HOH C 32 332 164 HOH HOH . H 3 HOH C 33 333 124 HOH HOH . H 3 HOH C 34 334 139 HOH HOH . H 3 HOH C 35 335 144 HOH HOH . H 3 HOH C 36 336 30 HOH HOH . H 3 HOH C 37 337 101 HOH HOH . H 3 HOH C 38 338 20 HOH HOH . H 3 HOH C 39 339 236 HOH HOH . H 3 HOH C 40 340 250 HOH HOH . H 3 HOH C 41 341 213 HOH HOH . H 3 HOH C 42 342 169 HOH HOH . H 3 HOH C 43 343 226 HOH HOH . H 3 HOH C 44 344 185 HOH HOH . H 3 HOH C 45 345 198 HOH HOH . H 3 HOH C 46 346 15 HOH HOH . H 3 HOH C 47 347 259 HOH HOH . H 3 HOH C 48 348 212 HOH HOH . H 3 HOH C 49 349 105 HOH HOH . H 3 HOH C 50 350 223 HOH HOH . H 3 HOH C 51 351 158 HOH HOH . H 3 HOH C 52 352 72 HOH HOH . H 3 HOH C 53 353 207 HOH HOH . H 3 HOH C 54 354 147 HOH HOH . H 3 HOH C 55 355 84 HOH HOH . H 3 HOH C 56 356 229 HOH HOH . H 3 HOH C 57 357 173 HOH HOH . H 3 HOH C 58 358 202 HOH HOH . H 3 HOH C 59 359 132 HOH HOH . H 3 HOH C 60 360 141 HOH HOH . H 3 HOH C 61 361 161 HOH HOH . H 3 HOH C 62 362 203 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 -8.131 _atom_site.Cartn_y -46.169 _atom_site.Cartn_z 16.293 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 35.33 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 301 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #