data_8VYD # _model_server_result.job_id LvnObzbBuZMitsNgcUAkzQ _model_server_result.datetime_utc '2024-12-01 03:43:29' _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 8vyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 8VYD # _exptl.entry_id 8VYD _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.642 _cell.angle_gamma 90 _cell.entry_id 8VYD _cell.length_a 37.67 _cell.length_b 97.28 _cell.length_c 89.02 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # 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,I 1 1 B,J 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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 OE2 GLU 129 A GLU 129 1_555 H NA NA . A NA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc2 A OD1 ASP 133 A ASP 133 1_555 C NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc3 A O CYS 135 A CYS 135 1_555 C NA NA . A NA 301 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc4 A O CYS 135 A CYS 135 1_555 C NA NA . A NA 301 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc5 A O MET 136 A MET 136 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc6 A O TYR 140 A TYR 140 1_555 D NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc7 A OD1 ASP 186 A ASP 186 1_555 F NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc8 C NA NA . A NA 301 1_555 I O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc9 C NA NA . A NA 301 1_555 I O HOH . A HOH 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc10 D NA NA . A NA 302 1_555 I O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc11 D NA NA . A NA 302 1_555 I O HOH . A HOH 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc12 E NA NA . A NA 303 1_555 I O HOH . A HOH 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc13 E NA NA . A NA 303 1_555 I O HOH . A HOH 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc14 G NA NA . A NA 305 1_555 I O HOH . A HOH 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc15 H NA NA . A NA 306 1_555 I O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? # _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 8VYD _atom_sites.fract_transf_matrix[1][1] 0.026546 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00451 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01028 _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] 0.011394 _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 NA A 1 301 1 NA NA . D 2 NA A 1 302 2 NA NA . E 2 NA A 1 303 3 NA NA . F 2 NA A 1 304 4 NA NA . G 2 NA A 1 305 5 NA NA . H 2 NA A 1 306 8 NA NA . I 3 HOH A 1 401 85 HOH HOH . I 3 HOH A 2 402 167 HOH HOH . I 3 HOH A 3 403 137 HOH HOH . I 3 HOH A 4 404 3 HOH HOH . I 3 HOH A 5 405 73 HOH HOH . I 3 HOH A 6 406 186 HOH HOH . I 3 HOH A 7 407 90 HOH HOH . I 3 HOH A 8 408 123 HOH HOH . I 3 HOH A 9 409 152 HOH HOH . I 3 HOH A 10 410 33 HOH HOH . I 3 HOH A 11 411 7 HOH HOH . I 3 HOH A 12 412 30 HOH HOH . I 3 HOH A 13 413 8 HOH HOH . I 3 HOH A 14 414 67 HOH HOH . I 3 HOH A 15 415 165 HOH HOH . I 3 HOH A 16 416 34 HOH HOH . I 3 HOH A 17 417 124 HOH HOH . I 3 HOH A 18 418 162 HOH HOH . I 3 HOH A 19 419 4 HOH HOH . I 3 HOH A 20 420 17 HOH HOH . I 3 HOH A 21 421 84 HOH HOH . I 3 HOH A 22 422 25 HOH HOH . I 3 HOH A 23 423 32 HOH HOH . I 3 HOH A 24 424 147 HOH HOH . I 3 HOH A 25 425 99 HOH HOH . I 3 HOH A 26 426 68 HOH HOH . I 3 HOH A 27 427 114 HOH HOH . I 3 HOH A 28 428 5 HOH HOH . I 3 HOH A 29 429 160 HOH HOH . I 3 HOH A 30 430 97 HOH HOH . I 3 HOH A 31 431 72 HOH HOH . I 3 HOH A 32 432 6 HOH HOH . I 3 HOH A 33 433 94 HOH HOH . I 3 HOH A 34 434 150 HOH HOH . I 3 HOH A 35 435 48 HOH HOH . I 3 HOH A 36 436 31 HOH HOH . I 3 HOH A 37 437 155 HOH HOH . I 3 HOH A 38 438 115 HOH HOH . I 3 HOH A 39 439 1 HOH HOH . I 3 HOH A 40 440 27 HOH HOH . I 3 HOH A 41 441 63 HOH HOH . I 3 HOH A 42 442 133 HOH HOH . I 3 HOH A 43 443 176 HOH HOH . I 3 HOH A 44 444 135 HOH HOH . I 3 HOH A 45 445 55 HOH HOH . I 3 HOH A 46 446 145 HOH HOH . I 3 HOH A 47 447 83 HOH HOH . I 3 HOH A 48 448 54 HOH HOH . I 3 HOH A 49 449 125 HOH HOH . I 3 HOH A 50 450 13 HOH HOH . I 3 HOH A 51 451 46 HOH HOH . I 3 HOH A 52 452 82 HOH HOH . I 3 HOH A 53 453 2 HOH HOH . I 3 HOH A 54 454 86 HOH HOH . I 3 HOH A 55 455 101 HOH HOH . I 3 HOH A 56 456 49 HOH HOH . I 3 HOH A 57 457 18 HOH HOH . I 3 HOH A 58 458 110 HOH HOH . I 3 HOH A 59 459 93 HOH HOH . I 3 HOH A 60 460 9 HOH HOH . I 3 HOH A 61 461 166 HOH HOH . I 3 HOH A 62 462 51 HOH HOH . I 3 HOH A 63 463 53 HOH HOH . I 3 HOH A 64 464 172 HOH HOH . I 3 HOH A 65 465 69 HOH HOH . I 3 HOH A 66 466 92 HOH HOH . I 3 HOH A 67 467 29 HOH HOH . I 3 HOH A 68 468 16 HOH HOH . I 3 HOH A 69 469 78 HOH HOH . I 3 HOH A 70 470 127 HOH HOH . I 3 HOH A 71 471 142 HOH HOH . I 3 HOH A 72 472 178 HOH HOH . I 3 HOH A 73 473 58 HOH HOH . I 3 HOH A 74 474 26 HOH HOH . I 3 HOH A 75 475 59 HOH HOH . I 3 HOH A 76 476 159 HOH HOH . I 3 HOH A 77 477 10 HOH HOH . I 3 HOH A 78 478 128 HOH HOH . I 3 HOH A 79 479 151 HOH HOH . I 3 HOH A 80 480 11 HOH HOH . I 3 HOH A 81 481 47 HOH HOH . I 3 HOH A 82 482 154 HOH HOH . I 3 HOH A 83 483 143 HOH HOH . I 3 HOH A 84 484 118 HOH HOH . I 3 HOH A 85 485 71 HOH HOH . I 3 HOH A 86 486 148 HOH HOH . I 3 HOH A 87 487 170 HOH HOH . I 3 HOH A 88 488 35 HOH HOH . I 3 HOH A 89 489 52 HOH HOH . I 3 HOH A 90 490 168 HOH HOH . I 3 HOH A 91 491 77 HOH HOH . I 3 HOH A 92 492 180 HOH HOH . I 3 HOH A 93 493 153 HOH HOH . I 3 HOH A 94 494 12 HOH HOH . I 3 HOH A 95 495 80 HOH HOH . I 3 HOH A 96 496 161 HOH HOH . I 3 HOH A 97 497 50 HOH HOH . I 3 HOH A 98 498 107 HOH HOH . I 3 HOH A 99 499 76 HOH HOH . I 3 HOH A 100 500 60 HOH HOH . I 3 HOH A 101 501 129 HOH HOH . I 3 HOH A 102 502 116 HOH HOH . I 3 HOH A 103 503 98 HOH HOH . I 3 HOH A 104 504 81 HOH HOH . I 3 HOH A 105 505 79 HOH HOH . I 3 HOH A 106 506 132 HOH HOH . I 3 HOH A 107 507 126 HOH HOH . I 3 HOH A 108 508 130 HOH HOH . I 3 HOH A 109 509 174 HOH HOH . I 3 HOH A 110 510 181 HOH HOH . I 3 HOH A 111 511 102 HOH HOH . I 3 HOH A 112 512 173 HOH HOH . I 3 HOH A 113 513 177 HOH HOH . J 3 HOH B 1 301 36 HOH HOH . J 3 HOH B 2 302 23 HOH HOH . J 3 HOH B 3 303 100 HOH HOH . J 3 HOH B 4 304 119 HOH HOH . J 3 HOH B 5 305 108 HOH HOH . J 3 HOH B 6 306 120 HOH HOH . J 3 HOH B 7 307 42 HOH HOH . J 3 HOH B 8 308 105 HOH HOH . J 3 HOH B 9 309 21 HOH HOH . J 3 HOH B 10 310 40 HOH HOH . J 3 HOH B 11 311 74 HOH HOH . J 3 HOH B 12 312 136 HOH HOH . J 3 HOH B 13 313 41 HOH HOH . J 3 HOH B 14 314 19 HOH HOH . J 3 HOH B 15 315 38 HOH HOH . J 3 HOH B 16 316 66 HOH HOH . J 3 HOH B 17 317 43 HOH HOH . J 3 HOH B 18 318 157 HOH HOH . J 3 HOH B 19 319 88 HOH HOH . J 3 HOH B 20 320 57 HOH HOH . J 3 HOH B 21 321 96 HOH HOH . J 3 HOH B 22 322 163 HOH HOH . J 3 HOH B 23 323 139 HOH HOH . J 3 HOH B 24 324 146 HOH HOH . J 3 HOH B 25 325 61 HOH HOH . J 3 HOH B 26 326 109 HOH HOH . J 3 HOH B 27 327 158 HOH HOH . J 3 HOH B 28 328 56 HOH HOH . J 3 HOH B 29 329 106 HOH HOH . J 3 HOH B 30 330 22 HOH HOH . J 3 HOH B 31 331 39 HOH HOH . J 3 HOH B 32 332 28 HOH HOH . J 3 HOH B 33 333 113 HOH HOH . J 3 HOH B 34 334 95 HOH HOH . J 3 HOH B 35 335 91 HOH HOH . J 3 HOH B 36 336 175 HOH HOH . J 3 HOH B 37 337 20 HOH HOH . J 3 HOH B 38 338 64 HOH HOH . J 3 HOH B 39 339 75 HOH HOH . J 3 HOH B 40 340 112 HOH HOH . J 3 HOH B 41 341 45 HOH HOH . J 3 HOH B 42 342 15 HOH HOH . J 3 HOH B 43 343 141 HOH HOH . J 3 HOH B 44 344 103 HOH HOH . J 3 HOH B 45 345 89 HOH HOH . J 3 HOH B 46 346 122 HOH HOH . J 3 HOH B 47 347 44 HOH HOH . J 3 HOH B 48 348 182 HOH HOH . J 3 HOH B 49 349 156 HOH HOH . J 3 HOH B 50 350 117 HOH HOH . J 3 HOH B 51 351 134 HOH HOH . J 3 HOH B 52 352 65 HOH HOH . J 3 HOH B 53 353 104 HOH HOH . J 3 HOH B 54 354 62 HOH HOH . J 3 HOH B 55 355 144 HOH HOH . J 3 HOH B 56 356 149 HOH HOH . J 3 HOH B 57 357 169 HOH HOH . J 3 HOH B 58 358 131 HOH HOH . J 3 HOH B 59 359 121 HOH HOH . J 3 HOH B 60 360 37 HOH HOH . J 3 HOH B 61 361 70 HOH HOH . J 3 HOH B 62 362 140 HOH HOH . J 3 HOH B 63 363 138 HOH HOH . J 3 HOH B 64 364 164 HOH HOH . J 3 HOH B 65 365 87 HOH HOH . J 3 HOH B 66 366 24 HOH HOH . J 3 HOH B 67 367 179 HOH HOH . J 3 HOH B 68 368 184 HOH HOH . J 3 HOH B 69 369 183 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 7.814 _atom_site.Cartn_y -0.033 _atom_site.Cartn_z 17.448 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 35.28 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 302 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #