data_5XPF # _model_server_result.job_id OlX3bpv7UYAraP3IXaD-6g _model_server_result.datetime_utc '2024-11-27 12:30:18' _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 5xpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5XPF # _exptl.entry_id 5XPF _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 3 _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 5XPF _cell.length_a 59.839 _cell.length_b 59.839 _cell.length_c 95.828 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,Q _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 B N N ? 2 C N N ? 2 D 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 GLU 11 A GLU 11 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc2 A OH TYR 25 A TYR 25 1_555 B NA NA . A NA 201 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc3 A OH TYR 25 A TYR 25 1_555 B NA NA . A NA 201 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc4 A O GLY 30 A GLY 30 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc5 A O PRO 37 A PRO 37 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc6 A O PHE 104 A PHE 104 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? metalc ? metalc7 B NA NA . A NA 201 1_555 Q O HOH . A HOH 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc8 B NA NA . A NA 201 1_555 Q O HOH . A HOH 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc9 C NA NA . A NA 202 1_555 Q O HOH . A HOH 403 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.719 ? metalc ? metalc10 C NA NA . A NA 202 1_555 Q O HOH . A HOH 443 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.952 ? metalc ? metalc11 C NA NA . A NA 202 1_555 Q O HOH . A HOH 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.148 ? metalc ? metalc12 C NA NA . A NA 202 1_555 Q O HOH . A HOH 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc13 D NA NA . A NA 203 1_555 Q O HOH . A HOH 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc14 D NA NA . A NA 203 1_555 Q O HOH . A HOH 408 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.418 ? metalc ? metalc15 D NA NA . A NA 203 1_555 Q O HOH . A HOH 418 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.318 ? metalc ? metalc16 D NA NA . A NA 203 1_555 Q O HOH . A HOH 418 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.374 ? metalc ? metalc17 D NA NA . A NA 203 1_555 Q O HOH . A HOH 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc18 D NA NA . A NA 203 1_555 Q O HOH . A HOH 509 4_565 ? ? ? ? A ? ? ? ? ? ? ? 2.76 ? # _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 5XPF _atom_sites.fract_transf_matrix[1][1] 0.016712 _atom_sites.fract_transf_matrix[1][2] 0.009648 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019297 _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] 0.010435 _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 B 2 NA A 1 201 1 NA NA . C 2 NA A 1 202 2 NA NA . D 2 NA A 1 203 3 NA NA . E 3 CL A 1 204 4 CL CL . F 3 CL A 1 205 5 CL CL . G 3 CL A 1 206 6 CL CL . H 3 CL A 1 207 7 CL CL . I 3 CL A 1 208 8 CL CL . J 4 HEZ A 1 209 9 HEZ HEZ . K 4 HEZ A 1 210 10 HEZ HEZ . L 4 HEZ A 1 211 11 HEZ HEZ . M 4 HEZ A 1 212 12 HEZ HEZ . N 5 GOL A 1 213 13 GOL GOL . O 5 GOL A 1 214 14 GOL GOL . P 5 GOL A 1 215 15 GOL GOL . Q 6 HOH A 1 301 181 HOH HOH . Q 6 HOH A 2 302 221 HOH HOH . Q 6 HOH A 3 303 125 HOH HOH . Q 6 HOH A 4 304 216 HOH HOH . Q 6 HOH A 5 305 227 HOH HOH . Q 6 HOH A 6 306 198 HOH HOH . Q 6 HOH A 7 307 117 HOH HOH . Q 6 HOH A 8 308 167 HOH HOH . Q 6 HOH A 9 309 104 HOH HOH . Q 6 HOH A 10 310 67 HOH HOH . Q 6 HOH A 11 311 225 HOH HOH . Q 6 HOH A 12 312 156 HOH HOH . Q 6 HOH A 13 313 194 HOH HOH . Q 6 HOH A 14 314 71 HOH HOH . Q 6 HOH A 15 315 206 HOH HOH . Q 6 HOH A 16 316 126 HOH HOH . Q 6 HOH A 17 317 190 HOH HOH . Q 6 HOH A 18 318 48 HOH HOH . Q 6 HOH A 19 319 101 HOH HOH . Q 6 HOH A 20 320 155 HOH HOH . Q 6 HOH A 21 321 1 HOH HOH . Q 6 HOH A 22 322 97 HOH HOH . Q 6 HOH A 23 323 66 HOH HOH . Q 6 HOH A 24 324 228 HOH HOH . Q 6 HOH A 25 325 152 HOH HOH . Q 6 HOH A 26 326 76 HOH HOH . Q 6 HOH A 27 327 136 HOH HOH . Q 6 HOH A 28 328 120 HOH HOH . Q 6 HOH A 29 329 204 HOH HOH . Q 6 HOH A 30 330 107 HOH HOH . Q 6 HOH A 31 331 53 HOH HOH . Q 6 HOH A 32 332 47 HOH HOH . Q 6 HOH A 33 333 199 HOH HOH . Q 6 HOH A 34 334 133 HOH HOH . Q 6 HOH A 35 335 215 HOH HOH . Q 6 HOH A 36 336 35 HOH HOH . Q 6 HOH A 37 337 124 HOH HOH . Q 6 HOH A 38 338 37 HOH HOH . Q 6 HOH A 39 339 56 HOH HOH . Q 6 HOH A 40 340 62 HOH HOH . Q 6 HOH A 41 341 220 HOH HOH . Q 6 HOH A 42 342 79 HOH HOH . Q 6 HOH A 43 343 65 HOH HOH . Q 6 HOH A 44 344 72 HOH HOH . Q 6 HOH A 45 345 183 HOH HOH . Q 6 HOH A 46 346 110 HOH HOH . Q 6 HOH A 47 347 150 HOH HOH . Q 6 HOH A 48 348 12 HOH HOH . Q 6 HOH A 49 349 80 HOH HOH . Q 6 HOH A 50 350 73 HOH HOH . Q 6 HOH A 51 351 131 HOH HOH . Q 6 HOH A 52 352 57 HOH HOH . Q 6 HOH A 53 353 33 HOH HOH . Q 6 HOH A 54 354 68 HOH HOH . Q 6 HOH A 55 355 19 HOH HOH . Q 6 HOH A 56 356 3 HOH HOH . Q 6 HOH A 57 357 28 HOH HOH . Q 6 HOH A 58 358 64 HOH HOH . Q 6 HOH A 59 359 176 HOH HOH . Q 6 HOH A 60 360 94 HOH HOH . Q 6 HOH A 61 361 11 HOH HOH . Q 6 HOH A 62 362 179 HOH HOH . Q 6 HOH A 63 363 51 HOH HOH . Q 6 HOH A 64 364 102 HOH HOH . Q 6 HOH A 65 365 205 HOH HOH . Q 6 HOH A 66 366 177 HOH HOH . Q 6 HOH A 67 367 99 HOH HOH . Q 6 HOH A 68 368 34 HOH HOH . Q 6 HOH A 69 369 109 HOH HOH . Q 6 HOH A 70 370 22 HOH HOH . Q 6 HOH A 71 371 84 HOH HOH . Q 6 HOH A 72 372 26 HOH HOH . Q 6 HOH A 73 373 38 HOH HOH . Q 6 HOH A 74 374 77 HOH HOH . Q 6 HOH A 75 375 93 HOH HOH . Q 6 HOH A 76 376 13 HOH HOH . Q 6 HOH A 77 377 49 HOH HOH . Q 6 HOH A 78 378 21 HOH HOH . Q 6 HOH A 79 379 137 HOH HOH . Q 6 HOH A 80 380 2 HOH HOH . Q 6 HOH A 81 381 69 HOH HOH . Q 6 HOH A 82 382 189 HOH HOH . Q 6 HOH A 83 383 115 HOH HOH . Q 6 HOH A 84 384 81 HOH HOH . Q 6 HOH A 85 385 223 HOH HOH . Q 6 HOH A 86 386 44 HOH HOH . Q 6 HOH A 87 387 29 HOH HOH . Q 6 HOH A 88 388 59 HOH HOH . Q 6 HOH A 89 389 32 HOH HOH . Q 6 HOH A 90 390 118 HOH HOH . Q 6 HOH A 91 391 217 HOH HOH . Q 6 HOH A 92 392 241 HOH HOH . Q 6 HOH A 93 393 128 HOH HOH . Q 6 HOH A 94 394 45 HOH HOH . Q 6 HOH A 95 395 143 HOH HOH . Q 6 HOH A 96 396 43 HOH HOH . Q 6 HOH A 97 397 222 HOH HOH . Q 6 HOH A 98 398 14 HOH HOH . Q 6 HOH A 99 399 83 HOH HOH . Q 6 HOH A 100 400 114 HOH HOH . Q 6 HOH A 101 401 103 HOH HOH . Q 6 HOH A 102 402 108 HOH HOH . Q 6 HOH A 103 403 192 HOH HOH . Q 6 HOH A 104 404 89 HOH HOH . Q 6 HOH A 105 405 9 HOH HOH . Q 6 HOH A 106 406 178 HOH HOH . Q 6 HOH A 107 407 17 HOH HOH . Q 6 HOH A 108 408 207 HOH HOH . Q 6 HOH A 109 409 27 HOH HOH . Q 6 HOH A 110 410 50 HOH HOH . Q 6 HOH A 111 411 8 HOH HOH . Q 6 HOH A 112 412 95 HOH HOH . Q 6 HOH A 113 413 15 HOH HOH . Q 6 HOH A 114 414 151 HOH HOH . Q 6 HOH A 115 415 7 HOH HOH . Q 6 HOH A 116 416 18 HOH HOH . Q 6 HOH A 117 417 113 HOH HOH . Q 6 HOH A 118 418 195 HOH HOH . Q 6 HOH A 119 419 30 HOH HOH . Q 6 HOH A 120 420 119 HOH HOH . Q 6 HOH A 121 421 135 HOH HOH . Q 6 HOH A 122 422 172 HOH HOH . Q 6 HOH A 123 423 112 HOH HOH . Q 6 HOH A 124 424 42 HOH HOH . Q 6 HOH A 125 425 122 HOH HOH . Q 6 HOH A 126 426 16 HOH HOH . Q 6 HOH A 127 427 25 HOH HOH . Q 6 HOH A 128 428 6 HOH HOH . Q 6 HOH A 129 429 148 HOH HOH . Q 6 HOH A 130 430 170 HOH HOH . Q 6 HOH A 131 431 74 HOH HOH . Q 6 HOH A 132 432 46 HOH HOH . Q 6 HOH A 133 433 91 HOH HOH . Q 6 HOH A 134 434 41 HOH HOH . Q 6 HOH A 135 435 31 HOH HOH . Q 6 HOH A 136 436 58 HOH HOH . Q 6 HOH A 137 437 4 HOH HOH . Q 6 HOH A 138 438 123 HOH HOH . Q 6 HOH A 139 439 20 HOH HOH . Q 6 HOH A 140 440 214 HOH HOH . Q 6 HOH A 141 441 147 HOH HOH . Q 6 HOH A 142 442 55 HOH HOH . Q 6 HOH A 143 443 188 HOH HOH . Q 6 HOH A 144 444 39 HOH HOH . Q 6 HOH A 145 445 75 HOH HOH . Q 6 HOH A 146 446 203 HOH HOH . Q 6 HOH A 147 447 185 HOH HOH . Q 6 HOH A 148 448 24 HOH HOH . Q 6 HOH A 149 449 174 HOH HOH . Q 6 HOH A 150 450 36 HOH HOH . Q 6 HOH A 151 451 129 HOH HOH . Q 6 HOH A 152 452 10 HOH HOH . Q 6 HOH A 153 453 134 HOH HOH . Q 6 HOH A 154 454 193 HOH HOH . Q 6 HOH A 155 455 63 HOH HOH . Q 6 HOH A 156 456 5 HOH HOH . Q 6 HOH A 157 457 138 HOH HOH . Q 6 HOH A 158 458 52 HOH HOH . Q 6 HOH A 159 459 153 HOH HOH . Q 6 HOH A 160 460 132 HOH HOH . Q 6 HOH A 161 461 169 HOH HOH . Q 6 HOH A 162 462 210 HOH HOH . Q 6 HOH A 163 463 209 HOH HOH . Q 6 HOH A 164 464 213 HOH HOH . Q 6 HOH A 165 465 88 HOH HOH . Q 6 HOH A 166 466 208 HOH HOH . Q 6 HOH A 167 467 87 HOH HOH . Q 6 HOH A 168 468 231 HOH HOH . Q 6 HOH A 169 469 111 HOH HOH . Q 6 HOH A 170 470 90 HOH HOH . Q 6 HOH A 171 471 127 HOH HOH . Q 6 HOH A 172 472 86 HOH HOH . Q 6 HOH A 173 473 234 HOH HOH . Q 6 HOH A 174 474 196 HOH HOH . Q 6 HOH A 175 475 242 HOH HOH . Q 6 HOH A 176 476 154 HOH HOH . Q 6 HOH A 177 477 182 HOH HOH . Q 6 HOH A 178 478 98 HOH HOH . Q 6 HOH A 179 479 100 HOH HOH . Q 6 HOH A 180 480 82 HOH HOH . Q 6 HOH A 181 481 149 HOH HOH . Q 6 HOH A 182 482 218 HOH HOH . Q 6 HOH A 183 483 105 HOH HOH . Q 6 HOH A 184 484 139 HOH HOH . Q 6 HOH A 185 485 211 HOH HOH . Q 6 HOH A 186 486 160 HOH HOH . Q 6 HOH A 187 487 191 HOH HOH . Q 6 HOH A 188 488 237 HOH HOH . Q 6 HOH A 189 489 78 HOH HOH . Q 6 HOH A 190 490 239 HOH HOH . Q 6 HOH A 191 491 219 HOH HOH . Q 6 HOH A 192 492 85 HOH HOH . Q 6 HOH A 193 493 159 HOH HOH . Q 6 HOH A 194 494 96 HOH HOH . Q 6 HOH A 195 495 146 HOH HOH . Q 6 HOH A 196 496 144 HOH HOH . Q 6 HOH A 197 497 226 HOH HOH . Q 6 HOH A 198 498 116 HOH HOH . Q 6 HOH A 199 499 200 HOH HOH . Q 6 HOH A 200 500 158 HOH HOH . Q 6 HOH A 201 501 166 HOH HOH . Q 6 HOH A 202 502 140 HOH HOH . Q 6 HOH A 203 503 161 HOH HOH . Q 6 HOH A 204 504 197 HOH HOH . Q 6 HOH A 205 505 141 HOH HOH . Q 6 HOH A 206 506 162 HOH HOH . Q 6 HOH A 207 507 142 HOH HOH . Q 6 HOH A 208 508 240 HOH HOH . Q 6 HOH A 209 509 171 HOH HOH . Q 6 HOH A 210 510 130 HOH HOH . Q 6 HOH A 211 511 168 HOH HOH . Q 6 HOH A 212 512 54 HOH HOH . Q 6 HOH A 213 513 238 HOH HOH . Q 6 HOH A 214 514 70 HOH HOH . Q 6 HOH A 215 515 61 HOH HOH . Q 6 HOH A 216 516 121 HOH HOH . Q 6 HOH A 217 517 163 HOH HOH . Q 6 HOH A 218 518 236 HOH HOH . Q 6 HOH A 219 519 235 HOH HOH . Q 6 HOH A 220 520 180 HOH HOH . Q 6 HOH A 221 521 212 HOH HOH . Q 6 HOH A 222 522 40 HOH HOH . Q 6 HOH A 223 523 145 HOH HOH . Q 6 HOH A 224 524 186 HOH HOH . Q 6 HOH A 225 525 232 HOH HOH . Q 6 HOH A 226 526 60 HOH HOH . Q 6 HOH A 227 527 175 HOH HOH . Q 6 HOH A 228 528 23 HOH HOH . Q 6 HOH A 229 529 187 HOH HOH . Q 6 HOH A 230 530 173 HOH HOH . Q 6 HOH A 231 531 157 HOH HOH . Q 6 HOH A 232 532 165 HOH HOH . Q 6 HOH A 233 533 184 HOH HOH . Q 6 HOH A 234 534 229 HOH HOH . Q 6 HOH A 235 535 106 HOH HOH . Q 6 HOH A 236 536 92 HOH HOH . Q 6 HOH A 237 537 230 HOH HOH . Q 6 HOH A 238 538 233 HOH HOH . Q 6 HOH A 239 539 224 HOH HOH . Q 6 HOH A 240 540 202 HOH HOH . Q 6 HOH A 241 541 201 HOH HOH . Q 6 HOH A 242 542 164 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 -16.446 _atom_site.Cartn_y 16.863 _atom_site.Cartn_z 10.668 _atom_site.occupancy 0.53 _atom_site.B_iso_or_equiv 20.32 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 203 _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 38 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #