data_5CVK # _model_server_result.job_id YYzH2SaSLd3KMXarJaqjrw _model_server_result.datetime_utc '2025-01-10 08:48:16' _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 5cvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":207}' # _entry.id 5CVK # _exptl.entry_id 5CVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _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 5CVK _cell.length_a 59.002 _cell.length_b 59.002 _cell.length_c 264.653 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J _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' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 LEU 14 A LEU 14 1_555 H NA NA . A NA 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A OE2 GLU 37 A GLU 37 1_555 C CD CD . A CD 202 8_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 A NE2 HIS 43 A HIS 43 1_555 D CD CD . A CD 203 8_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc4 A SG CYS 99 A CYS 99 1_555 B CD CD . A CD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 A O LEU 105 A LEU 105 1_555 I CD CD . A CD 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc6 A OE1 GLU 128 A GLU 128 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc7 A OE2 GLU 128 A GLU 128 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc8 A OE1 GLU 130 A GLU 130 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc9 A OE2 GLU 130 A GLU 130 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc10 A OE1 GLU 132 A GLU 132 1_555 C CD CD . A CD 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc11 A NE2 HIS 141 A HIS 141 1_555 B CD CD . A CD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc12 A NE2 HIS 145 A HIS 145 1_555 B CD CD . A CD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc13 A NE2 HIS 145 A HIS 145 1_555 E CD CD . A CD 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc14 A OD1 ASP 164 A ASP 164 1_555 I CD CD . A CD 208 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc15 A OD2 ASP 164 A ASP 164 1_555 I CD CD . A CD 208 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc16 C CD CD . A CD 202 1_555 J O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc17 D CD CD . A CD 203 1_555 J O HOH . A HOH 369 8_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc18 D CD CD . A CD 203 1_555 J O HOH . A HOH 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc19 E CD CD . A CD 204 1_555 J O HOH . A HOH 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc20 H NA NA . A NA 207 1_555 J O HOH . A HOH 370 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc21 H NA NA . A NA 207 1_555 J O HOH . A HOH 388 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc22 H NA NA . A NA 207 1_555 J O HOH . A HOH 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc23 H NA NA . A NA 207 1_555 J O HOH . A HOH 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc24 H NA NA . A NA 207 1_555 J O HOH . A HOH 469 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc25 I CD CD . A CD 208 1_555 J O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc26 I CD CD . A CD 208 1_555 J O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? # _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 5CVK _atom_sites.fract_transf_matrix[1][1] 0.016949 _atom_sites.fract_transf_matrix[1][2] 0.009785 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019571 _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] 0.003779 _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 CD A 1 201 1 CD CD . C 2 CD A 1 202 3 CD CD . D 2 CD A 1 203 2 CD CD . E 2 CD A 1 204 4 CD CD . F 3 56E A 1 205 1 56E 493 . G 4 ACT A 1 206 1 ACT ACT . H 5 NA A 1 207 1 NA NA . I 2 CD A 1 208 1 CD CD . J 6 HOH A 1 301 151 HOH HOH . J 6 HOH A 2 302 216 HOH HOH . J 6 HOH A 3 303 193 HOH HOH . J 6 HOH A 4 304 34 HOH HOH . J 6 HOH A 5 305 54 HOH HOH . J 6 HOH A 6 306 215 HOH HOH . J 6 HOH A 7 307 5 HOH HOH . J 6 HOH A 8 308 113 HOH HOH . J 6 HOH A 9 309 64 HOH HOH . J 6 HOH A 10 310 68 HOH HOH . J 6 HOH A 11 311 73 HOH HOH . J 6 HOH A 12 312 94 HOH HOH . J 6 HOH A 13 313 171 HOH HOH . J 6 HOH A 14 314 79 HOH HOH . J 6 HOH A 15 315 100 HOH HOH . J 6 HOH A 16 316 147 HOH HOH . J 6 HOH A 17 317 70 HOH HOH . J 6 HOH A 18 318 98 HOH HOH . J 6 HOH A 19 319 91 HOH HOH . J 6 HOH A 20 320 41 HOH HOH . J 6 HOH A 21 321 45 HOH HOH . J 6 HOH A 22 322 22 HOH HOH . J 6 HOH A 23 323 3 HOH HOH . J 6 HOH A 24 324 75 HOH HOH . J 6 HOH A 25 325 114 HOH HOH . J 6 HOH A 26 326 69 HOH HOH . J 6 HOH A 27 327 187 HOH HOH . J 6 HOH A 28 328 119 HOH HOH . J 6 HOH A 29 329 33 HOH HOH . J 6 HOH A 30 330 51 HOH HOH . J 6 HOH A 31 331 11 HOH HOH . J 6 HOH A 32 332 36 HOH HOH . J 6 HOH A 33 333 31 HOH HOH . J 6 HOH A 34 334 47 HOH HOH . J 6 HOH A 35 335 12 HOH HOH . J 6 HOH A 36 336 71 HOH HOH . J 6 HOH A 37 337 18 HOH HOH . J 6 HOH A 38 338 3 HOH HOH . J 6 HOH A 39 339 87 HOH HOH . J 6 HOH A 40 340 72 HOH HOH . J 6 HOH A 41 341 128 HOH HOH . J 6 HOH A 42 342 28 HOH HOH . J 6 HOH A 43 343 86 HOH HOH . J 6 HOH A 44 344 59 HOH HOH . J 6 HOH A 45 345 40 HOH HOH . J 6 HOH A 46 346 60 HOH HOH . J 6 HOH A 47 347 44 HOH HOH . J 6 HOH A 48 348 7 HOH HOH . J 6 HOH A 49 349 17 HOH HOH . J 6 HOH A 50 350 107 HOH HOH . J 6 HOH A 51 351 20 HOH HOH . J 6 HOH A 52 352 15 HOH HOH . J 6 HOH A 53 353 1 HOH HOH . J 6 HOH A 54 354 77 HOH HOH . J 6 HOH A 55 355 4 HOH HOH . J 6 HOH A 56 356 188 HOH HOH . J 6 HOH A 57 357 217 HOH HOH . J 6 HOH A 58 358 26 HOH HOH . J 6 HOH A 59 359 9 HOH HOH . J 6 HOH A 60 360 4 HOH HOH . J 6 HOH A 61 361 115 HOH HOH . J 6 HOH A 62 362 88 HOH HOH . J 6 HOH A 63 363 199 HOH HOH . J 6 HOH A 64 364 27 HOH HOH . J 6 HOH A 65 365 200 HOH HOH . J 6 HOH A 66 366 67 HOH HOH . J 6 HOH A 67 367 74 HOH HOH . J 6 HOH A 68 368 121 HOH HOH . J 6 HOH A 69 369 13 HOH HOH . J 6 HOH A 70 370 212 HOH HOH . J 6 HOH A 71 371 19 HOH HOH . J 6 HOH A 72 372 95 HOH HOH . J 6 HOH A 73 373 97 HOH HOH . J 6 HOH A 74 374 61 HOH HOH . J 6 HOH A 75 375 14 HOH HOH . J 6 HOH A 76 376 32 HOH HOH . J 6 HOH A 77 377 111 HOH HOH . J 6 HOH A 78 378 29 HOH HOH . J 6 HOH A 79 379 37 HOH HOH . J 6 HOH A 80 380 148 HOH HOH . J 6 HOH A 81 381 126 HOH HOH . J 6 HOH A 82 382 129 HOH HOH . J 6 HOH A 83 383 23 HOH HOH . J 6 HOH A 84 384 84 HOH HOH . J 6 HOH A 85 385 6 HOH HOH . J 6 HOH A 86 386 142 HOH HOH . J 6 HOH A 87 387 153 HOH HOH . J 6 HOH A 88 388 214 HOH HOH . J 6 HOH A 89 389 219 HOH HOH . J 6 HOH A 90 390 211 HOH HOH . J 6 HOH A 91 391 149 HOH HOH . J 6 HOH A 92 392 5 HOH HOH . J 6 HOH A 93 393 10 HOH HOH . J 6 HOH A 94 394 169 HOH HOH . J 6 HOH A 95 395 50 HOH HOH . J 6 HOH A 96 396 106 HOH HOH . J 6 HOH A 97 397 198 HOH HOH . J 6 HOH A 98 398 24 HOH HOH . J 6 HOH A 99 399 25 HOH HOH . J 6 HOH A 100 400 197 HOH HOH . J 6 HOH A 101 401 5 HOH HOH . J 6 HOH A 102 402 110 HOH HOH . J 6 HOH A 103 403 43 HOH HOH . J 6 HOH A 104 404 125 HOH HOH . J 6 HOH A 105 405 16 HOH HOH . J 6 HOH A 106 406 146 HOH HOH . J 6 HOH A 107 407 49 HOH HOH . J 6 HOH A 108 408 117 HOH HOH . J 6 HOH A 109 409 104 HOH HOH . J 6 HOH A 110 410 96 HOH HOH . J 6 HOH A 111 411 8 HOH HOH . J 6 HOH A 112 412 143 HOH HOH . J 6 HOH A 113 413 76 HOH HOH . J 6 HOH A 114 414 222 HOH HOH . J 6 HOH A 115 415 62 HOH HOH . J 6 HOH A 116 416 103 HOH HOH . J 6 HOH A 117 417 137 HOH HOH . J 6 HOH A 118 418 66 HOH HOH . J 6 HOH A 119 419 131 HOH HOH . J 6 HOH A 120 420 38 HOH HOH . J 6 HOH A 121 421 224 HOH HOH . J 6 HOH A 122 422 53 HOH HOH . J 6 HOH A 123 423 52 HOH HOH . J 6 HOH A 124 424 1 HOH HOH . J 6 HOH A 125 425 78 HOH HOH . J 6 HOH A 126 426 56 HOH HOH . J 6 HOH A 127 427 225 HOH HOH . J 6 HOH A 128 428 93 HOH HOH . J 6 HOH A 129 429 2 HOH HOH . J 6 HOH A 130 430 191 HOH HOH . J 6 HOH A 131 431 221 HOH HOH . J 6 HOH A 132 432 102 HOH HOH . J 6 HOH A 133 433 170 HOH HOH . J 6 HOH A 134 434 55 HOH HOH . J 6 HOH A 135 435 42 HOH HOH . J 6 HOH A 136 436 46 HOH HOH . J 6 HOH A 137 437 109 HOH HOH . J 6 HOH A 138 438 2 HOH HOH . J 6 HOH A 139 439 127 HOH HOH . J 6 HOH A 140 440 195 HOH HOH . J 6 HOH A 141 441 175 HOH HOH . J 6 HOH A 142 442 101 HOH HOH . J 6 HOH A 143 443 4 HOH HOH . J 6 HOH A 144 444 182 HOH HOH . J 6 HOH A 145 445 82 HOH HOH . J 6 HOH A 146 446 81 HOH HOH . J 6 HOH A 147 447 57 HOH HOH . J 6 HOH A 148 448 30 HOH HOH . J 6 HOH A 149 449 174 HOH HOH . J 6 HOH A 150 450 90 HOH HOH . J 6 HOH A 151 451 63 HOH HOH . J 6 HOH A 152 452 173 HOH HOH . J 6 HOH A 153 453 189 HOH HOH . J 6 HOH A 154 454 130 HOH HOH . J 6 HOH A 155 455 196 HOH HOH . J 6 HOH A 156 456 177 HOH HOH . J 6 HOH A 157 457 194 HOH HOH . J 6 HOH A 158 458 112 HOH HOH . J 6 HOH A 159 459 167 HOH HOH . J 6 HOH A 160 460 185 HOH HOH . J 6 HOH A 161 461 39 HOH HOH . J 6 HOH A 162 462 192 HOH HOH . J 6 HOH A 163 463 140 HOH HOH . J 6 HOH A 164 464 83 HOH HOH . J 6 HOH A 165 465 220 HOH HOH . J 6 HOH A 166 466 124 HOH HOH . J 6 HOH A 167 467 190 HOH HOH . J 6 HOH A 168 468 1 HOH HOH . J 6 HOH A 169 469 213 HOH HOH . J 6 HOH A 170 470 157 HOH HOH . J 6 HOH A 171 471 161 HOH HOH . J 6 HOH A 172 472 3 HOH HOH . J 6 HOH A 173 473 85 HOH HOH . J 6 HOH A 174 474 156 HOH HOH . J 6 HOH A 175 475 223 HOH HOH . J 6 HOH A 176 476 122 HOH HOH . J 6 HOH A 177 477 65 HOH HOH . J 6 HOH A 178 478 123 HOH HOH . J 6 HOH A 179 479 89 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 H _atom_site.label_entity_id 5 _atom_site.Cartn_x 14.858 _atom_site.Cartn_y -6.247 _atom_site.Cartn_z 14.334 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 35.73 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 207 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #