data_1VKG # _model_server_result.job_id bEf3R10xRuSSTGg0u2jWSg _model_server_result.datetime_utc '2024-11-23 23:41:25' _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 1vkg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 1VKG # _exptl.entry_id 1VKG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _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 1VKG _cell.length_a 82.63 _cell.length_b 92.71 _cell.length_c 98.76 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VKG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _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 ? 3 D N N ? 3 G 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 disulf ? disulf1 A SG CYS 244 A CYS 244 1_555 A SG CYS 287 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 B SG CYS 244 B CYS 244 1_555 B SG CYS 287 B CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc1 A O LEU 177 A LEU 177 1_555 D NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc2 A OD1 ASP 178 A ASP 178 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc3 A OD2 ASP 178 A ASP 178 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc4 A O ASP 178 A ASP 178 1_555 D NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc5 A ND1 HIS 180 A HIS 180 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc6 A O LEU 200 A LEU 200 1_555 D NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc7 A OH TYR 240 A TYR 240 1_555 D NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc8 A OD2 ASP 267 A ASP 267 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc9 C ZN ZN . A ZN 400 1_555 E O CRI . A CRI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? metalc ? metalc10 B O ASP 176 B ASP 176 1_555 G NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc11 B OD1 ASP 176 B ASP 176 1_555 G NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc12 B OD2 ASP 178 B ASP 178 1_555 F ZN ZN . B ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc13 B O ASP 178 B ASP 178 1_555 G NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc14 B ND1 HIS 180 B HIS 180 1_555 F ZN ZN . B ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc15 B O HIS 180 B HIS 180 1_555 G NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc16 B O LEU 200 B LEU 200 1_555 G NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc17 B OD2 ASP 267 B ASP 267 1_555 F ZN ZN . B ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc18 F ZN ZN . B ZN 400 1_555 H OH CRI . B CRI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc19 F ZN ZN . B ZN 400 1_555 H N CRI . B CRI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc20 F ZN ZN . B ZN 400 1_555 H O CRI . B CRI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? # _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 1VKG _atom_sites.fract_transf_matrix[1][1] 0.012102 _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] 0.010786 _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] 0.010126 _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 ZN A 1 400 400 ZN ZN . D 3 NA A 1 401 12 NA NA . E 4 CRI A 1 402 401 CRI INH . F 2 ZN B 1 400 400 ZN ZN . G 3 NA B 1 401 2 NA NA . H 4 CRI B 1 402 401 CRI INH . I 5 HOH A 1 403 6 HOH HOH . I 5 HOH A 2 404 7 HOH HOH . I 5 HOH A 3 405 9 HOH HOH . I 5 HOH A 4 406 10 HOH HOH . I 5 HOH A 5 407 11 HOH HOH . I 5 HOH A 6 408 13 HOH HOH . I 5 HOH A 7 409 16 HOH HOH . I 5 HOH A 8 410 17 HOH HOH . I 5 HOH A 9 411 18 HOH HOH . I 5 HOH A 10 412 19 HOH HOH . I 5 HOH A 11 413 20 HOH HOH . I 5 HOH A 12 414 21 HOH HOH . I 5 HOH A 13 415 24 HOH HOH . I 5 HOH A 14 416 26 HOH HOH . I 5 HOH A 15 417 28 HOH HOH . I 5 HOH A 16 418 32 HOH HOH . I 5 HOH A 17 419 33 HOH HOH . I 5 HOH A 18 420 37 HOH HOH . I 5 HOH A 19 421 43 HOH HOH . I 5 HOH A 20 422 51 HOH HOH . I 5 HOH A 21 423 59 HOH HOH . I 5 HOH A 22 424 60 HOH HOH . I 5 HOH A 23 425 69 HOH HOH . I 5 HOH A 24 426 70 HOH HOH . I 5 HOH A 25 427 72 HOH HOH . I 5 HOH A 26 428 75 HOH HOH . I 5 HOH A 27 429 87 HOH HOH . I 5 HOH A 28 430 88 HOH HOH . I 5 HOH A 29 431 89 HOH HOH . I 5 HOH A 30 432 91 HOH HOH . I 5 HOH A 31 433 92 HOH HOH . I 5 HOH A 32 434 93 HOH HOH . I 5 HOH A 33 435 94 HOH HOH . I 5 HOH A 34 436 95 HOH HOH . I 5 HOH A 35 437 97 HOH HOH . I 5 HOH A 36 438 98 HOH HOH . I 5 HOH A 37 439 100 HOH HOH . I 5 HOH A 38 440 101 HOH HOH . I 5 HOH A 39 441 108 HOH HOH . I 5 HOH A 40 442 110 HOH HOH . I 5 HOH A 41 443 115 HOH HOH . I 5 HOH A 42 444 118 HOH HOH . I 5 HOH A 43 445 120 HOH HOH . I 5 HOH A 44 446 125 HOH HOH . I 5 HOH A 45 447 133 HOH HOH . I 5 HOH A 46 448 134 HOH HOH . I 5 HOH A 47 449 137 HOH HOH . I 5 HOH A 48 450 142 HOH HOH . I 5 HOH A 49 451 147 HOH HOH . I 5 HOH A 50 452 154 HOH HOH . I 5 HOH A 51 453 158 HOH HOH . I 5 HOH A 52 454 161 HOH HOH . I 5 HOH A 53 455 169 HOH HOH . I 5 HOH A 54 456 172 HOH HOH . I 5 HOH A 55 457 178 HOH HOH . I 5 HOH A 56 458 184 HOH HOH . I 5 HOH A 57 459 192 HOH HOH . I 5 HOH A 58 460 194 HOH HOH . I 5 HOH A 59 461 195 HOH HOH . I 5 HOH A 60 462 199 HOH HOH . I 5 HOH A 61 463 200 HOH HOH . I 5 HOH A 62 464 201 HOH HOH . I 5 HOH A 63 465 209 HOH HOH . I 5 HOH A 64 466 217 HOH HOH . I 5 HOH A 65 467 219 HOH HOH . I 5 HOH A 66 468 223 HOH HOH . I 5 HOH A 67 469 224 HOH HOH . I 5 HOH A 68 470 230 HOH HOH . I 5 HOH A 69 471 231 HOH HOH . I 5 HOH A 70 472 233 HOH HOH . I 5 HOH A 71 473 237 HOH HOH . I 5 HOH A 72 474 238 HOH HOH . I 5 HOH A 73 475 242 HOH HOH . I 5 HOH A 74 476 247 HOH HOH . I 5 HOH A 75 477 260 HOH HOH . I 5 HOH A 76 478 263 HOH HOH . I 5 HOH A 77 479 267 HOH HOH . I 5 HOH A 78 480 268 HOH HOH . I 5 HOH A 79 481 275 HOH HOH . I 5 HOH A 80 482 282 HOH HOH . I 5 HOH A 81 483 284 HOH HOH . I 5 HOH A 82 484 288 HOH HOH . I 5 HOH A 83 485 292 HOH HOH . I 5 HOH A 84 486 293 HOH HOH . I 5 HOH A 85 487 294 HOH HOH . I 5 HOH A 86 488 295 HOH HOH . I 5 HOH A 87 489 305 HOH HOH . I 5 HOH A 88 490 307 HOH HOH . I 5 HOH A 89 491 312 HOH HOH . I 5 HOH A 90 492 314 HOH HOH . I 5 HOH A 91 493 318 HOH HOH . I 5 HOH A 92 494 323 HOH HOH . I 5 HOH A 93 495 325 HOH HOH . I 5 HOH A 94 496 326 HOH HOH . I 5 HOH A 95 497 329 HOH HOH . I 5 HOH A 96 498 331 HOH HOH . I 5 HOH A 97 499 336 HOH HOH . I 5 HOH A 98 500 337 HOH HOH . I 5 HOH A 99 501 341 HOH HOH . I 5 HOH A 100 502 353 HOH HOH . I 5 HOH A 101 503 357 HOH HOH . I 5 HOH A 102 504 358 HOH HOH . I 5 HOH A 103 505 360 HOH HOH . I 5 HOH A 104 506 361 HOH HOH . I 5 HOH A 105 507 374 HOH HOH . I 5 HOH A 106 508 387 HOH HOH . I 5 HOH A 107 509 399 HOH HOH . I 5 HOH A 108 510 405 HOH HOH . I 5 HOH A 109 511 411 HOH HOH . I 5 HOH A 110 512 429 HOH HOH . I 5 HOH A 111 513 430 HOH HOH . I 5 HOH A 112 514 431 HOH HOH . I 5 HOH A 113 515 432 HOH HOH . I 5 HOH A 114 516 460 HOH HOH . I 5 HOH A 115 517 461 HOH HOH . I 5 HOH A 116 518 465 HOH HOH . I 5 HOH A 117 519 466 HOH HOH . I 5 HOH A 118 520 473 HOH HOH . I 5 HOH A 119 521 475 HOH HOH . I 5 HOH A 120 522 478 HOH HOH . I 5 HOH A 121 523 482 HOH HOH . I 5 HOH A 122 524 496 HOH HOH . I 5 HOH A 123 525 509 HOH HOH . I 5 HOH A 124 526 515 HOH HOH . I 5 HOH A 125 527 517 HOH HOH . I 5 HOH A 126 528 518 HOH HOH . I 5 HOH A 127 529 526 HOH HOH . I 5 HOH A 128 530 544 HOH HOH . I 5 HOH A 129 531 546 HOH HOH . J 5 HOH B 1 403 1 HOH HOH . J 5 HOH B 2 404 3 HOH HOH . J 5 HOH B 3 405 4 HOH HOH . J 5 HOH B 4 406 5 HOH HOH . J 5 HOH B 5 407 8 HOH HOH . J 5 HOH B 6 408 14 HOH HOH . J 5 HOH B 7 409 22 HOH HOH . J 5 HOH B 8 410 23 HOH HOH . J 5 HOH B 9 411 29 HOH HOH . J 5 HOH B 10 412 31 HOH HOH . J 5 HOH B 11 413 34 HOH HOH . J 5 HOH B 12 414 36 HOH HOH . J 5 HOH B 13 415 39 HOH HOH . J 5 HOH B 14 416 41 HOH HOH . J 5 HOH B 15 417 42 HOH HOH . J 5 HOH B 16 418 44 HOH HOH . J 5 HOH B 17 419 45 HOH HOH . J 5 HOH B 18 420 46 HOH HOH . J 5 HOH B 19 421 47 HOH HOH . J 5 HOH B 20 422 48 HOH HOH . J 5 HOH B 21 423 52 HOH HOH . J 5 HOH B 22 424 53 HOH HOH . J 5 HOH B 23 425 54 HOH HOH . J 5 HOH B 24 426 56 HOH HOH . J 5 HOH B 25 427 57 HOH HOH . J 5 HOH B 26 428 58 HOH HOH . J 5 HOH B 27 429 61 HOH HOH . J 5 HOH B 28 430 63 HOH HOH . J 5 HOH B 29 431 64 HOH HOH . J 5 HOH B 30 432 65 HOH HOH . J 5 HOH B 31 433 66 HOH HOH . J 5 HOH B 32 434 68 HOH HOH . J 5 HOH B 33 435 71 HOH HOH . J 5 HOH B 34 436 74 HOH HOH . J 5 HOH B 35 437 77 HOH HOH . J 5 HOH B 36 438 78 HOH HOH . J 5 HOH B 37 439 80 HOH HOH . J 5 HOH B 38 440 82 HOH HOH . J 5 HOH B 39 441 84 HOH HOH . J 5 HOH B 40 442 85 HOH HOH . J 5 HOH B 41 443 86 HOH HOH . J 5 HOH B 42 444 102 HOH HOH . J 5 HOH B 43 445 103 HOH HOH . J 5 HOH B 44 446 107 HOH HOH . J 5 HOH B 45 447 111 HOH HOH . J 5 HOH B 46 448 112 HOH HOH . J 5 HOH B 47 449 117 HOH HOH . J 5 HOH B 48 450 127 HOH HOH . J 5 HOH B 49 451 131 HOH HOH . J 5 HOH B 50 452 135 HOH HOH . J 5 HOH B 51 453 136 HOH HOH . J 5 HOH B 52 454 140 HOH HOH . J 5 HOH B 53 455 143 HOH HOH . J 5 HOH B 54 456 145 HOH HOH . J 5 HOH B 55 457 148 HOH HOH . J 5 HOH B 56 458 149 HOH HOH . J 5 HOH B 57 459 151 HOH HOH . J 5 HOH B 58 460 152 HOH HOH . J 5 HOH B 59 461 160 HOH HOH . J 5 HOH B 60 462 163 HOH HOH . J 5 HOH B 61 463 164 HOH HOH . J 5 HOH B 62 464 165 HOH HOH . J 5 HOH B 63 465 166 HOH HOH . J 5 HOH B 64 466 167 HOH HOH . J 5 HOH B 65 467 175 HOH HOH . J 5 HOH B 66 468 179 HOH HOH . J 5 HOH B 67 469 182 HOH HOH . J 5 HOH B 68 470 190 HOH HOH . J 5 HOH B 69 471 191 HOH HOH . J 5 HOH B 70 472 204 HOH HOH . J 5 HOH B 71 473 212 HOH HOH . J 5 HOH B 72 474 216 HOH HOH . J 5 HOH B 73 475 221 HOH HOH . J 5 HOH B 74 476 222 HOH HOH . J 5 HOH B 75 477 225 HOH HOH . J 5 HOH B 76 478 235 HOH HOH . J 5 HOH B 77 479 240 HOH HOH . J 5 HOH B 78 480 243 HOH HOH . J 5 HOH B 79 481 254 HOH HOH . J 5 HOH B 80 482 256 HOH HOH . J 5 HOH B 81 483 264 HOH HOH . J 5 HOH B 82 484 266 HOH HOH . J 5 HOH B 83 485 285 HOH HOH . J 5 HOH B 84 486 286 HOH HOH . J 5 HOH B 85 487 311 HOH HOH . J 5 HOH B 86 488 317 HOH HOH . J 5 HOH B 87 489 319 HOH HOH . J 5 HOH B 88 490 334 HOH HOH . J 5 HOH B 89 491 345 HOH HOH . J 5 HOH B 90 492 355 HOH HOH . J 5 HOH B 91 493 363 HOH HOH . J 5 HOH B 92 494 364 HOH HOH . J 5 HOH B 93 495 368 HOH HOH . J 5 HOH B 94 496 369 HOH HOH . J 5 HOH B 95 497 371 HOH HOH . J 5 HOH B 96 498 408 HOH HOH . J 5 HOH B 97 499 415 HOH HOH . J 5 HOH B 98 500 419 HOH HOH . J 5 HOH B 99 501 420 HOH HOH . J 5 HOH B 100 502 422 HOH HOH . J 5 HOH B 101 503 424 HOH HOH . J 5 HOH B 102 504 445 HOH HOH . J 5 HOH B 103 505 446 HOH HOH . J 5 HOH B 104 506 448 HOH HOH . J 5 HOH B 105 507 449 HOH HOH . J 5 HOH B 106 508 450 HOH HOH . J 5 HOH B 107 509 468 HOH HOH . J 5 HOH B 108 510 470 HOH HOH . J 5 HOH B 109 511 472 HOH HOH . J 5 HOH B 110 512 480 HOH HOH . J 5 HOH B 111 513 481 HOH HOH . J 5 HOH B 112 514 487 HOH HOH . J 5 HOH B 113 515 498 HOH HOH . J 5 HOH B 114 516 527 HOH HOH . J 5 HOH B 115 517 538 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 3 _atom_site.Cartn_x 25.915 _atom_site.Cartn_y 55.373 _atom_site.Cartn_z 68.318 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.64 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #