data_5YKJ
#
_model_server_result.job_id            jP5uH00DAE2PCfAKj5a63A 
_model_server_result.datetime_utc      '2025-02-18 02:13:08' 
_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          5ykj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    5YKJ 
#
_exptl.entry_id    5YKJ 
_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    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         90 
_cell.entry_id            5YKJ 
_cell.length_a            84.03 
_cell.length_b            84.03 
_cell.length_c            62.784 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YKJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
covale ? covale1 A C VAL 43 A VAL 90 1_555 A N CSO 44 A CSO 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? 
covale ? covale2 A C CSO 44 A CSO 91 1_555 A N THR 45 A THR 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? 
#
_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                     5YKJ 
_atom_sites.fract_transf_matrix[1][1]    0.011901 
_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]    0.011901 
_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]    0.015928 
_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 GOL A 1 301 1 GOL GOL . 
C 3 NA A 1 302 1 NA NA . 
D 4 HOH A 1 401 116 HOH HOH . 
D 4 HOH A 2 402 131 HOH HOH . 
D 4 HOH A 3 403 53 HOH HOH . 
D 4 HOH A 4 404 155 HOH HOH . 
D 4 HOH A 5 405 191 HOH HOH . 
D 4 HOH A 6 406 172 HOH HOH . 
D 4 HOH A 7 407 112 HOH HOH . 
D 4 HOH A 8 408 60 HOH HOH . 
D 4 HOH A 9 409 171 HOH HOH . 
D 4 HOH A 10 410 154 HOH HOH . 
D 4 HOH A 11 411 68 HOH HOH . 
D 4 HOH A 12 412 46 HOH HOH . 
D 4 HOH A 13 413 220 HOH HOH . 
D 4 HOH A 14 414 195 HOH HOH . 
D 4 HOH A 15 415 118 HOH HOH . 
D 4 HOH A 16 416 54 HOH HOH . 
D 4 HOH A 17 417 98 HOH HOH . 
D 4 HOH A 18 418 32 HOH HOH . 
D 4 HOH A 19 419 188 HOH HOH . 
D 4 HOH A 20 420 82 HOH HOH . 
D 4 HOH A 21 421 204 HOH HOH . 
D 4 HOH A 22 422 207 HOH HOH . 
D 4 HOH A 23 423 23 HOH HOH . 
D 4 HOH A 24 424 136 HOH HOH . 
D 4 HOH A 25 425 33 HOH HOH . 
D 4 HOH A 26 426 177 HOH HOH . 
D 4 HOH A 27 427 7 HOH HOH . 
D 4 HOH A 28 428 73 HOH HOH . 
D 4 HOH A 29 429 28 HOH HOH . 
D 4 HOH A 30 430 142 HOH HOH . 
D 4 HOH A 31 431 139 HOH HOH . 
D 4 HOH A 32 432 17 HOH HOH . 
D 4 HOH A 33 433 128 HOH HOH . 
D 4 HOH A 34 434 156 HOH HOH . 
D 4 HOH A 35 435 3 HOH HOH . 
D 4 HOH A 36 436 105 HOH HOH . 
D 4 HOH A 37 437 29 HOH HOH . 
D 4 HOH A 38 438 78 HOH HOH . 
D 4 HOH A 39 439 50 HOH HOH . 
D 4 HOH A 40 440 185 HOH HOH . 
D 4 HOH A 41 441 194 HOH HOH . 
D 4 HOH A 42 442 119 HOH HOH . 
D 4 HOH A 43 443 85 HOH HOH . 
D 4 HOH A 44 444 34 HOH HOH . 
D 4 HOH A 45 445 25 HOH HOH . 
D 4 HOH A 46 446 84 HOH HOH . 
D 4 HOH A 47 447 144 HOH HOH . 
D 4 HOH A 48 448 79 HOH HOH . 
D 4 HOH A 49 449 30 HOH HOH . 
D 4 HOH A 50 450 19 HOH HOH . 
D 4 HOH A 51 451 127 HOH HOH . 
D 4 HOH A 52 452 99 HOH HOH . 
D 4 HOH A 53 453 26 HOH HOH . 
D 4 HOH A 54 454 153 HOH HOH . 
D 4 HOH A 55 455 134 HOH HOH . 
D 4 HOH A 56 456 180 HOH HOH . 
D 4 HOH A 57 457 4 HOH HOH . 
D 4 HOH A 58 458 137 HOH HOH . 
D 4 HOH A 59 459 36 HOH HOH . 
D 4 HOH A 60 460 45 HOH HOH . 
D 4 HOH A 61 461 16 HOH HOH . 
D 4 HOH A 62 462 143 HOH HOH . 
D 4 HOH A 63 463 219 HOH HOH . 
D 4 HOH A 64 464 141 HOH HOH . 
D 4 HOH A 65 465 9 HOH HOH . 
D 4 HOH A 66 466 217 HOH HOH . 
D 4 HOH A 67 467 24 HOH HOH . 
D 4 HOH A 68 468 6 HOH HOH . 
D 4 HOH A 69 469 62 HOH HOH . 
D 4 HOH A 70 470 149 HOH HOH . 
D 4 HOH A 71 471 95 HOH HOH . 
D 4 HOH A 72 472 63 HOH HOH . 
D 4 HOH A 73 473 22 HOH HOH . 
D 4 HOH A 74 474 86 HOH HOH . 
D 4 HOH A 75 475 130 HOH HOH . 
D 4 HOH A 76 476 14 HOH HOH . 
D 4 HOH A 77 477 94 HOH HOH . 
D 4 HOH A 78 478 176 HOH HOH . 
D 4 HOH A 79 479 77 HOH HOH . 
D 4 HOH A 80 480 51 HOH HOH . 
D 4 HOH A 81 481 101 HOH HOH . 
D 4 HOH A 82 482 49 HOH HOH . 
D 4 HOH A 83 483 31 HOH HOH . 
D 4 HOH A 84 484 218 HOH HOH . 
D 4 HOH A 85 485 83 HOH HOH . 
D 4 HOH A 86 486 114 HOH HOH . 
D 4 HOH A 87 487 132 HOH HOH . 
D 4 HOH A 88 488 1 HOH HOH . 
D 4 HOH A 89 489 76 HOH HOH . 
D 4 HOH A 90 490 165 HOH HOH . 
D 4 HOH A 91 491 74 HOH HOH . 
D 4 HOH A 92 492 15 HOH HOH . 
D 4 HOH A 93 493 10 HOH HOH . 
D 4 HOH A 94 494 27 HOH HOH . 
D 4 HOH A 95 495 37 HOH HOH . 
D 4 HOH A 96 496 72 HOH HOH . 
D 4 HOH A 97 497 47 HOH HOH . 
D 4 HOH A 98 498 18 HOH HOH . 
D 4 HOH A 99 499 184 HOH HOH . 
D 4 HOH A 100 500 106 HOH HOH . 
D 4 HOH A 101 501 150 HOH HOH . 
D 4 HOH A 102 502 196 HOH HOH . 
D 4 HOH A 103 503 40 HOH HOH . 
D 4 HOH A 104 504 20 HOH HOH . 
D 4 HOH A 105 505 111 HOH HOH . 
D 4 HOH A 106 506 5 HOH HOH . 
D 4 HOH A 107 507 164 HOH HOH . 
D 4 HOH A 108 508 57 HOH HOH . 
D 4 HOH A 109 509 113 HOH HOH . 
D 4 HOH A 110 510 93 HOH HOH . 
D 4 HOH A 111 511 58 HOH HOH . 
D 4 HOH A 112 512 152 HOH HOH . 
D 4 HOH A 113 513 189 HOH HOH . 
D 4 HOH A 114 514 39 HOH HOH . 
D 4 HOH A 115 515 35 HOH HOH . 
D 4 HOH A 116 516 122 HOH HOH . 
D 4 HOH A 117 517 124 HOH HOH . 
D 4 HOH A 118 518 13 HOH HOH . 
D 4 HOH A 119 519 90 HOH HOH . 
D 4 HOH A 120 520 52 HOH HOH . 
D 4 HOH A 121 521 11 HOH HOH . 
D 4 HOH A 122 522 21 HOH HOH . 
D 4 HOH A 123 523 133 HOH HOH . 
D 4 HOH A 124 524 108 HOH HOH . 
D 4 HOH A 125 525 97 HOH HOH . 
D 4 HOH A 126 526 48 HOH HOH . 
D 4 HOH A 127 527 211 HOH HOH . 
D 4 HOH A 128 528 91 HOH HOH . 
D 4 HOH A 129 529 59 HOH HOH . 
D 4 HOH A 130 530 102 HOH HOH . 
D 4 HOH A 131 531 92 HOH HOH . 
D 4 HOH A 132 532 71 HOH HOH . 
D 4 HOH A 133 533 43 HOH HOH . 
D 4 HOH A 134 534 55 HOH HOH . 
D 4 HOH A 135 535 222 HOH HOH . 
D 4 HOH A 136 536 2 HOH HOH . 
D 4 HOH A 137 537 66 HOH HOH . 
D 4 HOH A 138 538 38 HOH HOH . 
D 4 HOH A 139 539 168 HOH HOH . 
D 4 HOH A 140 540 182 HOH HOH . 
D 4 HOH A 141 541 44 HOH HOH . 
D 4 HOH A 142 542 89 HOH HOH . 
D 4 HOH A 143 543 41 HOH HOH . 
D 4 HOH A 144 544 161 HOH HOH . 
D 4 HOH A 145 545 75 HOH HOH . 
D 4 HOH A 146 546 87 HOH HOH . 
D 4 HOH A 147 547 125 HOH HOH . 
D 4 HOH A 148 548 80 HOH HOH . 
D 4 HOH A 149 549 145 HOH HOH . 
D 4 HOH A 150 550 64 HOH HOH . 
D 4 HOH A 151 551 104 HOH HOH . 
D 4 HOH A 152 552 103 HOH HOH . 
D 4 HOH A 153 553 110 HOH HOH . 
D 4 HOH A 154 554 183 HOH HOH . 
D 4 HOH A 155 555 187 HOH HOH . 
D 4 HOH A 156 556 140 HOH HOH . 
D 4 HOH A 157 557 158 HOH HOH . 
D 4 HOH A 158 558 88 HOH HOH . 
D 4 HOH A 159 559 42 HOH HOH . 
D 4 HOH A 160 560 209 HOH HOH . 
D 4 HOH A 161 561 232 HOH HOH . 
D 4 HOH A 162 562 65 HOH HOH . 
D 4 HOH A 163 563 230 HOH HOH . 
D 4 HOH A 164 564 226 HOH HOH . 
D 4 HOH A 165 565 228 HOH HOH . 
D 4 HOH A 166 566 173 HOH HOH . 
D 4 HOH A 167 567 224 HOH HOH . 
D 4 HOH A 168 568 160 HOH HOH . 
D 4 HOH A 169 569 210 HOH HOH . 
D 4 HOH A 170 570 69 HOH HOH . 
D 4 HOH A 171 571 56 HOH HOH . 
D 4 HOH A 172 572 67 HOH HOH . 
D 4 HOH A 173 573 147 HOH HOH . 
D 4 HOH A 174 574 186 HOH HOH . 
D 4 HOH A 175 575 129 HOH HOH . 
D 4 HOH A 176 576 193 HOH HOH . 
D 4 HOH A 177 577 70 HOH HOH . 
D 4 HOH A 178 578 123 HOH HOH . 
D 4 HOH A 179 579 199 HOH HOH . 
D 4 HOH A 180 580 201 HOH HOH . 
D 4 HOH A 181 581 229 HOH HOH . 
D 4 HOH A 182 582 198 HOH HOH . 
D 4 HOH A 183 583 221 HOH HOH . 
D 4 HOH A 184 584 175 HOH HOH . 
D 4 HOH A 185 585 100 HOH HOH . 
D 4 HOH A 186 586 202 HOH HOH . 
D 4 HOH A 187 587 61 HOH HOH . 
D 4 HOH A 188 588 192 HOH HOH . 
D 4 HOH A 189 589 203 HOH HOH . 
D 4 HOH A 190 590 174 HOH HOH . 
D 4 HOH A 191 591 159 HOH HOH . 
D 4 HOH A 192 592 178 HOH HOH . 
D 4 HOH A 193 593 117 HOH HOH . 
D 4 HOH A 194 594 212 HOH HOH . 
D 4 HOH A 195 595 121 HOH HOH . 
D 4 HOH A 196 596 179 HOH HOH . 
D 4 HOH A 197 597 107 HOH HOH . 
D 4 HOH A 198 598 225 HOH HOH . 
D 4 HOH A 199 599 227 HOH HOH . 
D 4 HOH A 200 600 215 HOH HOH . 
D 4 HOH A 201 601 234 HOH HOH . 
D 4 HOH A 202 602 169 HOH HOH . 
D 4 HOH A 203 603 231 HOH HOH . 
D 4 HOH A 204 604 138 HOH HOH . 
D 4 HOH A 205 605 170 HOH HOH . 
D 4 HOH A 206 606 120 HOH HOH . 
D 4 HOH A 207 607 135 HOH HOH . 
D 4 HOH A 208 608 126 HOH HOH . 
D 4 HOH A 209 609 181 HOH HOH . 
D 4 HOH A 210 610 216 HOH HOH . 
D 4 HOH A 211 611 146 HOH HOH . 
D 4 HOH A 212 612 206 HOH HOH . 
D 4 HOH A 213 613 115 HOH HOH . 
D 4 HOH A 214 614 205 HOH HOH . 
D 4 HOH A 215 615 197 HOH HOH . 
D 4 HOH A 216 616 213 HOH HOH . 
D 4 HOH A 217 617 200 HOH HOH . 
D 4 HOH A 218 618 96 HOH HOH . 
D 4 HOH A 219 619 166 HOH HOH . 
D 4 HOH A 220 620 81 HOH HOH . 
D 4 HOH A 221 621 148 HOH HOH . 
D 4 HOH A 222 622 167 HOH HOH . 
D 4 HOH A 223 623 208 HOH HOH . 
D 4 HOH A 224 624 163 HOH HOH . 
D 4 HOH A 225 625 223 HOH HOH . 
D 4 HOH A 226 626 233 HOH HOH . 
D 4 HOH A 227 627 151 HOH HOH . 
D 4 HOH A 228 628 190 HOH HOH . 
D 4 HOH A 229 629 235 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         C 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               13.124 
_atom_site.Cartn_y               -2.258 
_atom_site.Cartn_z               -29.486 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        41.3 
_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              68 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           1 
#