data_5YR7
#
_model_server_result.job_id            GmuIH-Q39lH3sQFc8QGhRg 
_model_server_result.datetime_utc      '2024-12-23 10:30:35' 
_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          5yr7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":405}' 
#
_entry.id    5YR7 
#
_exptl.entry_id    5YR7 
_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          92.03 
_cell.angle_gamma         90 
_cell.entry_id            5YR7 
_cell.length_a            47.414 
_cell.length_b            77.193 
_cell.length_c            48.22 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YR7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                             F 
_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 NE2 HIS 32 A HIS 99 1_555 E CO CO . A CO 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc2 A O ASN 140 A ASN 207 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc3 A O VAL 142 A VAL 209 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc4 A NE2 HIS 145 A HIS 212 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc5 A OD1 ASP 162 A ASP 229 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc6 A OD2 ASP 162 A ASP 229 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc7 A OD1 ASP 173 A ASP 240 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc8 A OD2 ASP 173 A ASP 240 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc9 A NE2 HIS 236 A HIS 303 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc10 A OE1 GLU 269 A GLU 336 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc11 A O SER 296 A SER 363 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc12 A OE1 GLU 300 A GLU 367 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc13 A OE2 GLU 300 A GLU 367 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc14 B CO CO . A CO 401 1_555 G N MET . A MET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc15 B CO CO . A CO 401 1_555 G O MET . A MET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc16 C CO CO . A CO 402 1_555 G O MET . A MET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? 
metalc ? metalc17 D CO CO . A CO 403 1_555 G OXT MET . A MET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc18 D CO CO . A CO 403 1_555 H O HOH . A HOH 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc19 D CO CO . A CO 403 1_555 H O HOH . A HOH 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc20 E CO CO . A CO 404 1_555 H O HOH . A HOH 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc21 E CO CO . A CO 404 1_555 H O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc22 F NA NA . A NA 405 1_555 H O HOH . A HOH 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc23 F NA NA . A NA 405 1_555 H O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.078 ? 
#
_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                     5YR7 
_atom_sites.fract_transf_matrix[1][1]    0.021091 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000747 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012955 
_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]    0.020751 
_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 CO A 1 401 401 CO CO . 
C 2 CO A 1 402 402 CO CO . 
D 2 CO A 1 403 403 CO CO . 
E 2 CO A 1 404 404 CO CO . 
F 3 NA A 1 405 405 NA NA . 
G 4 MET A 1 406 406 MET MET . 
H 5 HOH A 1 501 451 HOH HOH . 
H 5 HOH A 2 502 463 HOH HOH . 
H 5 HOH A 3 503 429 HOH HOH . 
H 5 HOH A 4 504 413 HOH HOH . 
H 5 HOH A 5 505 474 HOH HOH . 
H 5 HOH A 6 506 477 HOH HOH . 
H 5 HOH A 7 507 415 HOH HOH . 
H 5 HOH A 8 508 412 HOH HOH . 
H 5 HOH A 9 509 434 HOH HOH . 
H 5 HOH A 10 510 460 HOH HOH . 
H 5 HOH A 11 511 445 HOH HOH . 
H 5 HOH A 12 512 423 HOH HOH . 
H 5 HOH A 13 513 420 HOH HOH . 
H 5 HOH A 14 514 427 HOH HOH . 
H 5 HOH A 15 515 458 HOH HOH . 
H 5 HOH A 16 516 468 HOH HOH . 
H 5 HOH A 17 517 442 HOH HOH . 
H 5 HOH A 18 518 437 HOH HOH . 
H 5 HOH A 19 519 457 HOH HOH . 
H 5 HOH A 20 520 424 HOH HOH . 
H 5 HOH A 21 521 416 HOH HOH . 
H 5 HOH A 22 522 448 HOH HOH . 
H 5 HOH A 23 523 473 HOH HOH . 
H 5 HOH A 24 524 476 HOH HOH . 
H 5 HOH A 25 525 456 HOH HOH . 
H 5 HOH A 26 526 475 HOH HOH . 
H 5 HOH A 27 527 426 HOH HOH . 
H 5 HOH A 28 528 422 HOH HOH . 
H 5 HOH A 29 529 467 HOH HOH . 
H 5 HOH A 30 530 438 HOH HOH . 
H 5 HOH A 31 531 446 HOH HOH . 
H 5 HOH A 32 532 414 HOH HOH . 
H 5 HOH A 33 533 469 HOH HOH . 
H 5 HOH A 34 534 440 HOH HOH . 
H 5 HOH A 35 535 428 HOH HOH . 
H 5 HOH A 36 536 411 HOH HOH . 
H 5 HOH A 37 537 439 HOH HOH . 
H 5 HOH A 38 538 452 HOH HOH . 
H 5 HOH A 39 539 419 HOH HOH . 
H 5 HOH A 40 540 441 HOH HOH . 
H 5 HOH A 41 541 432 HOH HOH . 
H 5 HOH A 42 542 478 HOH HOH . 
H 5 HOH A 43 543 462 HOH HOH . 
H 5 HOH A 44 544 435 HOH HOH . 
H 5 HOH A 45 545 449 HOH HOH . 
H 5 HOH A 46 546 453 HOH HOH . 
H 5 HOH A 47 547 447 HOH HOH . 
H 5 HOH A 48 548 455 HOH HOH . 
H 5 HOH A 49 549 417 HOH HOH . 
H 5 HOH A 50 550 471 HOH HOH . 
H 5 HOH A 51 551 459 HOH HOH . 
H 5 HOH A 52 552 421 HOH HOH . 
H 5 HOH A 53 553 433 HOH HOH . 
H 5 HOH A 54 554 466 HOH HOH . 
H 5 HOH A 55 555 418 HOH HOH . 
H 5 HOH A 56 556 444 HOH HOH . 
H 5 HOH A 57 557 461 HOH HOH . 
H 5 HOH A 58 558 443 HOH HOH . 
H 5 HOH A 59 559 430 HOH HOH . 
H 5 HOH A 60 560 436 HOH HOH . 
H 5 HOH A 61 561 450 HOH HOH . 
H 5 HOH A 62 562 480 HOH HOH . 
H 5 HOH A 63 563 470 HOH HOH . 
H 5 HOH A 64 564 431 HOH HOH . 
H 5 HOH A 65 565 425 HOH HOH . 
H 5 HOH A 66 566 465 HOH HOH . 
H 5 HOH A 67 567 479 HOH HOH . 
H 5 HOH A 68 568 464 HOH HOH . 
H 5 HOH A 69 569 454 HOH HOH . 
H 5 HOH A 70 570 472 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         F 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               12.862 
_atom_site.Cartn_y               -3.809 
_atom_site.Cartn_z               0.75 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        31.35 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           405 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#