data_5B8D
#
_model_server_result.job_id            K1tZh592CXbXMIXNI0dCjA 
_model_server_result.datetime_utc      '2024-11-05 08:38:55' 
_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          5b8d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"RA","auth_seq_id":1343}' 
#
_entry.id    5B8D 
#
_exptl.entry_id    5B8D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          6 
_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            5B8D 
_cell.length_a            41.434 
_cell.length_b            44.157 
_cell.length_c            56.549 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5B8D 
_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    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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA 
_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                      6 
_struct_asym.id                             RA 
_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 SG CYS 7 A CYS 1113 1_555 D ZN ZN . A ZN 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc2 A ND1 HIS 9 A HIS 1115 1_555 D ZN ZN . A ZN 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc3 A SG CYS 27 A CYS 1133 1_555 C ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc4 A SG CYS 30 A CYS 1136 1_555 C ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc5 A SG CYS 39 A CYS 1145 1_555 B ZN ZN . A ZN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc6 A SG CYS 47 A CYS 1153 1_555 C ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc7 A O TYR 50 A TYR 1156 1_555 RA NA NA . A NA 1343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
metalc ? metalc8 A O ILE 51 A ILE 1157 1_555 RA NA NA . A NA 1343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc9 A ND1 HIS 54 A HIS 1160 1_555 C ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc10 A NE2 HIS 58 A HIS 1164 1_555 B ZN ZN . A ZN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc11 A ND1 HIS 64 A HIS 1170 1_555 B ZN ZN . A ZN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc12 A SG CYS 77 A CYS 1183 1_555 D ZN ZN . A ZN 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc13 A SG CYS 80 A CYS 1186 1_555 D ZN ZN . A ZN 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? 
metalc ? metalc14 RA NA NA . A NA 1343 1_555 SA O HOH . A HOH 1449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? 
metalc ? metalc15 RA NA NA . A NA 1343 1_555 SA O HOH . A HOH 1469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc16 RA NA NA . A NA 1343 1_555 SA O HOH . A HOH 1470 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
#
_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                     5B8D 
_atom_sites.fract_transf_matrix[1][1]    0.024135 
_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]    0.022646 
_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]    0.017684 
_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 ZN A 1 1301 201 ZN ZN . 
C 2 ZN A 1 1302 202 ZN ZN . 
D 2 ZN A 1 1303 203 ZN ZN . 
E 3 FMT A 1 1304 1 FMT FMT . 
F 3 FMT A 1 1305 2 FMT FMT . 
G 4 6T4 A 1 1306 1 6T4 304 . 
H 5 UNX A 1 1307 1 UNX UNX . 
I 5 UNX A 1 1308 2 UNX UNX . 
J 5 UNX A 1 1309 3 UNX UNX . 
K 5 UNX A 1 1310 4 UNX UNX . 
L 5 UNX A 1 1311 5 UNX UNX . 
M 5 UNX A 1 1312 6 UNX UNX . 
N 5 UNX A 1 1313 7 UNX UNX . 
O 5 UNX A 1 1314 8 UNX UNX . 
P 5 UNX A 1 1315 9 UNX UNX . 
Q 5 UNX A 1 1316 10 UNX UNX . 
R 5 UNX A 1 1317 11 UNX UNX . 
S 5 UNX A 1 1318 12 UNX UNX . 
T 5 UNX A 1 1319 13 UNX UNX . 
U 5 UNX A 1 1320 14 UNX UNX . 
V 5 UNX A 1 1321 15 UNX UNX . 
W 5 UNX A 1 1322 16 UNX UNX . 
X 5 UNX A 1 1323 17 UNX UNX . 
Y 5 UNX A 1 1324 18 UNX UNX . 
Z 5 UNX A 1 1325 19 UNX UNX . 
AA 5 UNX A 1 1326 20 UNX UNX . 
BA 5 UNX A 1 1327 21 UNX UNX . 
CA 5 UNX A 1 1328 22 UNX UNX . 
DA 5 UNX A 1 1329 23 UNX UNX . 
EA 5 UNX A 1 1330 24 UNX UNX . 
FA 5 UNX A 1 1331 25 UNX UNX . 
GA 5 UNX A 1 1332 26 UNX UNX . 
HA 5 UNX A 1 1333 27 UNX UNX . 
IA 5 UNX A 1 1334 28 UNX UNX . 
JA 5 UNX A 1 1335 29 UNX UNX . 
KA 5 UNX A 1 1336 30 UNX UNX . 
LA 5 UNX A 1 1337 31 UNX UNX . 
MA 5 UNX A 1 1338 32 UNX UNX . 
NA 5 UNX A 1 1339 33 UNX UNX . 
OA 5 UNX A 1 1340 34 UNX UNX . 
PA 5 UNX A 1 1341 35 UNX UNX . 
QA 5 UNX A 1 1342 36 UNX UNX . 
RA 6 NA A 1 1343 1 NA NA . 
SA 7 HOH A 1 1401 14 HOH HOH . 
SA 7 HOH A 2 1402 45 HOH HOH . 
SA 7 HOH A 3 1403 30 HOH HOH . 
SA 7 HOH A 4 1404 32 HOH HOH . 
SA 7 HOH A 5 1405 43 HOH HOH . 
SA 7 HOH A 6 1406 7 HOH HOH . 
SA 7 HOH A 7 1407 27 HOH HOH . 
SA 7 HOH A 8 1408 48 HOH HOH . 
SA 7 HOH A 9 1409 66 HOH HOH . 
SA 7 HOH A 10 1410 71 HOH HOH . 
SA 7 HOH A 11 1411 54 HOH HOH . 
SA 7 HOH A 12 1412 9 HOH HOH . 
SA 7 HOH A 13 1413 74 HOH HOH . 
SA 7 HOH A 14 1414 20 HOH HOH . 
SA 7 HOH A 15 1415 39 HOH HOH . 
SA 7 HOH A 16 1416 4 HOH HOH . 
SA 7 HOH A 17 1417 1 HOH HOH . 
SA 7 HOH A 18 1418 35 HOH HOH . 
SA 7 HOH A 19 1419 62 HOH HOH . 
SA 7 HOH A 20 1420 31 HOH HOH . 
SA 7 HOH A 21 1421 49 HOH HOH . 
SA 7 HOH A 22 1422 13 HOH HOH . 
SA 7 HOH A 23 1423 26 HOH HOH . 
SA 7 HOH A 24 1424 12 HOH HOH . 
SA 7 HOH A 25 1425 22 HOH HOH . 
SA 7 HOH A 26 1426 47 HOH HOH . 
SA 7 HOH A 27 1427 8 HOH HOH . 
SA 7 HOH A 28 1428 50 HOH HOH . 
SA 7 HOH A 29 1429 18 HOH HOH . 
SA 7 HOH A 30 1430 6 HOH HOH . 
SA 7 HOH A 31 1431 19 HOH HOH . 
SA 7 HOH A 32 1432 25 HOH HOH . 
SA 7 HOH A 33 1433 16 HOH HOH . 
SA 7 HOH A 34 1434 34 HOH HOH . 
SA 7 HOH A 35 1435 69 HOH HOH . 
SA 7 HOH A 36 1436 3 HOH HOH . 
SA 7 HOH A 37 1437 75 HOH HOH . 
SA 7 HOH A 38 1438 73 HOH HOH . 
SA 7 HOH A 39 1439 40 HOH HOH . 
SA 7 HOH A 40 1440 28 HOH HOH . 
SA 7 HOH A 41 1441 33 HOH HOH . 
SA 7 HOH A 42 1442 56 HOH HOH . 
SA 7 HOH A 43 1443 38 HOH HOH . 
SA 7 HOH A 44 1444 17 HOH HOH . 
SA 7 HOH A 45 1445 63 HOH HOH . 
SA 7 HOH A 46 1446 21 HOH HOH . 
SA 7 HOH A 47 1447 36 HOH HOH . 
SA 7 HOH A 48 1448 68 HOH HOH . 
SA 7 HOH A 49 1449 41 HOH HOH . 
SA 7 HOH A 50 1450 10 HOH HOH . 
SA 7 HOH A 51 1451 65 HOH HOH . 
SA 7 HOH A 52 1452 59 HOH HOH . 
SA 7 HOH A 53 1453 5 HOH HOH . 
SA 7 HOH A 54 1454 67 HOH HOH . 
SA 7 HOH A 55 1455 44 HOH HOH . 
SA 7 HOH A 56 1456 2 HOH HOH . 
SA 7 HOH A 57 1457 79 HOH HOH . 
SA 7 HOH A 58 1458 60 HOH HOH . 
SA 7 HOH A 59 1459 24 HOH HOH . 
SA 7 HOH A 60 1460 46 HOH HOH . 
SA 7 HOH A 61 1461 29 HOH HOH . 
SA 7 HOH A 62 1462 23 HOH HOH . 
SA 7 HOH A 63 1463 53 HOH HOH . 
SA 7 HOH A 64 1464 15 HOH HOH . 
SA 7 HOH A 65 1465 57 HOH HOH . 
SA 7 HOH A 66 1466 11 HOH HOH . 
SA 7 HOH A 67 1467 72 HOH HOH . 
SA 7 HOH A 68 1468 64 HOH HOH . 
SA 7 HOH A 69 1469 70 HOH HOH . 
SA 7 HOH A 70 1470 61 HOH HOH . 
SA 7 HOH A 71 1471 76 HOH HOH . 
SA 7 HOH A 72 1472 51 HOH HOH . 
SA 7 HOH A 73 1473 52 HOH HOH . 
SA 7 HOH A 74 1474 37 HOH HOH . 
SA 7 HOH A 75 1475 55 HOH HOH . 
SA 7 HOH A 76 1476 58 HOH HOH . 
SA 7 HOH A 77 1477 78 HOH HOH . 
SA 7 HOH A 78 1478 42 HOH HOH . 
SA 7 HOH A 79 1479 77 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         RA 
_atom_site.label_entity_id       6 
_atom_site.Cartn_x               5.349 
_atom_site.Cartn_y               13.934 
_atom_site.Cartn_z               13.224 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        18.04 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           1343 
_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    2 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#