data_1D5M
#
_model_server_result.job_id            a-tdbW1N2290GSsgceYN-g 
_model_server_result.datetime_utc      '2025-01-03 05:23:30' 
_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          1d5m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1201}' 
#
_entry.id    1D5M 
#
_exptl.entry_id    1D5M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          5 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_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            1D5M 
_cell.length_a            82.38 
_cell.length_b            93.34 
_cell.length_c            99.68 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1D5M 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I 
_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                      5 
_struct_asym.id                             E 
_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
disulf ? disulf1 A SG CYS 107 A CYS 107 1_555 A SG CYS 163 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 15 B CYS 15 1_555 B SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf3 B SG CYS 117 B CYS 117 1_555 B SG CYS 173 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
disulf ? disulf4 C SG CYS 93 C CYS 93 1_555 C SG CYS 113 C CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
covale ? covale1 A ND2 ASN 118 A ASN 118 1_555 E C1 NAG . A NAG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale2 D C ACE 1 D ACE 803 1_555 D N ALC 2 D ALC 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale3 D C ALC 2 D ALC 804 1_555 D N ARG 3 D ARG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale4 D C MET 5 D MET 807 1_555 D N CY1 6 D CY1 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? 
covale ? covale5 D C CY1 6 D CY1 808 1_555 D N SER 7 D SER 809 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale6 D C LEU 8 D LEU 810 1_555 D N NH2 9 D NH2 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NAG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-beta-D-glucopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C1 C2 NAG sing 295 n n 
C1 O1 NAG sing 296 n n 
C1 O5 NAG sing 297 n n 
C1 H1 NAG sing 298 n n 
C2 C3 NAG sing 299 n n 
C2 N2 NAG sing 300 n n 
C2 H2 NAG sing 301 n n 
C3 C4 NAG sing 302 n n 
C3 O3 NAG sing 303 n n 
C3 H3 NAG sing 304 n n 
C4 C5 NAG sing 305 n n 
C4 O4 NAG sing 306 n n 
C4 H4 NAG sing 307 n n 
C5 C6 NAG sing 308 n n 
C5 O5 NAG sing 309 n n 
C5 H5 NAG sing 310 n n 
C6 O6 NAG sing 311 n n 
C6 H61 NAG sing 312 n n 
C6 H62 NAG sing 313 n n 
C7 C8 NAG sing 314 n n 
C7 N2 NAG sing 315 n n 
C7 O7 NAG doub 316 n n 
C8 H81 NAG sing 317 n n 
C8 H82 NAG sing 318 n n 
C8 H83 NAG sing 319 n n 
N2 HN2 NAG sing 320 n n 
O1 HO1 NAG sing 321 n n 
O3 HO3 NAG sing 322 n n 
O4 HO4 NAG sing 323 n n 
O6 HO6 NAG sing 324 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 
NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     1D5M 
_atom_sites.fract_transf_matrix[1][1]    0.012139 
_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]    0.010714 
_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]    0.010032 
_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
E 5 NAG A 1 1201 1201 NAG NAG . 
F 6 HOH A 1 1302 1302 HOH HOH . 
F 6 HOH A 2 1303 1303 HOH HOH . 
F 6 HOH A 3 1305 1305 HOH HOH . 
F 6 HOH A 4 1306 1306 HOH HOH . 
F 6 HOH A 5 1307 1307 HOH HOH . 
F 6 HOH A 6 1309 1309 HOH HOH . 
F 6 HOH A 7 1310 1310 HOH HOH . 
F 6 HOH A 8 1312 1312 HOH HOH . 
F 6 HOH A 9 1315 1315 HOH HOH . 
F 6 HOH A 10 1316 1316 HOH HOH . 
F 6 HOH A 11 1317 1317 HOH HOH . 
F 6 HOH A 12 1319 1319 HOH HOH . 
F 6 HOH A 13 1320 1320 HOH HOH . 
F 6 HOH A 14 1321 1321 HOH HOH . 
F 6 HOH A 15 1323 1323 HOH HOH . 
F 6 HOH A 16 1324 1324 HOH HOH . 
F 6 HOH A 17 1325 1325 HOH HOH . 
F 6 HOH A 18 1326 1326 HOH HOH . 
F 6 HOH A 19 1327 1327 HOH HOH . 
F 6 HOH A 20 1328 1328 HOH HOH . 
F 6 HOH A 21 1329 1329 HOH HOH . 
F 6 HOH A 22 1330 1330 HOH HOH . 
F 6 HOH A 23 1333 1333 HOH HOH . 
F 6 HOH A 24 1334 1334 HOH HOH . 
F 6 HOH A 25 1335 1335 HOH HOH . 
F 6 HOH A 26 1380 1380 HOH HOH . 
F 6 HOH A 27 1381 1381 HOH HOH . 
F 6 HOH A 28 1382 1382 HOH HOH . 
F 6 HOH A 29 1383 1383 HOH HOH . 
F 6 HOH A 30 1384 1384 HOH HOH . 
F 6 HOH A 31 1385 1385 HOH HOH . 
F 6 HOH A 32 1387 1387 HOH HOH . 
F 6 HOH A 33 1388 1388 HOH HOH . 
F 6 HOH A 34 1389 1389 HOH HOH . 
F 6 HOH A 35 1390 1390 HOH HOH . 
F 6 HOH A 36 1391 1391 HOH HOH . 
F 6 HOH A 37 1392 1392 HOH HOH . 
F 6 HOH A 38 1393 1393 HOH HOH . 
F 6 HOH A 39 1394 1394 HOH HOH . 
F 6 HOH A 40 1395 1395 HOH HOH . 
F 6 HOH A 41 1397 1397 HOH HOH . 
F 6 HOH A 42 1398 1398 HOH HOH . 
F 6 HOH A 43 1399 1399 HOH HOH . 
F 6 HOH A 44 1400 1400 HOH HOH . 
F 6 HOH A 45 1430 1430 HOH HOH . 
F 6 HOH A 46 1431 1431 HOH HOH . 
F 6 HOH A 47 1432 1432 HOH HOH . 
F 6 HOH A 48 1433 1433 HOH HOH . 
F 6 HOH A 49 1434 1434 HOH HOH . 
F 6 HOH A 50 1436 1436 HOH HOH . 
F 6 HOH A 51 1437 1437 HOH HOH . 
F 6 HOH A 52 1438 1438 HOH HOH . 
G 6 HOH B 1 1304 1304 HOH HOH . 
G 6 HOH B 2 1308 1308 HOH HOH . 
G 6 HOH B 3 1311 1311 HOH HOH . 
G 6 HOH B 4 1322 1322 HOH HOH . 
G 6 HOH B 5 1331 1331 HOH HOH . 
G 6 HOH B 6 1332 1332 HOH HOH . 
G 6 HOH B 7 1336 1336 HOH HOH . 
G 6 HOH B 8 1337 1337 HOH HOH . 
G 6 HOH B 9 1338 1338 HOH HOH . 
G 6 HOH B 10 1339 1339 HOH HOH . 
G 6 HOH B 11 1340 1340 HOH HOH . 
G 6 HOH B 12 1341 1341 HOH HOH . 
G 6 HOH B 13 1342 1342 HOH HOH . 
G 6 HOH B 14 1343 1343 HOH HOH . 
G 6 HOH B 15 1344 1344 HOH HOH . 
G 6 HOH B 16 1345 1345 HOH HOH . 
G 6 HOH B 17 1346 1346 HOH HOH . 
G 6 HOH B 18 1347 1347 HOH HOH . 
G 6 HOH B 19 1348 1348 HOH HOH . 
G 6 HOH B 20 1349 1349 HOH HOH . 
G 6 HOH B 21 1350 1350 HOH HOH . 
G 6 HOH B 22 1351 1351 HOH HOH . 
G 6 HOH B 23 1352 1352 HOH HOH . 
G 6 HOH B 24 1353 1353 HOH HOH . 
G 6 HOH B 25 1354 1354 HOH HOH . 
G 6 HOH B 26 1401 1401 HOH HOH . 
G 6 HOH B 27 1402 1402 HOH HOH . 
G 6 HOH B 28 1403 1403 HOH HOH . 
G 6 HOH B 29 1404 1404 HOH HOH . 
G 6 HOH B 30 1405 1405 HOH HOH . 
G 6 HOH B 31 1406 1406 HOH HOH . 
G 6 HOH B 32 1407 1407 HOH HOH . 
G 6 HOH B 33 1408 1408 HOH HOH . 
G 6 HOH B 34 1409 1409 HOH HOH . 
G 6 HOH B 35 1435 1435 HOH HOH . 
G 6 HOH B 36 1440 1440 HOH HOH . 
G 6 HOH B 37 1442 1442 HOH HOH . 
G 6 HOH B 38 1444 1444 HOH HOH . 
H 6 HOH C 1 1313 1313 HOH HOH . 
H 6 HOH C 2 1314 1314 HOH HOH . 
H 6 HOH C 3 1318 1318 HOH HOH . 
H 6 HOH C 4 1355 1355 HOH HOH . 
H 6 HOH C 5 1356 1356 HOH HOH . 
H 6 HOH C 6 1357 1357 HOH HOH . 
H 6 HOH C 7 1358 1358 HOH HOH . 
H 6 HOH C 8 1359 1359 HOH HOH . 
H 6 HOH C 9 1360 1360 HOH HOH . 
H 6 HOH C 10 1361 1361 HOH HOH . 
H 6 HOH C 11 1362 1362 HOH HOH . 
H 6 HOH C 12 1363 1363 HOH HOH . 
H 6 HOH C 13 1364 1364 HOH HOH . 
H 6 HOH C 14 1365 1365 HOH HOH . 
H 6 HOH C 15 1366 1366 HOH HOH . 
H 6 HOH C 16 1367 1367 HOH HOH . 
H 6 HOH C 17 1368 1368 HOH HOH . 
H 6 HOH C 18 1369 1369 HOH HOH . 
H 6 HOH C 19 1370 1370 HOH HOH . 
H 6 HOH C 20 1371 1371 HOH HOH . 
H 6 HOH C 21 1372 1372 HOH HOH . 
H 6 HOH C 22 1373 1373 HOH HOH . 
H 6 HOH C 23 1374 1374 HOH HOH . 
H 6 HOH C 24 1375 1375 HOH HOH . 
H 6 HOH C 25 1376 1376 HOH HOH . 
H 6 HOH C 26 1377 1377 HOH HOH . 
H 6 HOH C 27 1378 1378 HOH HOH . 
H 6 HOH C 28 1379 1379 HOH HOH . 
H 6 HOH C 29 1386 1386 HOH HOH . 
H 6 HOH C 30 1396 1396 HOH HOH . 
H 6 HOH C 31 1410 1410 HOH HOH . 
H 6 HOH C 32 1411 1411 HOH HOH . 
H 6 HOH C 33 1412 1412 HOH HOH . 
H 6 HOH C 34 1413 1413 HOH HOH . 
H 6 HOH C 35 1414 1414 HOH HOH . 
H 6 HOH C 36 1415 1415 HOH HOH . 
H 6 HOH C 37 1416 1416 HOH HOH . 
H 6 HOH C 38 1417 1417 HOH HOH . 
H 6 HOH C 39 1418 1418 HOH HOH . 
H 6 HOH C 40 1419 1419 HOH HOH . 
H 6 HOH C 41 1420 1420 HOH HOH . 
H 6 HOH C 42 1421 1421 HOH HOH . 
H 6 HOH C 43 1422 1422 HOH HOH . 
H 6 HOH C 44 1423 1423 HOH HOH . 
H 6 HOH C 45 1424 1424 HOH HOH . 
H 6 HOH C 46 1425 1425 HOH HOH . 
H 6 HOH C 47 1426 1426 HOH HOH . 
H 6 HOH C 48 1427 1427 HOH HOH . 
H 6 HOH C 49 1428 1428 HOH HOH . 
H 6 HOH C 50 1429 1429 HOH HOH . 
H 6 HOH C 51 1441 1441 HOH HOH . 
I 6 HOH D 1 1301 1301 HOH HOH . 
I 6 HOH D 2 1439 1439 HOH HOH . 
I 6 HOH D 3 1443 1443 HOH HOH . 
I 6 HOH D 4 1445 1445 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C1 NAG . . . E 5 34.396 34.239 0.064 1 34.2 ? C1 NAG 1201 A 1 
HETATM 2 C C2 NAG . . . E 5 33.914 33.194 -0.933 1 36.4 ? C2 NAG 1201 A 1 
HETATM 3 C C3 NAG . . . E 5 34.665 31.905 -0.623 1 36.8 ? C3 NAG 1201 A 1 
HETATM 4 C C4 NAG . . . E 5 36.151 32.171 -0.865 1 36.5 ? C4 NAG 1201 A 1 
HETATM 5 C C5 NAG . . . E 5 36.634 33.351 0.004 1 37.04 ? C5 NAG 1201 A 1 
HETATM 6 C C6 NAG . . . E 5 38.042 33.779 -0.359 1 37.38 ? C6 NAG 1201 A 1 
HETATM 7 C C7 NAG . . . E 5 31.886 32.648 0.253 1 39.53 ? C7 NAG 1201 A 1 
HETATM 8 C C8 NAG . . . E 5 30.37 32.551 0.245 1 39.14 ? C8 NAG 1201 A 1 
HETATM 9 N N2 NAG . . . E 5 32.475 33.014 -0.877 1 39.35 ? N2 NAG 1201 A 1 
HETATM 10 O O3 NAG . . . E 5 34.207 30.85 -1.456 1 37.03 ? O3 NAG 1201 A 1 
HETATM 11 O O4 NAG . . . E 5 36.904 31.006 -0.562 1 37.05 ? O4 NAG 1201 A 1 
HETATM 12 O O5 NAG . . . E 5 35.785 34.516 -0.178 1 35.12 ? O5 NAG 1201 A 1 
HETATM 13 O O6 NAG . . . E 5 38.068 34.438 -1.617 1 38.08 ? O6 NAG 1201 A 1 
HETATM 14 O O7 NAG . . . E 5 32.513 32.393 1.277 1 43.14 ? O7 NAG 1201 A 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#