data_8QEE # _model_server_result.job_id jzxVnYIB4UPKS-uZP8zuWA _model_server_result.datetime_utc '2024-10-18 17:17:11' _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 8qee # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1202}' # _entry.id 8QEE # _exptl.entry_id 8QEE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 8QEE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QEE _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _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 _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 ? 4 D N N ? 4 E N N ? 4 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 1205 NAG 2 n B NAG 2 B 2 NAG A 1206 NAG # 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 438 A CYS 438 1_555 A SG CYS 447 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 473 A CYS 473 1_555 A SG CYS 480 A CYS 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 822 A CYS 822 1_555 A SG CYS 828 A CYS 828 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 868 A CYS 868 1_555 A SG CYS 925 A CYS 925 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 869 A CYS 869 1_555 A SG CYS 891 A CYS 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 A SG CYS 879 A CYS 879 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 401 A ASN 401 1_555 D C1 NAG . A NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 513 A ASN 513 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 A ND2 ASN 900 A ASN 900 1_555 F C1 NAG . A NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 940 A ASN 940 1_555 E C1 NAG . A NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 8QEE _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 Y01 A 1 1201 1200 Y01 Y01 . D 4 NAG A 1 1202 1207 NAG NAG . E 4 NAG A 1 1203 1208 NAG NAG . F 4 NAG A 1 1204 1209 NAG NAG . G 5 HOH A 1 1301 1447 HOH HOH . G 5 HOH A 2 1302 1323 HOH HOH . G 5 HOH A 3 1303 1332 HOH HOH . G 5 HOH A 4 1304 1438 HOH HOH . G 5 HOH A 5 1305 1343 HOH HOH . G 5 HOH A 6 1306 1303 HOH HOH . G 5 HOH A 7 1307 1300 HOH HOH . G 5 HOH A 8 1308 1403 HOH HOH . G 5 HOH A 9 1309 1328 HOH HOH . G 5 HOH A 10 1310 1330 HOH HOH . G 5 HOH A 11 1311 1361 HOH HOH . G 5 HOH A 12 1312 1308 HOH HOH . G 5 HOH A 13 1313 1321 HOH HOH . G 5 HOH A 14 1314 1324 HOH HOH . G 5 HOH A 15 1315 1374 HOH HOH . G 5 HOH A 16 1316 1313 HOH HOH . G 5 HOH A 17 1317 1335 HOH HOH . G 5 HOH A 18 1318 1329 HOH HOH . G 5 HOH A 19 1319 1439 HOH HOH . G 5 HOH A 20 1320 1367 HOH HOH . G 5 HOH A 21 1321 1377 HOH HOH . G 5 HOH A 22 1322 1331 HOH HOH . G 5 HOH A 23 1323 1306 HOH HOH . G 5 HOH A 24 1324 1426 HOH HOH . G 5 HOH A 25 1325 1417 HOH HOH . G 5 HOH A 26 1326 1430 HOH HOH . G 5 HOH A 27 1327 1365 HOH HOH . G 5 HOH A 28 1328 1325 HOH HOH . G 5 HOH A 29 1329 1408 HOH HOH . G 5 HOH A 30 1330 1394 HOH HOH . G 5 HOH A 31 1331 1354 HOH HOH . G 5 HOH A 32 1332 1349 HOH HOH . G 5 HOH A 33 1333 1322 HOH HOH . G 5 HOH A 34 1334 1389 HOH HOH . G 5 HOH A 35 1335 1358 HOH HOH . G 5 HOH A 36 1336 1387 HOH HOH . G 5 HOH A 37 1337 1400 HOH HOH . G 5 HOH A 38 1338 1373 HOH HOH . G 5 HOH A 39 1339 1382 HOH HOH . G 5 HOH A 40 1340 1333 HOH HOH . G 5 HOH A 41 1341 1412 HOH HOH . G 5 HOH A 42 1342 1409 HOH HOH . G 5 HOH A 43 1343 1359 HOH HOH . G 5 HOH A 44 1344 1423 HOH HOH . G 5 HOH A 45 1345 1402 HOH HOH . G 5 HOH A 46 1346 1302 HOH HOH . G 5 HOH A 47 1347 1376 HOH HOH . G 5 HOH A 48 1348 1310 HOH HOH . G 5 HOH A 49 1349 1381 HOH HOH . G 5 HOH A 50 1350 1445 HOH HOH . G 5 HOH A 51 1351 1427 HOH HOH . G 5 HOH A 52 1352 1435 HOH HOH . G 5 HOH A 53 1353 1398 HOH HOH . G 5 HOH A 54 1354 1399 HOH HOH . G 5 HOH A 55 1355 1384 HOH HOH . G 5 HOH A 56 1356 1425 HOH HOH . G 5 HOH A 57 1357 1411 HOH HOH . G 5 HOH A 58 1358 1353 HOH HOH . G 5 HOH A 59 1359 1424 HOH HOH . G 5 HOH A 60 1360 1422 HOH HOH . G 5 HOH A 61 1361 1318 HOH HOH . G 5 HOH A 62 1362 1429 HOH HOH . G 5 HOH A 63 1363 1344 HOH HOH . G 5 HOH A 64 1364 1397 HOH HOH . G 5 HOH A 65 1365 1364 HOH HOH . G 5 HOH A 66 1366 1418 HOH HOH . G 5 HOH A 67 1367 1356 HOH HOH . G 5 HOH A 68 1368 1383 HOH HOH . G 5 HOH A 69 1369 1366 HOH HOH . G 5 HOH A 70 1370 1355 HOH HOH . G 5 HOH A 71 1371 1375 HOH HOH . G 5 HOH A 72 1372 1386 HOH HOH . G 5 HOH A 73 1373 1385 HOH HOH . G 5 HOH A 74 1374 1371 HOH HOH . G 5 HOH A 75 1375 1337 HOH HOH . G 5 HOH A 76 1376 1369 HOH HOH . G 5 HOH A 77 1377 1345 HOH HOH . G 5 HOH A 78 1378 1317 HOH HOH . G 5 HOH A 79 1379 1396 HOH HOH . G 5 HOH A 80 1380 1301 HOH HOH . G 5 HOH A 81 1381 1413 HOH HOH . G 5 HOH A 82 1382 1442 HOH HOH . G 5 HOH A 83 1383 1395 HOH HOH . G 5 HOH A 84 1384 1363 HOH HOH . G 5 HOH A 85 1385 1362 HOH HOH . G 5 HOH A 86 1386 1421 HOH HOH . G 5 HOH A 87 1387 1391 HOH HOH . G 5 HOH A 88 1388 1406 HOH HOH . G 5 HOH A 89 1389 1342 HOH HOH . G 5 HOH A 90 1390 1420 HOH HOH . G 5 HOH A 91 1391 1414 HOH HOH . G 5 HOH A 92 1392 1405 HOH HOH . G 5 HOH A 93 1393 1339 HOH HOH . G 5 HOH A 94 1394 1401 HOH HOH . G 5 HOH A 95 1395 1437 HOH HOH . G 5 HOH A 96 1396 1307 HOH HOH . G 5 HOH A 97 1397 1390 HOH HOH . G 5 HOH A 98 1398 1379 HOH HOH . G 5 HOH A 99 1399 1340 HOH HOH . G 5 HOH A 100 1400 1352 HOH HOH . G 5 HOH A 101 1401 1393 HOH HOH . G 5 HOH A 102 1402 1415 HOH HOH . G 5 HOH A 103 1403 1357 HOH HOH . G 5 HOH A 104 1404 1378 HOH HOH . G 5 HOH A 105 1405 1392 HOH HOH . G 5 HOH A 106 1406 1360 HOH HOH . G 5 HOH A 107 1407 1370 HOH HOH . G 5 HOH A 108 1408 1368 HOH HOH . G 5 HOH A 109 1409 1326 HOH HOH . G 5 HOH A 110 1410 1372 HOH HOH . G 5 HOH A 111 1411 1351 HOH HOH . G 5 HOH A 112 1412 1305 HOH HOH . G 5 HOH A 113 1413 1346 HOH HOH . G 5 HOH A 114 1414 1380 HOH HOH . G 5 HOH A 115 1415 1347 HOH HOH . G 5 HOH A 116 1416 1388 HOH HOH . G 5 HOH A 117 1417 1309 HOH HOH . G 5 HOH A 118 1418 1431 HOH HOH . G 5 HOH A 119 1419 1404 HOH HOH . G 5 HOH A 120 1420 1334 HOH HOH . G 5 HOH A 121 1421 1441 HOH HOH . G 5 HOH A 122 1422 1327 HOH HOH . G 5 HOH A 123 1423 1443 HOH HOH . G 5 HOH A 124 1424 1434 HOH HOH . G 5 HOH A 125 1425 1341 HOH HOH . G 5 HOH A 126 1426 1432 HOH HOH . G 5 HOH A 127 1427 1416 HOH HOH . G 5 HOH A 128 1428 1444 HOH HOH . G 5 HOH A 129 1429 1433 HOH HOH . G 5 HOH A 130 1430 1436 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 . . . D 4 113.231 134.498 166.359 1 36.71 ? C1 NAG 1202 A 1 HETATM 2 C C2 NAG . . . D 4 112.872 133.649 167.579 1 37.62 ? C2 NAG 1202 A 1 HETATM 3 C C3 NAG . . . D 4 111.363 133.46 167.664 1 37.72 ? C3 NAG 1202 A 1 HETATM 4 C C4 NAG . . . D 4 110.67 134.814 167.684 1 37.71 ? C4 NAG 1202 A 1 HETATM 5 C C5 NAG . . . D 4 111.086 135.63 166.465 1 37.22 ? C5 NAG 1202 A 1 HETATM 6 C C6 NAG . . . D 4 110.525 137.032 166.486 1 42.02 ? C6 NAG 1202 A 1 HETATM 7 C C7 NAG . . . D 4 113.739 131.618 168.64 1 38.64 ? C7 NAG 1202 A 1 HETATM 8 C C8 NAG . . . D 4 114.445 130.315 168.433 1 41.17 ? C8 NAG 1202 A 1 HETATM 9 N N2 NAG . . . D 4 113.546 132.362 167.546 1 36.98 ? N2 NAG 1202 A 1 HETATM 10 O O3 NAG . . . D 4 111.04 132.731 168.842 1 37.04 ? O3 NAG 1202 A 1 HETATM 11 O O4 NAG . . . D 4 109.257 134.642 167.675 1 40.59 ? O4 NAG 1202 A 1 HETATM 12 O O5 NAG . . . D 4 112.517 135.755 166.416 1 33.49 ? O5 NAG 1202 A 1 HETATM 13 O O6 NAG . . . D 4 109.922 137.333 167.737 1 42.5 ? O6 NAG 1202 A 1 HETATM 14 O O7 NAG . . . D 4 113.36 131.983 169.747 1 46.08 ? O7 NAG 1202 A 1 HETATM 15 H H1 NAG . . . D 4 112.972 134.02 165.549 1 37.59 ? H1 NAG 1202 A 1 HETATM 16 H H2 NAG . . . D 4 113.16 134.129 168.379 1 36.71 ? H2 NAG 1202 A 1 HETATM 17 H H3 NAG . . . D 4 111.06 132.958 166.884 1 37.54 ? H3 NAG 1202 A 1 HETATM 18 H H4 NAG . . . D 4 110.93 135.29 168.495 1 37.34 ? H4 NAG 1202 A 1 HETATM 19 H H5 NAG . . . D 4 110.778 135.176 165.658 1 36.8 ? H5 NAG 1202 A 1 HETATM 20 H H61 NAG . . . D 4 109.857 137.121 165.78 1 37.56 ? H61 NAG 1202 A 1 HETATM 21 H H62 NAG . . . D 4 111.248 137.664 166.326 1 36.97 ? H62 NAG 1202 A 1 HETATM 22 H H81 NAG . . . D 4 113.942 129.599 168.867 1 37.57 ? H81 NAG 1202 A 1 HETATM 23 H H82 NAG . . . D 4 115.339 130.365 168.821 1 37.56 ? H82 NAG 1202 A 1 HETATM 24 H H83 NAG . . . D 4 114.513 130.131 167.476 1 37.74 ? H83 NAG 1202 A 1 HETATM 25 H HN2 NAG . . . D 4 113.845 132.045 166.745 1 36.73 ? HN2 NAG 1202 A 1 HETATM 26 H HO3 NAG . . . D 4 110.192 132.47 168.806 1 37.03 ? HO3 NAG 1202 A 1 HETATM 27 H HO4 NAG . . . D 4 108.866 135.406 167.9 1 37.31 ? HO4 NAG 1202 A 1 HETATM 28 H HO6 NAG . . . D 4 110.146 138.156 167.983 1 37.5 ? HO6 NAG 1202 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #