data_1YKB # _model_server_result.job_id 6FuzgXtRWj-Rw11Tx6NR3g _model_server_result.datetime_utc '2025-03-06 07:04:06' _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 1ykb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1531}' # _entry.id 1YKB # _exptl.entry_id 1YKB _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.35 _cell.angle_gamma 90 _cell.entry_id 1YKB _cell.length_a 64.877 _cell.length_b 62.227 _cell.length_c 139.524 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YKB _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,J,K,L,M,N,O,P,Q,R,S,T,U _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 ? 5 M N N ? 5 N N N ? 5 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 1 FUC NAG C1 O1 . O6 HO6 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 6 ? 4 4 3 MAN MAN C1 O1 . O6 HO6 . sing 7 ? 4 5 1 FUC NAG C1 O1 . O6 HO6 . 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 G NAG 1 G 1 NAG G 1111 NAG 2 n G NAG 2 G 2 NAG G 1113 NAG 2 n G FUC 3 G 3 FUC G 1112 FUC 3 n H NAG 1 H 1 NAG H 1331 NAG 3 n H NAG 2 H 2 NAG H 1332 NAG 4 n I NAG 1 I 1 NAG I 1411 NAG 4 n I NAG 2 I 2 NAG I 1412 NAG 4 n I MAN 3 I 3 MAN I 1413 MAN 4 n I MAN 4 I 4 MAN I 1414 MAN 4 n I FUC 5 I 5 FUC I 1415 FUC 3 n J NAG 1 J 1 NAG J 1431 NAG 3 n J NAG 2 J 2 NAG J 1432 NAG 3 n K NAG 1 K 1 NAG K 1611 NAG 3 n K NAG 2 K 2 NAG K 1612 NAG 3 n L NAG 1 L 1 NAG L 1631 NAG 3 n L NAG 2 L 2 NAG L 1632 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 3 A CYS 40 1_555 A SG CYS 95 A CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 A SG CYS 52 A CYS 89 1_555 A SG CYS 141 A CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 B SG CYS 3 B CYS 40 1_555 B SG CYS 95 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 B SG CYS 52 B CYS 89 1_555 B SG CYS 141 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf5 C SG CYS 3 C CYS 40 1_555 C SG CYS 95 C CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 C SG CYS 52 C CYS 89 1_555 C SG CYS 141 C CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 D SG CYS 3 D CYS 40 1_555 D SG CYS 95 D CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf8 D SG CYS 52 D CYS 89 1_555 D SG CYS 141 D CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf9 E SG CYS 3 E CYS 40 1_555 E SG CYS 95 E CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 E SG CYS 52 E CYS 89 1_555 E SG CYS 141 E CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf11 F SG CYS 3 F CYS 40 1_555 F SG CYS 95 F CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf12 F SG CYS 52 F CYS 89 1_555 F SG CYS 141 F CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 17 A ASN 54 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 60 A ASN 97 1_555 M C1 NAG . A NAG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 B ND2 ASN 60 B ASN 97 1_555 N C1 NAG . B NAG 1231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale4 C ND2 ASN 60 C ASN 97 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 D ND2 ASN 17 D ASN 54 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 D ND2 ASN 60 D ASN 97 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale7 E ND2 ASN 60 E ASN 97 1_555 O C1 NAG . E NAG 1531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 F ND2 ASN 17 F ASN 54 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 F ND2 ASN 60 F ASN 97 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale11 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale13 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale14 I O6 NAG . I NAG 1 1_555 I C1 FUC . I FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale15 I O4 NAG . I NAG 2 1_555 I C1 MAN . I MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale16 I O6 MAN . I MAN 3 1_555 I C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale17 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale18 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale19 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? # _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 284 n n C1 O1 NAG sing 285 n n C1 O5 NAG sing 286 n n C1 H1 NAG sing 287 n n C2 C3 NAG sing 288 n n C2 N2 NAG sing 289 n n C2 H2 NAG sing 290 n n C3 C4 NAG sing 291 n n C3 O3 NAG sing 292 n n C3 H3 NAG sing 293 n n C4 C5 NAG sing 294 n n C4 O4 NAG sing 295 n n C4 H4 NAG sing 296 n n C5 C6 NAG sing 297 n n C5 O5 NAG sing 298 n n C5 H5 NAG sing 299 n n C6 O6 NAG sing 300 n n C6 H61 NAG sing 301 n n C6 H62 NAG sing 302 n n C7 C8 NAG sing 303 n n C7 N2 NAG sing 304 n n C7 O7 NAG doub 305 n n C8 H81 NAG sing 306 n n C8 H82 NAG sing 307 n n C8 H83 NAG sing 308 n n N2 HN2 NAG sing 309 n n O1 HO1 NAG sing 310 n n O3 HO3 NAG sing 311 n n O4 HO4 NAG sing 312 n n O6 HO6 NAG sing 313 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 1YKB _atom_sites.fract_transf_matrix[1][1] 0.015414 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000363 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01607 _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] 0.007169 _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 M 5 NAG A 1 1131 1131 NAG NAG . N 5 NAG B 1 1231 1231 NAG NAG . O 5 NAG E 1 1531 1531 NAG NAG . P 6 HOH A 1 4 4 HOH HOH . P 6 HOH A 2 245 245 HOH HOH . P 6 HOH A 3 323 323 HOH HOH . P 6 HOH A 4 325 325 HOH HOH . P 6 HOH A 5 347 347 HOH HOH . P 6 HOH A 6 349 349 HOH HOH . P 6 HOH A 7 394 394 HOH HOH . P 6 HOH A 8 416 416 HOH HOH . Q 6 HOH B 1 1232 36 HOH HOH . Q 6 HOH B 2 1233 107 HOH HOH . Q 6 HOH B 3 1234 154 HOH HOH . Q 6 HOH B 4 1235 285 HOH HOH . Q 6 HOH B 5 1236 315 HOH HOH . Q 6 HOH B 6 1237 335 HOH HOH . Q 6 HOH B 7 1238 343 HOH HOH . Q 6 HOH B 8 1239 350 HOH HOH . R 6 HOH C 1 206 206 HOH HOH . R 6 HOH C 2 226 226 HOH HOH . R 6 HOH C 3 260 260 HOH HOH . R 6 HOH C 4 263 263 HOH HOH . R 6 HOH C 5 268 268 HOH HOH . R 6 HOH C 6 273 273 HOH HOH . R 6 HOH C 7 287 287 HOH HOH . R 6 HOH C 8 312 312 HOH HOH . R 6 HOH C 9 337 337 HOH HOH . R 6 HOH C 10 402 402 HOH HOH . R 6 HOH C 11 412 412 HOH HOH . S 6 HOH D 1 1433 1 HOH HOH . S 6 HOH D 2 1434 15 HOH HOH . S 6 HOH D 3 1435 48 HOH HOH . S 6 HOH D 4 1436 111 HOH HOH . S 6 HOH D 5 1437 113 HOH HOH . S 6 HOH D 6 1438 134 HOH HOH . S 6 HOH D 7 1439 219 HOH HOH . S 6 HOH D 8 1440 222 HOH HOH . S 6 HOH D 9 1441 317 HOH HOH . S 6 HOH D 10 1442 322 HOH HOH . S 6 HOH D 11 1443 330 HOH HOH . S 6 HOH D 12 1444 334 HOH HOH . S 6 HOH D 13 1445 361 HOH HOH . S 6 HOH D 14 1446 401 HOH HOH . S 6 HOH D 15 1447 405 HOH HOH . T 6 HOH E 1 230 230 HOH HOH . T 6 HOH E 2 231 231 HOH HOH . T 6 HOH E 3 388 388 HOH HOH . T 6 HOH E 4 403 403 HOH HOH . T 6 HOH E 5 410 410 HOH HOH . U 6 HOH F 1 1633 101 HOH HOH . U 6 HOH F 2 1634 227 HOH HOH . U 6 HOH F 3 1635 353 HOH HOH . U 6 HOH F 4 1636 369 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 . . . O 5 63.063 13.348 56.418 1 57.72 ? C1 NAG 1531 E 1 HETATM 2 C C2 NAG . . . O 5 63.377 11.848 56.486 1 59.08 ? C2 NAG 1531 E 1 HETATM 3 C C3 NAG . . . O 5 63.064 11.251 57.885 1 61.58 ? C3 NAG 1531 E 1 HETATM 4 C C4 NAG . . . O 5 63.626 12.141 59.01 1 60.9 ? C4 NAG 1531 E 1 HETATM 5 C C5 NAG . . . O 5 63.124 13.57 58.805 1 60.37 ? C5 NAG 1531 E 1 HETATM 6 C C6 NAG . . . O 5 63.624 14.523 59.87 1 59.02 ? C6 NAG 1531 E 1 HETATM 7 C C7 NAG . . . O 5 63.06 10.766 54.328 1 57.82 ? C7 NAG 1531 E 1 HETATM 8 C C8 NAG . . . O 5 62.043 10.289 53.295 1 55.26 ? C8 NAG 1531 E 1 HETATM 9 N N2 NAG . . . O 5 62.556 11.177 55.491 1 58.62 ? N2 NAG 1531 E 1 HETATM 10 O O3 NAG . . . O 5 63.607 9.932 57.99 1 61.86 ? O3 NAG 1531 E 1 HETATM 11 O O4 NAG . . . O 5 63.204 11.657 60.283 1 63.62 ? O4 NAG 1531 E 1 HETATM 12 O O5 NAG . . . O 5 63.599 14.065 57.538 1 60.09 ? O5 NAG 1531 E 1 HETATM 13 O O6 NAG . . . O 5 65.043 14.548 59.894 1 57.83 ? O6 NAG 1531 E 1 HETATM 14 O O7 NAG . . . O 5 64.272 10.747 54.067 1 57.76 ? O7 NAG 1531 E 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #