data_9DIQ # _model_server_result.job_id XR5Sd_idz9b3dz0KOCx3pw _model_server_result.datetime_utc '2025-07-14 01:44:24' _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 9diq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 9DIQ # _exptl.entry_id 9DIQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _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 91.66 _cell.angle_gamma 90 _cell.entry_id 9DIQ _cell.length_a 130.367 _cell.length_b 72.061 _cell.length_c 206.859 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DIQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,M,N,O,S,T,U,V,W 1 1 G,H,I,J,K,L,P,Q,R,X,Y,Z,AA,BA,CA 2 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 R _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . 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 3 n M NAG 1 M 1 NAG M 1 NAG 3 n M NAG 2 M 2 NAG M 2 NAG 3 n M BMA 3 M 3 BMA M 3 BMA 4 n N NAG 1 N 1 NAG N 1 NAG 4 n N NAG 2 N 2 NAG N 2 NAG 3 n O NAG 1 O 1 NAG O 1 NAG 3 n O NAG 2 O 2 NAG O 2 NAG 3 n O BMA 3 O 3 BMA O 3 BMA 4 n P NAG 1 P 1 NAG P 1 NAG 4 n P NAG 2 P 2 NAG P 2 NAG 3 n Q NAG 1 Q 1 NAG Q 1 NAG 3 n Q NAG 2 Q 2 NAG Q 2 NAG 3 n Q BMA 3 Q 3 BMA Q 3 BMA # 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 46 I CYS 52 1_555 A SG CYS 278 I CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 59 I CYS 64 1_555 A SG CYS 71 I CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 94 I CYS 97 1_555 A SG CYS 139 I CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 282 I CYS 281 1_555 A SG CYS 306 I CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 C SG CYS 8 A CYS 14 1_555 D SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 46 A CYS 52 1_555 C SG CYS 278 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 C SG CYS 59 A CYS 64 1_555 C SG CYS 71 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 94 A CYS 97 1_555 C SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf9 C SG CYS 282 A CYS 281 1_555 C SG CYS 306 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 D SG CYS 144 B CYS 144 1_555 D SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 E SG CYS 8 C CYS 14 1_555 F SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 E SG CYS 59 C CYS 64 1_555 E SG CYS 71 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 E SG CYS 94 C CYS 97 1_555 E SG CYS 139 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf14 E SG CYS 282 C CYS 281 1_555 E SG CYS 306 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 G SG CYS 8 E CYS 14 1_555 H SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 G SG CYS 46 E CYS 52 1_555 G SG CYS 278 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 G SG CYS 59 E CYS 64 1_555 G SG CYS 71 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 G SG CYS 94 E CYS 97 1_555 G SG CYS 139 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf19 G SG CYS 282 E CYS 281 1_555 G SG CYS 306 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf20 H SG CYS 144 F CYS 144 1_555 H SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf21 I SG CYS 46 G CYS 52 1_555 I SG CYS 278 G CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf22 I SG CYS 59 G CYS 64 1_555 I SG CYS 71 G CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf23 I SG CYS 94 G CYS 97 1_555 I SG CYS 139 G CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf24 I SG CYS 282 G CYS 281 1_555 I SG CYS 306 G CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf25 K SG CYS 59 K CYS 64 1_555 K SG CYS 71 K CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf26 K SG CYS 94 K CYS 97 1_555 K SG CYS 139 K CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf27 K SG CYS 282 K CYS 281 1_555 K SG CYS 306 K CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 169 I ASN 169 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 C ND2 ASN 169 A ASN 169 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 E ND2 ASN 169 C ASN 169 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 G ND2 ASN 169 E ASN 169 1_555 R C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 I ND2 ASN 169 G ASN 169 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 K ND2 ASN 169 K ASN 169 1_555 Q C1 NAG . Q NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 M O4 NAG . M NAG 2 1_555 M C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 O O4 NAG . O NAG 2 1_555 O C1 BMA . O BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale13 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale14 Q O4 NAG . Q NAG 2 1_555 Q C1 BMA . Q BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 9DIQ _atom_sites.fract_transf_matrix[1][1] 0.007671 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000222 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013877 _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] 0.004836 _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 R 5 NAG E 1 401 325 NAG NAG . S 6 HOH I 1 401 7 HOH HOH . S 6 HOH I 2 402 80 HOH HOH . S 6 HOH I 3 403 28 HOH HOH . S 6 HOH I 4 404 12 HOH HOH . S 6 HOH I 5 405 23 HOH HOH . T 6 HOH A 1 401 64 HOH HOH . T 6 HOH A 2 402 41 HOH HOH . T 6 HOH A 3 403 35 HOH HOH . T 6 HOH A 4 404 47 HOH HOH . T 6 HOH A 5 405 82 HOH HOH . T 6 HOH A 6 406 72 HOH HOH . U 6 HOH B 1 201 69 HOH HOH . V 6 HOH C 1 401 3 HOH HOH . V 6 HOH C 2 402 96 HOH HOH . V 6 HOH C 3 403 84 HOH HOH . V 6 HOH C 4 404 46 HOH HOH . V 6 HOH C 5 405 39 HOH HOH . V 6 HOH C 6 406 71 HOH HOH . V 6 HOH C 7 407 50 HOH HOH . W 6 HOH D 1 201 59 HOH HOH . X 6 HOH E 1 501 58 HOH HOH . X 6 HOH E 2 502 86 HOH HOH . X 6 HOH E 3 503 99 HOH HOH . X 6 HOH E 4 504 65 HOH HOH . X 6 HOH E 5 505 93 HOH HOH . X 6 HOH E 6 506 14 HOH HOH . X 6 HOH E 7 507 66 HOH HOH . Y 6 HOH F 1 201 98 HOH HOH . Y 6 HOH F 2 202 76 HOH HOH . Z 6 HOH G 1 401 38 HOH HOH . Z 6 HOH G 2 402 37 HOH HOH . Z 6 HOH G 3 403 57 HOH HOH . Z 6 HOH G 4 404 94 HOH HOH . AA 6 HOH H 1 201 91 HOH HOH . BA 6 HOH K 1 401 100 HOH HOH . BA 6 HOH K 2 402 56 HOH HOH . BA 6 HOH K 3 403 6 HOH HOH . BA 6 HOH K 4 404 27 HOH HOH . BA 6 HOH K 5 405 87 HOH HOH . CA 6 HOH L 1 201 44 HOH HOH . CA 6 HOH L 2 202 85 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 . . . R 5 70.415 5.485 -31.169 1 75.73 ? C1 NAG 401 E 1 HETATM 2 C C2 NAG . . . R 5 70.837 5.051 -29.767 1 69.64 ? C2 NAG 401 E 1 HETATM 3 C C3 NAG . . . R 5 70.551 6.163 -28.76 1 82.6 ? C3 NAG 401 E 1 HETATM 4 C C4 NAG . . . R 5 71.217 7.46 -29.201 1 95.46 ? C4 NAG 401 E 1 HETATM 5 C C5 NAG . . . R 5 70.779 7.81 -30.62 1 92.38 ? C5 NAG 401 E 1 HETATM 6 C C6 NAG . . . R 5 71.491 9.022 -31.173 1 103.27 ? C6 NAG 401 E 1 HETATM 7 C C7 NAG . . . R 5 70.812 2.673 -29.164 1 74.74 ? C7 NAG 401 E 1 HETATM 8 C C8 NAG . . . R 5 72.296 2.701 -29.383 1 80.89 ? C8 NAG 401 E 1 HETATM 9 N N2 NAG . . . R 5 70.166 3.824 -29.372 1 70.58 ? N2 NAG 401 E 1 HETATM 10 O O3 NAG . . . R 5 71.017 5.777 -27.472 1 70.73 ? O3 NAG 401 E 1 HETATM 11 O O4 NAG . . . R 5 70.86 8.523 -28.323 1 106.69 ? O4 NAG 401 E 1 HETATM 12 O O5 NAG . . . R 5 71.07 6.72 -31.509 1 92 ? O5 NAG 401 E 1 HETATM 13 O O6 NAG . . . R 5 71.521 8.995 -32.594 1 111.77 ? O6 NAG 401 E 1 HETATM 14 O O7 NAG . . . R 5 70.225 1.653 -28.818 1 76.57 ? O7 NAG 401 E 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #