data_9KUD # _model_server_result.job_id 7hzFFSpn-wxdHp2maaZe6Q _model_server_result.datetime_utc '2025-08-13 22:25:08' _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 9kud # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":602}' # _entry.id 9KUD # _exptl.entry_id 9KUD _exptl.method 'X-RAY DIFFRACTION' # _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 6 _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 9KUD _cell.length_a 128.674 _cell.length_b 129.157 _cell.length_c 138.062 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9KUD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F,G,H,I,K,L 1 1 B,D,E,J,M 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N ? 4 H N N ? 4 K N N ? 4 L N N ? 4 M N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 4 3 MAN BMA 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 3 n E NAG 1 C 1 NAG C 1 NAG 3 n E NAG 2 C 2 NAG C 2 NAG 3 n E BMA 3 C 3 BMA C 3 BMA 3 n E MAN 4 C 4 MAN C 4 MAN # 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 115 A CYS 133 1_555 A SG CYS 123 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf3 A SG CYS 512 A CYS 533 1_555 A SG CYS 524 A CYS 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 115 B CYS 133 1_555 B SG CYS 123 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 B SG CYS 326 B CYS 344 1_555 B SG CYS 343 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 B SG CYS 512 B CYS 533 1_555 B SG CYS 524 B CYS 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf7 C SG CYS 5 E CYS 336 1_555 C SG CYS 30 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 C SG CYS 48 E CYS 379 1_555 C SG CYS 101 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf9 C SG CYS 60 E CYS 391 1_555 C SG CYS 193 E CYS 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf10 C SG CYS 149 E CYS 480 1_555 C SG CYS 156 E CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf11 D SG CYS 5 F CYS 336 1_555 D SG CYS 30 F CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 D SG CYS 48 F CYS 379 1_555 D SG CYS 101 F CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf13 D SG CYS 60 F CYS 391 1_555 D SG CYS 193 F CYS 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf14 D SG CYS 149 F CYS 480 1_555 D SG CYS 156 F CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A ND2 ASN 35 A ASN 53 1_555 F C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 72 A ASN 90 1_555 G C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 528 A ASN 549 1_555 H C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 35 B ASN 53 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale5 C ND2 ASN 12 E ASN 343 1_555 L C1 NAG . E NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale6 C ND2 ASN 23 E ASN 354 1_555 K C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 D ND2 ASN 23 F ASN 354 1_555 M C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale8 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 E O6 BMA . C BMA 3 1_555 E C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? metalc ? metalc1 A NE2 HIS 356 A HIS 374 1_555 I ZN ZN . A ZN 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc2 A NE2 HIS 360 A HIS 378 1_555 I ZN ZN . A ZN 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc3 A OE1 GLU 384 A GLU 402 1_555 I ZN ZN . A ZN 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc4 B NE2 HIS 356 B HIS 374 1_555 J ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc5 B NE2 HIS 360 B HIS 378 1_555 J ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc6 B OE1 GLU 384 B GLU 402 1_555 J ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 9KUD _atom_sites.fract_transf_matrix[1][1] 0.007772 _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] 0.007743 _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] 0.007243 _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 F 4 NAG A 1 701 618 NAG NAG . G 4 NAG A 1 702 619 NAG NAG . H 4 NAG A 1 703 620 NAG NAG . I 5 ZN A 1 704 1 ZN ZN . J 5 ZN B 1 701 2 ZN ZN . K 4 NAG E 1 601 529 NAG NAG . L 4 NAG E 1 602 530 NAG NAG . M 4 NAG F 1 601 526 NAG NAG . # 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 . . . L 4 -28.902 -26.612 21.306 1 71.57 ? C1 NAG 602 E 1 HETATM 2 C C2 NAG . . . L 4 -28.852 -27.881 20.437 1 76.18 ? C2 NAG 602 E 1 HETATM 3 C C3 NAG . . . L 4 -30.14 -28.687 20.625 1 79.57 ? C3 NAG 602 E 1 HETATM 4 C C4 NAG . . . L 4 -30.312 -29.048 22.096 1 82.59 ? C4 NAG 602 E 1 HETATM 5 C C5 NAG . . . L 4 -30.284 -27.794 22.979 1 72.9 ? C5 NAG 602 E 1 HETATM 6 C C6 NAG . . . L 4 -30.284 -28.129 24.454 1 71.77 ? C6 NAG 602 E 1 HETATM 7 C C7 NAG . . . L 4 -28.04 -28.437 18.196 1 76.39 ? C7 NAG 602 E 1 HETATM 8 C C8 NAG . . . L 4 -27.885 -27.977 16.774 1 60.86 ? C8 NAG 602 E 1 HETATM 9 N N2 NAG . . . L 4 -28.633 -27.578 19.032 1 78.65 ? N2 NAG 602 E 1 HETATM 10 O O3 NAG . . . L 4 -30.136 -29.87 19.828 1 66.97 ? O3 NAG 602 E 1 HETATM 11 O O4 NAG . . . L 4 -31.538 -29.75 22.284 1 82.68 ? O4 NAG 602 E 1 HETATM 12 O O5 NAG . . . L 4 -29.107 -26.996 22.73 1 69.45 ? O5 NAG 602 E 1 HETATM 13 O O6 NAG . . . L 4 -31.353 -29.005 24.793 1 60.69 ? O6 NAG 602 E 1 HETATM 14 O O7 NAG . . . L 4 -27.651 -29.541 18.572 1 77.22 ? O7 NAG 602 E 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #