data_9KX8 # _model_server_result.job_id uGWqq8eSzKS1Eq_VHFGCgA _model_server_result.datetime_utc '2025-06-25 02:49:11' _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 9kx8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":304}' # _entry.id 9KX8 # _exptl.entry_id 9KX8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _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 120 _cell.entry_id 9KX8 _cell.length_a 107.859 _cell.length_b 107.859 _cell.length_c 311.386 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9KX8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 ? 6 I N N ? 6 R N N ? 6 S N 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 ? 4 2 1 GAL ZCD 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 C NAG 1 C 1 NAG C 1 NAG 3 n C NAG 2 C 2 NAG C 2 NAG 3 n D NAG 1 D 1 NAG D 1 NAG 3 n D NAG 2 D 2 NAG D 2 NAG 4 n E ZCD 1 E 1 ZCD E 1 ZCD 4 n E GAL 2 E 2 GAL E 2 GAL # 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 247 A CYS 247 1_555 B SG CYS 5 B CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 64 B CYS 64 1_555 B SG CYS 81 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf3 B SG CYS 152 B CYS 152 1_555 B SG CYS 165 B CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf4 B SG CYS 191 B CYS 191 1_555 B SG CYS 208 B CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 112 A ASN 112 1_555 I C1 NAG . A NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale2 B ND2 ASN 61 B ASN 61 1_555 R C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale3 B ND2 ASN 96 B ASN 96 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale4 B ND2 ASN 136 B ASN 136 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 E O4 ZCD . E ZCD 1 1_555 E C1 GAL . E GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? # _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 274 n n C1 O1 NAG sing 275 n n C1 O5 NAG sing 276 n n C1 H1 NAG sing 277 n n C2 C3 NAG sing 278 n n C2 N2 NAG sing 279 n n C2 H2 NAG sing 280 n n C3 C4 NAG sing 281 n n C3 O3 NAG sing 282 n n C3 H3 NAG sing 283 n n C4 C5 NAG sing 284 n n C4 O4 NAG sing 285 n n C4 H4 NAG sing 286 n n C5 C6 NAG sing 287 n n C5 O5 NAG sing 288 n n C5 H5 NAG sing 289 n n C6 O6 NAG sing 290 n n C6 H61 NAG sing 291 n n C6 H62 NAG sing 292 n n C7 C8 NAG sing 293 n n C7 N2 NAG sing 294 n n C7 O7 NAG doub 295 n n C8 H81 NAG sing 296 n n C8 H82 NAG sing 297 n n C8 H83 NAG sing 298 n n N2 HN2 NAG sing 299 n n O1 HO1 NAG sing 300 n n O3 HO3 NAG sing 301 n n O4 HO4 NAG sing 302 n n O6 HO6 NAG sing 303 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 9KX8 _atom_sites.fract_transf_matrix[1][1] 0.009271 _atom_sites.fract_transf_matrix[1][2] 0.005353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010706 _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] 0.003211 _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 5 GOL A 1 301 301 GOL GOL . G 5 GOL A 1 302 302 GOL GOL . H 5 GOL A 1 303 303 GOL GOL . I 6 NAG A 1 304 304 NAG NAG . J 7 SO4 A 1 305 305 SO4 SO4 . K 8 GLY A 1 306 306 GLY GLY . L 9 CL A 1 307 2 CL CL . M 9 CL A 1 308 1 CL CL . N 7 SO4 A 1 309 1 SO4 SO4 . O 10 NA A 1 310 1 NA NA . P 5 GOL B 1 301 301 GOL GOL . Q 5 GOL B 1 302 302 GOL GOL . R 6 NAG B 1 303 303 NAG NAG . S 6 NAG B 1 304 3 NAG NAG . T 7 SO4 B 1 305 4 SO4 SO4 . U 11 HOH A 1 401 401 HOH HOH . U 11 HOH A 2 402 448 HOH HOH . U 11 HOH A 3 403 404 HOH HOH . U 11 HOH A 4 404 403 HOH HOH . U 11 HOH A 5 405 405 HOH HOH . U 11 HOH A 6 406 402 HOH HOH . U 11 HOH A 7 407 406 HOH HOH . V 11 HOH B 1 401 503 HOH HOH . V 11 HOH B 2 402 403 HOH HOH . V 11 HOH B 3 403 436 HOH HOH . V 11 HOH B 4 404 447 HOH HOH . V 11 HOH B 5 405 413 HOH HOH . V 11 HOH B 6 406 407 HOH HOH . V 11 HOH B 7 407 406 HOH HOH . V 11 HOH B 8 408 410 HOH HOH . V 11 HOH B 9 409 404 HOH HOH . V 11 HOH B 10 410 405 HOH HOH . V 11 HOH B 11 411 822 HOH HOH . V 11 HOH B 12 412 432 HOH HOH . V 11 HOH B 13 413 759 HOH HOH . V 11 HOH B 14 414 407 HOH HOH . V 11 HOH B 15 415 408 HOH HOH . V 11 HOH B 16 416 438 HOH HOH . V 11 HOH B 17 417 409 HOH HOH . V 11 HOH B 18 418 435 HOH HOH . V 11 HOH B 19 419 440 HOH HOH . V 11 HOH B 20 420 840 HOH HOH . V 11 HOH B 21 421 683 HOH HOH . V 11 HOH B 22 422 433 HOH HOH . V 11 HOH B 23 423 726 HOH HOH . V 11 HOH B 24 424 898 HOH HOH . V 11 HOH B 25 425 412 HOH HOH . V 11 HOH B 26 426 417 HOH HOH . V 11 HOH B 27 427 415 HOH HOH . V 11 HOH B 28 428 647 HOH HOH . V 11 HOH B 29 429 936 HOH HOH . V 11 HOH B 30 430 739 HOH HOH . V 11 HOH B 31 431 798 HOH HOH . V 11 HOH B 32 432 821 HOH HOH . V 11 HOH B 33 433 509 HOH HOH . V 11 HOH B 34 434 703 HOH HOH . V 11 HOH B 35 435 490 HOH HOH . V 11 HOH B 36 436 804 HOH HOH . V 11 HOH B 37 437 1083 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 . . . S 6 3.326 -71.723 3.775 1 127 ? C1 NAG 304 B 1 HETATM 2 C C2 NAG . . . S 6 2.279 -71.029 4.665 1 127.95 ? C2 NAG 304 B 1 HETATM 3 C C3 NAG . . . S 6 0.921 -70.79 3.984 1 129.11 ? C3 NAG 304 B 1 HETATM 4 C C4 NAG . . . S 6 0.562 -71.723 2.82 1 128.14 ? C4 NAG 304 B 1 HETATM 5 C C5 NAG . . . S 6 1.761 -72.474 2.225 1 129.2 ? C5 NAG 304 B 1 HETATM 6 C C6 NAG . . . S 6 1.585 -72.685 0.744 1 123.8 ? C6 NAG 304 B 1 HETATM 7 C C7 NAG . . . S 6 1.975 -71.446 7.123 1 126.29 ? C7 NAG 304 B 1 HETATM 8 C C8 NAG . . . S 6 2.356 -70.013 7.404 1 121.7 ? C8 NAG 304 B 1 HETATM 9 N N2 NAG . . . S 6 1.983 -71.822 5.831 1 127.12 ? N2 NAG 304 B 1 HETATM 10 O O1 NAG . . . S 6 4.532 -71.06 3.887 1 123.8 ? O1 NAG 304 B 1 HETATM 11 O O3 NAG . . . S 6 0.842 -69.431 3.616 1 127.85 ? O3 NAG 304 B 1 HETATM 12 O O4 NAG . . . S 6 -0.428 -72.605 3.311 1 125 ? O4 NAG 304 B 1 HETATM 13 O O5 NAG . . . S 6 2.936 -71.719 2.426 1 127.94 ? O5 NAG 304 B 1 HETATM 14 O O6 NAG . . . S 6 1.046 -71.495 0.219 1 123.17 ? O6 NAG 304 B 1 HETATM 15 O O7 NAG . . . S 6 1.681 -72.219 8.024 1 122.95 ? O7 NAG 304 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #