data_8XY9 # _model_server_result.job_id QGY30JWVp8_bJlkDguryMw _model_server_result.datetime_utc '2025-01-22 09:55:59' _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 8xy9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":708}' # _entry.id 8XY9 # _exptl.entry_id 8XY9 _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 11 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.06 _cell.angle_gamma 90 _cell.entry_id 8XY9 _cell.length_a 73.467 _cell.length_b 152.681 _cell.length_c 116.695 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XY9 _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 ? 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,B,I,J,K,L,M,N,O,P,Q,R,S,T 1 1 C,D,E,F,G,H,U 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 ? 5 I N N ? 5 J N N ? 5 L N N ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 U 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 ? 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 E NAG 1 E 1 NAG E 1 NAG 3 n E NAG 2 E 2 NAG E 2 NAG 3 n E BMA 3 E 3 BMA E 3 BMA 4 n F NAG 1 F 1 NAG F 1 NAG 4 n F NAG 2 F 2 NAG F 2 NAG 4 n G NAG 1 G 1 NAG G 1 NAG 4 n G NAG 2 G 2 NAG G 2 NAG 3 n H NAG 1 H 1 NAG H 1 NAG 3 n H NAG 2 H 2 NAG H 2 NAG 3 n H BMA 3 H 3 BMA H 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 115 A CYS 133 1_555 A SG CYS 123 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 512 A CYS 530 1_555 A SG CYS 524 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 B SG CYS 4 B CYS 336 1_555 B SG CYS 29 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 47 B CYS 379 1_555 B SG CYS 100 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 59 B CYS 391 1_555 B SG CYS 193 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 148 B CYS 480 1_555 B SG CYS 156 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 C SG CYS 115 C CYS 133 1_555 C SG CYS 123 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 326 C CYS 344 1_555 C SG CYS 343 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 512 C CYS 530 1_555 C SG CYS 524 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 D SG CYS 4 D CYS 336 1_555 D SG CYS 29 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 D SG CYS 47 D CYS 379 1_555 D SG CYS 100 D CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 D SG CYS 59 D CYS 391 1_555 D SG CYS 193 D CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 D SG CYS 148 D CYS 480 1_555 D SG CYS 156 D CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 35 A ASN 53 1_555 I C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 72 A ASN 90 1_555 L C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 304 A ASN 322 1_555 O C1 NAG . A NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 414 A ASN 432 1_555 S C1 NAG . A NAG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 A ND2 ASN 528 A ASN 546 1_555 Q C1 NAG . A NAG 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale6 I O4 NAG . A NAG 701 1_555 J C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale7 J O4 NAG . A NAG 702 1_555 K C1 BMA . A BMA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 L O4 NAG . A NAG 704 1_555 M C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale9 M O4 NAG . A NAG 705 1_555 T C1 BMA . B BMA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale10 O O4 NAG . A NAG 707 1_555 P C1 NAG . A NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale11 Q O4 NAG . A NAG 709 1_555 R C1 NAG . A NAG 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 C ND2 ASN 35 C ASN 53 1_555 U C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale13 C ND2 ASN 72 C ASN 90 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale14 C ND2 ASN 304 C ASN 322 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale15 C ND2 ASN 528 C ASN 546 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale16 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale17 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale18 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale19 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale20 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale21 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 8XY9 _atom_sites.fract_transf_matrix[1][1] 0.013612 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003156 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00655 _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] 0.008797 _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 I 5 NAG A 1 701 906 NAG NAG . J 5 NAG A 1 702 907 NAG NAG . K 6 BMA A 1 703 908 BMA BMA . L 5 NAG A 1 704 909 NAG NAG . M 5 NAG A 1 705 910 NAG NAG . N 5 NAG A 1 706 912 NAG NAG . O 5 NAG A 1 707 913 NAG NAG . P 5 NAG A 1 708 914 NAG NAG . Q 5 NAG A 1 709 915 NAG NAG . R 5 NAG A 1 710 916 NAG NAG . S 5 NAG A 1 711 917 NAG NAG . T 6 BMA B 1 601 911 BMA BMA . U 5 NAG C 1 701 906 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 . . . P 5 50.133 -10.785 -69.365 1 132.12 ? C1 NAG 708 A 1 HETATM 2 C C2 NAG . . . P 5 51.656 -10.59 -69.244 1 132.15 ? C2 NAG 708 A 1 HETATM 3 C C3 NAG . . . P 5 52.225 -10.009 -70.542 1 133.97 ? C3 NAG 708 A 1 HETATM 4 C C4 NAG . . . P 5 51.806 -10.847 -71.75 1 132.26 ? C4 NAG 708 A 1 HETATM 5 C C5 NAG . . . P 5 50.277 -11.009 -71.782 1 134.23 ? C5 NAG 708 A 1 HETATM 6 C C6 NAG . . . P 5 49.779 -11.933 -72.877 1 131.11 ? C6 NAG 708 A 1 HETATM 7 C C7 NAG . . . P 5 52.015 -10.158 -66.842 1 140.17 ? C7 NAG 708 A 1 HETATM 8 C C8 NAG . . . P 5 52.39 -9.131 -65.812 1 141.31 ? C8 NAG 708 A 1 HETATM 9 N N2 NAG . . . P 5 51.995 -9.736 -68.115 1 131.83 ? N2 NAG 708 A 1 HETATM 10 O O3 NAG . . . P 5 53.646 -9.976 -70.44 1 153.22 ? O3 NAG 708 A 1 HETATM 11 O O4 NAG . . . P 5 52.31 -10.267 -72.954 1 130.6 ? O4 NAG 708 A 1 HETATM 12 O O5 NAG . . . P 5 49.836 -11.577 -70.537 1 131.21 ? O5 NAG 708 A 1 HETATM 13 O O6 NAG . . . P 5 49.492 -13.246 -72.409 1 129.2 ? O6 NAG 708 A 1 HETATM 14 O O7 NAG . . . P 5 51.759 -11.319 -66.533 1 141.56 ? O7 NAG 708 A 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 76 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #