data_8GK6 # _model_server_result.job_id MSBbuwAL0s2Mn6-SWD0l6w _model_server_result.datetime_utc '2024-10-19 16:26:40' _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 8gk6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":201}' # _entry.id 8GK6 # _exptl.entry_id 8GK6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.09 _cell.angle_gamma 90 _cell.entry_id 8GK6 _cell.length_a 55.338 _cell.length_b 120.764 _cell.length_c 95.254 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GK6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _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 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J,P,Q,T,X 1 1 B,H,N,U,AA 2 1 C,G,K,M,S,V,Z 3 1 D,F,L,O,R,W,Y 4 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 O N N ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 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 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 8 ? 5 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 I NAG 1 I 1 NAG A 153 NAG 2 n I FUC 2 I 2 FUC A 154 FUC 3 n J NAG 1 J 1 NAG A 155 NAG 3 n J NAG 2 J 2 NAG A 156 NAG 4 n K NAG 1 K 1 NAG C 154 NAG 4 n K NAG 2 K 2 NAG C 155 NAG 4 n K BMA 3 K 3 BMA C 156 BMA 3 n L NAG 1 L 1 NAG D 154 NAG 3 n L NAG 2 L 2 NAG D 155 NAG 3 n M NAG 1 M 1 NAG H 154 NAG 3 n M NAG 2 M 2 NAG H 155 NAG 5 n N NAG 1 N 1 NAG G 153 NAG 5 n N NAG 2 N 2 NAG G 155 NAG 5 n N BMA 3 N 3 BMA G 156 BMA 5 n N MAN 4 N 4 MAN G 157 MAN 5 n N FUC 5 N 5 FUC G 154 FUC # 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 66 A CYS 80 1_555 A SG CYS 104 A CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 66 B CYS 80 1_555 B SG CYS 104 B CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 C SG CYS 66 C CYS 80 1_555 C SG CYS 104 C CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 D SG CYS 66 D CYS 80 1_555 D SG CYS 104 D CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 E SG CYS 66 E CYS 80 1_555 E SG CYS 104 E CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 F SG CYS 66 F CYS 80 1_555 F SG CYS 104 F CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 G SG CYS 66 H CYS 80 1_555 G SG CYS 104 H CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 H SG CYS 66 G CYS 80 1_555 H SG CYS 104 G CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 49 A ASN 63 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? covale ? covale2 C ND2 ASN 49 C ASN 63 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale3 D ND2 ASN 49 D ASN 63 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale4 E ND2 ASN 37 E ASN 51 1_555 P C1 NAG . E NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale5 E ND2 ASN 49 E ASN 63 1_555 Q C1 NAG . E NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale6 F ND2 ASN 37 F ASN 51 1_555 R C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale7 G ND2 ASN 37 H ASN 51 1_555 S C1 NAG . H NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale8 G ND2 ASN 115 H ASN 129 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale9 I O6 NAG . I NAG 1 1_555 I C1 FUC . I FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale11 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale12 K O4 NAG . K NAG 2 1_555 K C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale13 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale14 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale15 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale16 N O6 NAG . N NAG 1 1_555 N C1 FUC . N FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale17 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale18 N O3 BMA . N BMA 3 1_555 N C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _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 289 n n C1 O1 NAG sing 290 n n C1 O5 NAG sing 291 n n C1 H1 NAG sing 292 n n C2 C3 NAG sing 293 n n C2 N2 NAG sing 294 n n C2 H2 NAG sing 295 n n C3 C4 NAG sing 296 n n C3 O3 NAG sing 297 n n C3 H3 NAG sing 298 n n C4 C5 NAG sing 299 n n C4 O4 NAG sing 300 n n C4 H4 NAG sing 301 n n C5 C6 NAG sing 302 n n C5 O5 NAG sing 303 n n C5 H5 NAG sing 304 n n C6 O6 NAG sing 305 n n C6 H61 NAG sing 306 n n C6 H62 NAG sing 307 n n C7 C8 NAG sing 308 n n C7 N2 NAG sing 309 n n C7 O7 NAG doub 310 n n C8 H81 NAG sing 311 n n C8 H82 NAG sing 312 n n C8 H83 NAG sing 313 n n N2 HN2 NAG sing 314 n n O1 HO1 NAG sing 315 n n O3 HO3 NAG sing 316 n n O4 HO4 NAG sing 317 n n O6 HO6 NAG sing 318 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 8GK6 _atom_sites.fract_transf_matrix[1][1] 0.018071 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002569 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008281 _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] 0.010604 _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 O 6 NAG D 1 201 153 NAG NAG . P 6 NAG E 1 201 153 NAG NAG . Q 6 NAG E 1 202 154 NAG NAG . R 6 NAG F 1 201 153 NAG NAG . S 6 NAG H 1 201 153 NAG NAG . T 7 HOH A 1 201 29 HOH HOH . T 7 HOH A 2 202 34 HOH HOH . T 7 HOH A 3 203 35 HOH HOH . T 7 HOH A 4 204 21 HOH HOH . T 7 HOH A 5 205 25 HOH HOH . T 7 HOH A 6 206 59 HOH HOH . T 7 HOH A 7 207 44 HOH HOH . U 7 HOH B 1 201 1 HOH HOH . U 7 HOH B 2 202 56 HOH HOH . U 7 HOH B 3 203 38 HOH HOH . U 7 HOH B 4 204 28 HOH HOH . U 7 HOH B 5 205 48 HOH HOH . U 7 HOH B 6 206 47 HOH HOH . U 7 HOH B 7 207 20 HOH HOH . U 7 HOH B 8 208 22 HOH HOH . V 7 HOH C 1 201 18 HOH HOH . V 7 HOH C 2 202 14 HOH HOH . V 7 HOH C 3 203 10 HOH HOH . V 7 HOH C 4 204 27 HOH HOH . V 7 HOH C 5 205 19 HOH HOH . V 7 HOH C 6 206 17 HOH HOH . V 7 HOH C 7 207 33 HOH HOH . W 7 HOH D 1 301 52 HOH HOH . W 7 HOH D 2 302 31 HOH HOH . W 7 HOH D 3 303 3 HOH HOH . W 7 HOH D 4 304 2 HOH HOH . W 7 HOH D 5 305 9 HOH HOH . W 7 HOH D 6 306 36 HOH HOH . X 7 HOH E 1 301 5 HOH HOH . X 7 HOH E 2 302 24 HOH HOH . X 7 HOH E 3 303 54 HOH HOH . X 7 HOH E 4 304 6 HOH HOH . X 7 HOH E 5 305 23 HOH HOH . Y 7 HOH F 1 301 12 HOH HOH . Y 7 HOH F 2 302 53 HOH HOH . Y 7 HOH F 3 303 8 HOH HOH . Z 7 HOH H 1 301 45 HOH HOH . Z 7 HOH H 2 302 50 HOH HOH . Z 7 HOH H 3 303 58 HOH HOH . AA 7 HOH G 1 201 15 HOH HOH . AA 7 HOH G 2 202 39 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 6 -9.417 2.23 61.093 1 83.64 ? C1 NAG 201 F 1 HETATM 2 C C2 NAG . . . R 6 -10.464 1.182 61.43 1 85.95 ? C2 NAG 201 F 1 HETATM 3 C C3 NAG . . . R 6 -9.922 0.24 62.485 1 78.07 ? C3 NAG 201 F 1 HETATM 4 C C4 NAG . . . R 6 -8.626 -0.384 61.981 1 81.85 ? C4 NAG 201 F 1 HETATM 5 C C5 NAG . . . R 6 -7.636 0.682 61.495 1 81.12 ? C5 NAG 201 F 1 HETATM 6 C C6 NAG . . . R 6 -6.441 0.083 60.783 1 78.77 ? C6 NAG 201 F 1 HETATM 7 C C7 NAG . . . R 6 -12.733 2.015 61.003 1 95.18 ? C7 NAG 201 F 1 HETATM 8 C C8 NAG . . . R 6 -13.944 2.687 61.578 1 69.33 ? C8 NAG 201 F 1 HETATM 9 N N2 NAG . . . R 6 -11.718 1.791 61.854 1 97.93 ? N2 NAG 201 F 1 HETATM 10 O O3 NAG . . . R 6 -10.887 -0.77 62.752 1 70.07 ? O3 NAG 201 F 1 HETATM 11 O O4 NAG . . . R 6 -8.022 -1.139 63.028 1 85.42 ? O4 NAG 201 F 1 HETATM 12 O O5 NAG . . . R 6 -8.254 1.589 60.564 1 71.65 ? O5 NAG 201 F 1 HETATM 13 O O6 NAG . . . R 6 -5.879 0.987 59.84 1 72.04 ? O6 NAG 201 F 1 HETATM 14 O O7 NAG . . . R 6 -12.656 1.719 59.811 1 90.19 ? O7 NAG 201 F 1 HETATM 15 H H3 NAG . . . R 6 -9.747 0.728 63.312 1 94.23 ? H3 NAG 201 F 1 HETATM 16 H H4 NAG . . . R 6 -8.836 -0.967 61.227 1 98.77 ? H4 NAG 201 F 1 HETATM 17 H H5 NAG . . . R 6 -7.343 1.201 62.268 1 97.9 ? H5 NAG 201 F 1 HETATM 18 H H61 NAG . . . R 6 -6.723 -0.727 60.317 1 95.08 ? H61 NAG 201 F 1 HETATM 19 H H62 NAG . . . R 6 -5.762 -0.149 61.444 1 95.08 ? H62 NAG 201 F 1 HETATM 20 H H81 NAG . . . R 6 -14.579 2.88 60.862 1 83.75 ? H81 NAG 201 F 1 HETATM 21 H H82 NAG . . . R 6 -13.679 3.52 62.012 1 83.75 ? H82 NAG 201 F 1 HETATM 22 H H83 NAG . . . R 6 -14.363 2.097 62.233 1 83.75 ? H83 NAG 201 F 1 HETATM 23 H HN2 NAG . . . R 6 -11.818 2.028 62.729 1 118.07 ? HN2 NAG 201 F 1 HETATM 24 H HO3 NAG . . . R 6 -10.594 -1.288 63.411 1 84.64 ? HO3 NAG 201 F 1 HETATM 25 H HO4 NAG . . . R 6 -7.404 -1.676 62.686 1 103.05 ? HO4 NAG 201 F 1 HETATM 26 H HO6 NAG . . . R 6 -6.483 1.598 59.622 1 87 ? HO6 NAG 201 F 1 # _model_server_stats.io_time_ms 180 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #