data_1DBN # _model_server_result.job_id 3izz7kQH4YwhPhuRyAvY0w _model_server_result.datetime_utc '2024-11-22 06:39:37' _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 1dbn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":921}' # _entry.id 1DBN # _exptl.entry_id 1DBN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 1DBN _cell.length_a 80.742 _cell.length_b 88.45 _cell.length_c 84.496 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DBN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 _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 ? 3 E N N ? 3 F N N ? 3 G N N ? 3 J N N ? 3 K N N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 GAL BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 SIA GAL C2 O2 . O3 HO3 . 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 C BGC 1 C 1 BGC S 103 BGC 2 n C GAL 2 C 2 GAL S 102 GAL 2 n C SIA 3 C 3 SIA S 101 SIA 2 n D BGC 1 D 1 BGC S 203 BGC 2 n D GAL 2 D 2 GAL S 202 GAL 2 n D SIA 3 D 3 SIA S 201 SIA # 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 covale ? covale1 A ND2 ASN 61 A ASN 61 1_555 E C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 113 A ASN 113 1_555 F C1 NAG . A NAG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale3 A ND2 ASN 179 A ASN 179 1_555 G C1 NAG . A NAG 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 113 B ASN 113 1_555 J C1 NAG . B NAG 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale5 B ND2 ASN 179 B ASN 179 1_555 K C1 NAG . B NAG 921 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 C O4 BGC . C BGC 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale7 C O3 GAL . C GAL 2 1_555 C C2 SIA . C SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale8 D O4 BGC . D BGC 1 1_555 D C1 GAL . D GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale9 D O3 GAL . D GAL 2 1_555 D C2 SIA . D SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? metalc ? metalc1 A OE1 GLU 127 A GLU 127 1_555 I MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 A OD1 ASP 129 A ASP 129 1_555 H CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc3 A OD2 ASP 129 A ASP 129 1_555 H CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc4 A OD2 ASP 129 A ASP 129 1_555 I MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc5 A O TYR 131 A TYR 131 1_555 H CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc6 A OD1 ASP 137 A ASP 137 1_555 H CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc7 A OD1 ASP 140 A ASP 140 1_555 H CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc8 A OD2 ASP 140 A ASP 140 1_555 I MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc9 A NE2 HIS 145 A HIS 145 1_555 I MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc10 H CA CA . A CA 301 1_555 N O HOH . A HOH 827 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc11 H CA CA . A CA 301 1_555 N O HOH . A HOH 828 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc12 I MN MN . A MN 302 1_555 N O HOH . A HOH 825 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc13 I MN MN . A MN 302 1_555 N O HOH . A HOH 826 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc14 B OE1 GLU 127 B GLU 127 1_555 M MN MN . B MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc15 B OD2 ASP 129 B ASP 129 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc16 B OD1 ASP 129 B ASP 129 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc17 B OD2 ASP 129 B ASP 129 1_555 M MN MN . B MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc18 B O TYR 131 B TYR 131 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc19 B OD1 ASP 137 B ASP 137 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc20 B OD1 ASP 140 B ASP 140 1_555 L CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc21 B OD2 ASP 140 B ASP 140 1_555 M MN MN . B MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc22 B NE2 HIS 145 B HIS 145 1_555 M MN MN . B MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc23 L CA CA . B CA 303 1_555 O O HOH . B HOH 927 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc24 L CA CA . B CA 303 1_555 O O HOH . B HOH 928 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc25 M MN MN . B MN 304 1_555 O O HOH . B HOH 925 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc26 M MN MN . B MN 304 1_555 O O HOH . B HOH 926 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? # _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 253 n n C1 O1 NAG sing 254 n n C1 O5 NAG sing 255 n n C1 H1 NAG sing 256 n n C2 C3 NAG sing 257 n n C2 N2 NAG sing 258 n n C2 H2 NAG sing 259 n n C3 C4 NAG sing 260 n n C3 O3 NAG sing 261 n n C3 H3 NAG sing 262 n n C4 C5 NAG sing 263 n n C4 O4 NAG sing 264 n n C4 H4 NAG sing 265 n n C5 C6 NAG sing 266 n n C5 O5 NAG sing 267 n n C5 H5 NAG sing 268 n n C6 O6 NAG sing 269 n n C6 H61 NAG sing 270 n n C6 H62 NAG sing 271 n n C7 C8 NAG sing 272 n n C7 N2 NAG sing 273 n n C7 O7 NAG doub 274 n n C8 H81 NAG sing 275 n n C8 H82 NAG sing 276 n n C8 H83 NAG sing 277 n n N2 HN2 NAG sing 278 n n O1 HO1 NAG sing 279 n n O3 HO3 NAG sing 280 n n O4 HO4 NAG sing 281 n n O6 HO6 NAG sing 282 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 1DBN _atom_sites.fract_transf_matrix[1][1] 0.012385 _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] 0.011306 _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] 0.011835 _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 E 3 NAG A 1 801 801 NAG NAG . F 3 NAG A 1 811 811 NAG NAG . G 3 NAG A 1 821 821 NAG NAG . H 4 CA A 1 301 301 CA CAL . I 5 MN A 1 302 302 MN MNG . J 3 NAG B 1 911 911 NAG NAG . K 3 NAG B 1 921 921 NAG NAG . L 4 CA B 1 303 303 CA CAL . M 5 MN B 1 304 304 MN MNG . N 6 HOH A 1 825 1 HOH HOH . N 6 HOH A 2 826 2 HOH HOH . N 6 HOH A 3 827 3 HOH HOH . N 6 HOH A 4 828 4 HOH HOH . N 6 HOH A 5 829 10 HOH HOH . N 6 HOH A 6 830 12 HOH HOH . N 6 HOH A 7 831 14 HOH HOH . N 6 HOH A 8 832 16 HOH HOH . N 6 HOH A 9 833 20 HOH HOH . N 6 HOH A 10 834 21 HOH HOH . N 6 HOH A 11 835 24 HOH HOH . N 6 HOH A 12 836 25 HOH HOH . N 6 HOH A 13 837 27 HOH HOH . N 6 HOH A 14 838 28 HOH HOH . N 6 HOH A 15 839 29 HOH HOH . N 6 HOH A 16 840 30 HOH HOH . O 6 HOH B 1 925 5 HOH HOH . O 6 HOH B 2 926 6 HOH HOH . O 6 HOH B 3 927 7 HOH HOH . O 6 HOH B 4 928 8 HOH HOH . O 6 HOH B 5 929 9 HOH HOH . O 6 HOH B 6 930 11 HOH HOH . O 6 HOH B 7 931 13 HOH HOH . O 6 HOH B 8 932 15 HOH HOH . O 6 HOH B 9 933 17 HOH HOH . O 6 HOH B 10 934 18 HOH HOH . O 6 HOH B 11 935 19 HOH HOH . O 6 HOH B 12 936 22 HOH HOH . O 6 HOH B 13 937 23 HOH HOH . O 6 HOH B 14 938 26 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 . . . K 3 22.251 13.453 22.939 1 41.07 ? C1 NAG 921 B 1 HETATM 2 C C2 NAG . . . K 3 22.137 14.188 24.289 1 39.23 ? C2 NAG 921 B 1 HETATM 3 C C3 NAG . . . K 3 21.483 13.317 25.381 1 44.98 ? C3 NAG 921 B 1 HETATM 4 C C4 NAG . . . K 3 20.184 12.697 24.845 1 46.69 ? C4 NAG 921 B 1 HETATM 5 C C5 NAG . . . K 3 20.555 11.894 23.594 1 47.35 ? C5 NAG 921 B 1 HETATM 6 C C6 NAG . . . K 3 19.423 11.095 22.992 1 42.71 ? C6 NAG 921 B 1 HETATM 7 C C7 NAG . . . K 3 23.893 15.817 24.616 1 44.22 ? C7 NAG 921 B 1 HETATM 8 C C8 NAG . . . K 3 25.326 16.098 25.039 1 42.48 ? C8 NAG 921 B 1 HETATM 9 N N2 NAG . . . K 3 23.478 14.556 24.699 1 42.37 ? N2 NAG 921 B 1 HETATM 10 O O3 NAG . . . K 3 21.205 14.114 26.527 1 44.5 ? O3 NAG 921 B 1 HETATM 11 O O4 NAG . . . K 3 19.562 11.867 25.827 1 43.7 ? O4 NAG 921 B 1 HETATM 12 O O5 NAG . . . K 3 21.025 12.804 22.577 1 45.56 ? O5 NAG 921 B 1 HETATM 13 O O6 NAG . . . K 3 18.757 11.848 21.991 1 46.92 ? O6 NAG 921 B 1 HETATM 14 O O7 NAG . . . K 3 23.171 16.74 24.241 1 48.44 ? O7 NAG 921 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #