data_9DIY # _model_server_result.job_id 8wBLoSx68gjqfjCIRVyEsg _model_server_result.datetime_utc '2024-12-03 16:43:29' _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 9diy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":404}' # _entry.id 9DIY # _exptl.entry_id 9DIY _exptl.method 'ELECTRON MICROSCOPY' # _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 9 _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 9DIY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DIY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 F N N ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 BMA 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 4 n D NAG 1 D 1 NAG A 708 NAG 4 n D NAG 2 D 2 NAG A 709 NAG 5 n E NAG 1 E 1 NAG B 256 NAG 5 n E NAG 2 E 2 NAG B 257 NAG 5 n E BMA 3 E 3 BMA B 258 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 167 A CYS 196 1_555 A SG CYS 183 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 B SG CYS 201 C CYS 225 1_555 B SG CYS 231 C CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 C SG CYS 38 B CYS 67 1_555 C SG CYS 114 B CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 C SG CYS 55 B CYS 84 1_555 C SG CYS 205 B CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 27 A ASN 56 1_555 G C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 34 A ASN 63 1_555 F C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 164 A ASN 193 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 B ND2 ASN 191 C ASN 215 1_555 J C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 198 C ASN 222 1_555 K C1 NAG . C NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 B ND2 ASN 227 C ASN 251 1_555 H C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 B ND2 ASN 230 C ASN 254 1_555 L C1 NAG . C NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 B ND2 ASN 243 C ASN 267 1_555 I C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 C ND2 ASN 88 B ASN 117 1_555 M C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 C ND2 ASN 103 B ASN 132 1_555 N C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 C ND2 ASN 118 B ASN 147 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale14 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 9DIY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 6 NAG A 1 801 710 NAG NAG . G 6 NAG A 1 802 711 NAG NAG . H 6 NAG C 1 401 315 NAG NAG . I 6 NAG C 1 402 316 NAG NAG . J 6 NAG C 1 403 317 NAG NAG . K 6 NAG C 1 404 319 NAG NAG . L 6 NAG C 1 405 320 NAG NAG . M 6 NAG B 1 401 254 NAG NAG . N 6 NAG B 1 402 255 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 . . . K 6 98.675 128.372 73.108 1 269.77 ? C1 NAG 404 C 1 HETATM 2 C C2 NAG . . . K 6 99.919 129.226 72.8 1 269.77 ? C2 NAG 404 C 1 HETATM 3 C C3 NAG . . . K 6 100.418 128.976 71.372 1 269.77 ? C3 NAG 404 C 1 HETATM 4 C C4 NAG . . . K 6 100.459 127.496 71.014 1 269.77 ? C4 NAG 404 C 1 HETATM 5 C C5 NAG . . . K 6 99.116 126.857 71.361 1 269.77 ? C5 NAG 404 C 1 HETATM 6 C C6 NAG . . . K 6 99.022 125.383 71.041 1 269.77 ? C6 NAG 404 C 1 HETATM 7 C C7 NAG . . . K 6 100.386 131.652 72.528 1 269.77 ? C7 NAG 404 C 1 HETATM 8 C C8 NAG . . . K 6 99.844 133.026 72.836 1 269.77 ? C8 NAG 404 C 1 HETATM 9 N N2 NAG . . . K 6 99.627 130.629 72.97 1 269.77 ? N2 NAG 404 C 1 HETATM 10 O O3 NAG . . . K 6 101.696 129.544 71.254 1 269.77 ? O3 NAG 404 C 1 HETATM 11 O O4 NAG . . . K 6 100.735 127.409 69.635 1 269.77 ? O4 NAG 404 C 1 HETATM 12 O O5 NAG . . . K 6 98.904 127.033 72.741 1 269.77 ? O5 NAG 404 C 1 HETATM 13 O O6 NAG . . . K 6 97.817 124.865 71.555 1 269.77 ? O6 NAG 404 C 1 HETATM 14 O O7 NAG . . . K 6 101.441 131.51 71.928 1 269.77 ? O7 NAG 404 C 1 HETATM 15 H H1 NAG . . . K 6 97.924 128.715 72.598 1 269.77 ? H1 NAG 404 C 1 HETATM 16 H H2 NAG . . . K 6 100.615 128.98 73.423 1 269.77 ? H2 NAG 404 C 1 HETATM 17 H H3 NAG . . . K 6 99.797 129.402 70.761 1 269.77 ? H3 NAG 404 C 1 HETATM 18 H H4 NAG . . . K 6 101.158 127.074 71.537 1 269.77 ? H4 NAG 404 C 1 HETATM 19 H H5 NAG . . . K 6 98.419 127.301 70.851 1 269.77 ? H5 NAG 404 C 1 HETATM 20 H H61 NAG . . . K 6 99.083 125.271 70.079 1 269.77 ? H61 NAG 404 C 1 HETATM 21 H H62 NAG . . . K 6 99.799 124.945 71.42 1 269.77 ? H62 NAG 404 C 1 HETATM 22 H H81 NAG . . . K 6 99.222 133.287 72.14 1 269.77 ? H81 NAG 404 C 1 HETATM 23 H H82 NAG . . . K 6 99.35 132.997 73.67 1 269.77 ? H82 NAG 404 C 1 HETATM 24 H H83 NAG . . . K 6 100.527 133.711 72.907 1 269.77 ? H83 NAG 404 C 1 HETATM 25 H HN2 NAG . . . K 6 98.9 130.826 73.381 1 269.77 ? HN2 NAG 404 C 1 HETATM 26 H HO3 NAG . . . K 6 101.632 130.232 70.759 1 269.77 ? HO3 NAG 404 C 1 HETATM 27 H HO4 NAG . . . K 6 101.228 128.064 69.41 1 269.77 ? HO4 NAG 404 C 1 HETATM 28 H HO6 NAG . . . K 6 97.766 125.077 72.377 1 269.77 ? HO6 NAG 404 C 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 904 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 28 #