data_8JJ5 # _model_server_result.job_id Jy54ZPxvV5ld2mVnHXTBxA _model_server_result.datetime_utc '2024-10-09 23:24:17' _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 8jj5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 8JJ5 # _exptl.entry_id 8JJ5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 8JJ5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JJ5 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? _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 ? 8 I N N ? 8 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide 7 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 7 4 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 7 5 3 MAN BMA 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 5 n E NAG 1 E 1 NAG A 258 NAG 5 n E NAG 2 E 2 NAG A 259 NAG 6 n F NAG 1 F 1 NAG B 185 NAG 6 n F NAG 2 F 2 NAG B 186 NAG 6 n F BMA 3 F 3 BMA B 187 BMA 7 n G NAG 1 G 1 NAG C 237 NAG 7 n G NAG 2 G 2 NAG C 238 NAG 7 n G BMA 3 G 3 BMA C 241 BMA 7 n G MAN 4 G 4 MAN C 242 MAN 7 n G MAN 5 G 5 MAN C 243 MAN 5 n H NAG 1 H 1 NAG C 239 NAG 5 n H NAG 2 H 2 NAG C 240 NAG # 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 158 A CYS 158 1_555 A SG CYS 217 A CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 A SG CYS 159 A CYS 159 1_555 A SG CYS 189 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf3 A SG CYS 190 A CYS 190 1_555 A SG CYS 204 A CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 47 C CYS 47 1_555 C SG CYS 110 C CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 C SG CYS 142 C CYS 142 1_555 C SG CYS 152 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf7 D SG CYS 159 D CYS 159 1_555 D SG CYS 218 D CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf8 D SG CYS 160 D CYS 160 1_555 D SG CYS 190 D CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 D SG CYS 191 D CYS 191 1_555 D SG CYS 205 D CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 169 A ASN 169 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B ND2 ASN 28 B ASN 28 1_555 I C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 B ND2 ASN 57 B ASN 57 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 C ND2 ASN 139 C ASN 139 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 C ND2 ASN 170 C ASN 170 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 D ND2 ASN 131 D ASN 131 1_555 J C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale9 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale10 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale11 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale12 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale13 G O6 BMA . G BMA 3 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 8JJ5 _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 I 8 NAG B 1 201 188 NAG NAG . J 8 NAG D 1 301 261 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 . . . J 8 128.165 106.078 156.076 1 30 ? C1 NAG 301 D 1 HETATM 2 C C2 NAG . . . J 8 128.942 106.93 157.094 1 30 ? C2 NAG 301 D 1 HETATM 3 C C3 NAG . . . J 8 128.982 108.37 156.563 1 30 ? C3 NAG 301 D 1 HETATM 4 C C4 NAG . . . J 8 129.607 108.397 155.162 1 30 ? C4 NAG 301 D 1 HETATM 5 C C5 NAG . . . J 8 128.882 107.468 154.183 1 30 ? C5 NAG 301 D 1 HETATM 6 C C6 NAG . . . J 8 129.578 107.398 152.828 1 30 ? C6 NAG 301 D 1 HETATM 7 C C7 NAG . . . J 8 128.846 107.098 159.548 1 30 ? C7 NAG 301 D 1 HETATM 8 C C8 NAG . . . J 8 128.091 106.736 160.765 1 30 ? C8 NAG 301 D 1 HETATM 9 N N2 NAG . . . J 8 128.269 106.851 158.389 1 30 ? N2 NAG 301 D 1 HETATM 10 O O3 NAG . . . J 8 129.741 109.243 157.431 1 30 ? O3 NAG 301 D 1 HETATM 11 O O4 NAG . . . J 8 129.51 109.738 154.662 1 30 ? O4 NAG 301 D 1 HETATM 12 O O5 NAG . . . J 8 128.816 106.12 154.778 1 30 ? O5 NAG 301 D 1 HETATM 13 O O6 NAG . . . J 8 129.083 106.28 152.085 1 30 ? O6 NAG 301 D 1 HETATM 14 O O7 NAG . . . J 8 129.951 107.614 159.594 1 30 ? O7 NAG 301 D 1 HETATM 15 H H1 NAG . . . J 8 127.151 106.462 155.969 1 30 ? H1 NAG 301 D 1 HETATM 16 H H2 NAG . . . J 8 129.957 106.544 157.196 1 30 ? H2 NAG 301 D 1 HETATM 17 H H3 NAG . . . J 8 127.961 108.747 156.513 1 30 ? H3 NAG 301 D 1 HETATM 18 H H4 NAG . . . J 8 130.657 108.113 155.224 1 30 ? H4 NAG 301 D 1 HETATM 19 H H5 NAG . . . J 8 127.862 107.819 154.031 1 30 ? H5 NAG 301 D 1 HETATM 20 H H61 NAG . . . J 8 129.402 108.31 152.258 1 30 ? H61 NAG 301 D 1 HETATM 21 H H62 NAG . . . J 8 130.653 107.276 152.962 1 30 ? H62 NAG 301 D 1 HETATM 22 H H81 NAG . . . J 8 127.01 106.72 160.624 1 30 ? H81 NAG 301 D 1 HETATM 23 H H82 NAG . . . J 8 128.347 105.744 161.138 1 30 ? H82 NAG 301 D 1 HETATM 24 H H83 NAG . . . J 8 128.264 107.423 161.593 1 30 ? H83 NAG 301 D 1 HETATM 25 H HN2 NAG . . . J 8 127.359 106.413 158.381 1 30 ? HN2 NAG 301 D 1 HETATM 26 H HO3 NAG . . . J 8 129.819 108.835 158.297 1 30 ? HO3 NAG 301 D 1 HETATM 27 H HO4 NAG . . . J 8 129.789 110.32 155.372 1 30 ? HO4 NAG 301 D 1 HETATM 28 H HO6 NAG . . . J 8 128.151 106.421 151.905 1 30 ? HO6 NAG 301 D 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #