data_8DPS # _model_server_result.job_id dDfCegZO7bj6oXVJJTXdcA _model_server_result.datetime_utc '2024-11-16 23:38:26' _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 8dps # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":401}' # _entry.id 8DPS # _exptl.entry_id 8DPS _exptl.method 'ELECTRON MICROSCOPY' # _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 4 _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 8DPS _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DPS _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 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 G NAG 1 G 1 NAG G 1 NAG 4 n G NAG 2 G 2 NAG G 2 NAG 5 n H NAG 1 H 1 NAG H 1 NAG 5 n H NAG 2 H 2 NAG H 2 NAG 5 n H BMA 3 H 3 BMA H 3 BMA 4 n I NAG 1 I 1 NAG I 1 NAG 4 n I NAG 2 I 2 NAG I 2 NAG 5 n J NAG 1 J 1 NAG J 1 NAG 5 n J NAG 2 J 2 NAG J 2 NAG 5 n J BMA 3 J 3 BMA J 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 7 A CYS 6 1_555 A SG CYS 33 A CYS 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 27 A CYS 26 1_555 A SG CYS 82 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 113 A CYS 112 1_555 A SG CYS 123 A CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 151 A CYS 150 1_555 A SG CYS 161 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 C SG CYS 99 C CYS 98 1_555 C SG CYS 109 C CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 C SG CYS 149 C CYS 148 1_555 C SG CYS 159 C CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 D SG CYS 7 D CYS 6 1_555 D SG CYS 33 D CYS 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 D SG CYS 27 D CYS 26 1_555 D SG CYS 82 D CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 D SG CYS 113 D CYS 112 1_555 D SG CYS 123 D CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 D SG CYS 151 D CYS 150 1_555 D SG CYS 161 D CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf11 F SG CYS 99 F CYS 98 1_555 F SG CYS 109 F CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 F SG CYS 149 F CYS 148 1_555 F SG CYS 159 F CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 22 A ASN 21 1_555 K C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 62 A ASN 61 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale3 A ND2 ASN 136 A ASN 135 1_555 L C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 C ND2 ASN 173 C ASN 172 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale5 D ND2 ASN 22 D ASN 21 1_555 M C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 D ND2 ASN 62 D ASN 61 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale7 D ND2 ASN 136 D ASN 135 1_555 N C1 NAG . D NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 F ND2 ASN 173 F ASN 172 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale12 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale13 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 8DPS _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 K 6 NAG A 1 401 401 NAG NAG . L 6 NAG A 1 402 402 NAG NAG . M 6 NAG D 1 401 401 NAG NAG . N 6 NAG D 1 402 402 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 . . . M 6 201.65 160.974 163.059 1 75.87 ? C1 NAG 401 D 1 HETATM 2 C C2 NAG . . . M 6 201.921 160.665 161.579 1 75.87 ? C2 NAG 401 D 1 HETATM 3 C C3 NAG . . . M 6 202.845 161.713 160.955 1 75.87 ? C3 NAG 401 D 1 HETATM 4 C C4 NAG . . . M 6 202.299 163.112 161.211 1 75.87 ? C4 NAG 401 D 1 HETATM 5 C C5 NAG . . . M 6 202.046 163.312 162.702 1 75.87 ? C5 NAG 401 D 1 HETATM 6 C C6 NAG . . . M 6 201.408 164.644 163.016 1 75.87 ? C6 NAG 401 D 1 HETATM 7 C C7 NAG . . . M 6 203.515 158.696 161.762 1 75.87 ? C7 NAG 401 D 1 HETATM 8 C C8 NAG . . . M 6 204.462 159.494 162.621 1 75.87 ? C8 NAG 401 D 1 HETATM 9 N N2 NAG . . . M 6 202.388 159.301 161.332 1 75.87 ? N2 NAG 401 D 1 HETATM 10 O O3 NAG . . . M 6 202.959 161.475 159.557 1 75.87 ? O3 NAG 401 D 1 HETATM 11 O O4 NAG . . . M 6 203.227 164.091 160.758 1 75.87 ? O4 NAG 401 D 1 HETATM 12 O O5 NAG . . . M 6 201.148 162.303 163.187 1 75.87 ? O5 NAG 401 D 1 HETATM 13 O O6 NAG . . . M 6 199.994 164.577 162.894 1 75.87 ? O6 NAG 401 D 1 HETATM 14 O O7 NAG . . . M 6 203.759 157.532 161.464 1 75.87 ? O7 NAG 401 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 14 #