data_8BPF # _model_server_result.job_id jwNrdqLNcZIqCuHH-aMHjA _model_server_result.datetime_utc '2025-01-22 08:52:29' _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 8bpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":601}' # _entry.id 8BPF # _exptl.entry_id 8BPF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 10 _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 8BPF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BPF _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,P,Q,R,S,T,U,V,W _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 ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 V N N ? 5 W N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 M NAG 1 M 1 NAG J 137 NAG 4 n M NAG 2 M 2 NAG J 138 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 139 A CYS 367 1_555 A SG CYS 198 A CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 246 A CYS 474 1_555 A SG CYS 308 A CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 347 A CYS 575 1_555 J SG CYS 91 J CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 139 B CYS 367 1_555 B SG CYS 198 B CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 186 B CYS 414 1_555 C SG CYS 186 C CYS 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 246 B CYS 474 1_555 B SG CYS 308 B CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 C SG CYS 139 C CYS 367 1_555 C SG CYS 198 C CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 246 C CYS 474 1_555 C SG CYS 308 C CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 D SG CYS 139 D CYS 367 1_555 D SG CYS 198 D CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 D SG CYS 186 D CYS 414 1_555 E SG CYS 186 E CYS 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 D SG CYS 246 D CYS 474 1_555 D SG CYS 308 D CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 E SG CYS 139 E CYS 367 1_555 E SG CYS 198 E CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 E SG CYS 246 E CYS 474 1_555 E SG CYS 308 E CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 F SG CYS 139 F CYS 367 1_555 F SG CYS 198 F CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 F SG CYS 186 F CYS 414 1_555 G SG CYS 186 G CYS 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 F SG CYS 246 F CYS 474 1_555 F SG CYS 308 F CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf17 G SG CYS 139 G CYS 367 1_555 G SG CYS 198 G CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 G SG CYS 246 G CYS 474 1_555 G SG CYS 308 G CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf19 H SG CYS 139 H CYS 367 1_555 H SG CYS 198 H CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf20 H SG CYS 186 H CYS 414 1_555 K SG CYS 186 K CYS 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 H SG CYS 246 H CYS 474 1_555 H SG CYS 308 H CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf22 I SG CYS 20 I CYS 37 1_555 I SG CYS 87 I CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf23 J SG CYS 35 J CYS 12 1_555 J SG CYS 123 J CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf24 J SG CYS 37 J CYS 14 1_555 L SG CYS 347 L CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf25 J SG CYS 131 J CYS 108 1_555 J SG CYS 156 J CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf26 K SG CYS 139 K CYS 367 1_555 K SG CYS 198 K CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf27 K SG CYS 246 K CYS 474 1_555 K SG CYS 308 K CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf28 L SG CYS 246 L CYS 474 1_555 L SG CYS 308 L CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 335 A ASN 563 1_555 N C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 B ND2 ASN 335 B ASN 563 1_555 O C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 C ND2 ASN 335 C ASN 563 1_555 P C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale4 D ND2 ASN 335 D ASN 563 1_555 Q C1 NAG . D NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 E ND2 ASN 335 E ASN 563 1_555 R C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 F ND2 ASN 335 F ASN 563 1_555 S C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale7 G ND2 ASN 335 G ASN 563 1_555 T C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 H ND2 ASN 335 H ASN 563 1_555 U C1 NAG . H NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale9 J ND2 ASN 71 J ASN 48 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale10 K ND2 ASN 335 K ASN 563 1_555 V C1 NAG . K NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale11 L ND2 ASN 335 L ASN 563 1_555 W C1 NAG . L NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale12 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 8BPF _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 N 5 NAG A 1 601 577 NAG NAG . O 5 NAG B 1 601 572 NAG NAG . P 5 NAG C 1 601 570 NAG NAG . Q 5 NAG D 1 601 569 NAG NAG . R 5 NAG E 1 601 569 NAG NAG . S 5 NAG F 1 601 569 NAG NAG . T 5 NAG G 1 601 569 NAG NAG . U 5 NAG H 1 601 571 NAG NAG . V 5 NAG K 1 601 576 NAG NAG . W 5 NAG L 1 601 577 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 . . . P 5 207.637 204.832 205.053 1 121.76 ? C1 NAG 601 C 1 HETATM 2 C C2 NAG . . . P 5 206.867 203.766 204.282 1 121.76 ? C2 NAG 601 C 1 HETATM 3 C C3 NAG . . . P 5 207.229 202.381 204.807 1 121.76 ? C3 NAG 601 C 1 HETATM 4 C C4 NAG . . . P 5 208.737 202.168 204.74 1 121.76 ? C4 NAG 601 C 1 HETATM 5 C C5 NAG . . . P 5 209.469 203.294 205.47 1 121.76 ? C5 NAG 601 C 1 HETATM 6 C C6 NAG . . . P 5 210.968 203.224 205.304 1 121.76 ? C6 NAG 601 C 1 HETATM 7 C C7 NAG . . . P 5 204.688 204.265 203.284 1 121.76 ? C7 NAG 601 C 1 HETATM 8 C C8 NAG . . . P 5 203.224 204.468 203.533 1 121.76 ? C8 NAG 601 C 1 HETATM 9 N N2 NAG . . . P 5 205.433 203.989 204.359 1 121.76 ? N2 NAG 601 C 1 HETATM 10 O O3 NAG . . . P 5 206.562 201.391 204.035 1 121.76 ? O3 NAG 601 C 1 HETATM 11 O O4 NAG . . . P 5 209.083 200.922 205.333 1 121.76 ? O4 NAG 601 C 1 HETATM 12 O O5 NAG . . . P 5 209.057 204.571 204.954 1 121.76 ? O5 NAG 601 C 1 HETATM 13 O O6 NAG . . . P 5 211.336 203.257 203.931 1 121.76 ? O6 NAG 601 C 1 HETATM 14 O O7 NAG . . . P 5 205.174 204.344 202.162 1 121.76 ? O7 NAG 601 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #