data_8DER # _model_server_result.job_id ij85KCXSDKVNst8lJp3W3g _model_server_result.datetime_utc '2025-02-26 15:51:21' _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 8der # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 8DER # _exptl.entry_id 8DER _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 8DER _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DER _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 _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 ? 7 P N N ? 7 Q N N ? 7 R N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 # 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 M NAG 1 D 1 NAG C 346 NAG 5 n M NAG 2 D 2 NAG C 347 NAG 5 n N NAG 1 I 1 NAG B 346 NAG 5 n N NAG 2 I 2 NAG B 347 NAG 6 n O NAG 1 J 1 NAG A 345 NAG 6 n O NAG 2 J 2 NAG A 346 NAG 6 n O BMA 3 J 3 BMA A 347 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 21 X CYS 22 1_555 A SG CYS 95 X CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 22 Y CYS 23 1_555 B SG CYS 87 Y CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 C SG CYS 49 G CYS 49 1_555 C SG CYS 114 G CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 C SG CYS 62 G CYS 62 1_555 C SG CYS 94 G CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 C SG CYS 63 G CYS 63 1_555 C SG CYS 96 G CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 C SG CYS 259 G CYS 259 1_555 C SG CYS 271 G CYS 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 C SG CYS 301 G CYS 301 1_555 C SG CYS 376 G CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 C SG CYS 306 G CYS 306 1_555 C SG CYS 380 G CYS 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 328 G CYS 328 1_555 C SG CYS 370 G CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 D SG CYS 49 E CYS 49 1_555 D SG CYS 114 E CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 D SG CYS 62 E CYS 62 1_555 D SG CYS 94 E CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 D SG CYS 63 E CYS 63 1_555 D SG CYS 96 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf13 D SG CYS 259 E CYS 259 1_555 D SG CYS 271 E CYS 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf14 D SG CYS 301 E CYS 301 1_555 D SG CYS 376 E CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf15 D SG CYS 306 E CYS 306 1_555 D SG CYS 380 E CYS 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 D SG CYS 328 E CYS 328 1_555 D SG CYS 370 E CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf17 E SG CYS 19 C CYS 19 1_555 E SG CYS 123 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 E SG CYS 22 C CYS 22 1_555 E SG CYS 27 C CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf19 E SG CYS 90 C CYS 90 1_555 E SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf20 E SG CYS 151 C CYS 151 1_555 E SG CYS 266 C CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf21 E SG CYS 200 C CYS 200 1_555 E SG CYS 226 C CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf22 E SG CYS 202 C CYS 202 1_555 E SG CYS 220 C CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf23 F SG CYS 49 F CYS 49 1_555 F SG CYS 114 F CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf24 F SG CYS 62 F CYS 62 1_555 F SG CYS 94 F CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf25 F SG CYS 63 F CYS 63 1_555 F SG CYS 96 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf26 F SG CYS 259 F CYS 259 1_555 F SG CYS 271 F CYS 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf27 F SG CYS 301 F CYS 301 1_555 F SG CYS 376 F CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf28 F SG CYS 306 F CYS 306 1_555 F SG CYS 380 F CYS 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf29 F SG CYS 328 F CYS 328 1_555 F SG CYS 370 F CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf30 G SG CYS 19 B CYS 19 1_555 G SG CYS 123 B CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf31 G SG CYS 22 B CYS 22 1_555 G SG CYS 27 B CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf32 G SG CYS 90 B CYS 90 1_555 G SG CYS 104 B CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf33 G SG CYS 151 B CYS 151 1_555 G SG CYS 266 B CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf34 G SG CYS 200 B CYS 200 1_555 G SG CYS 226 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf35 G SG CYS 202 B CYS 202 1_555 G SG CYS 220 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf36 H SG CYS 19 A CYS 19 1_555 H SG CYS 123 A CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf37 H SG CYS 22 A CYS 22 1_555 H SG CYS 27 A CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf38 H SG CYS 90 A CYS 90 1_555 H SG CYS 104 A CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf39 H SG CYS 151 A CYS 151 1_555 H SG CYS 266 A CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf40 H SG CYS 200 A CYS 200 1_555 H SG CYS 226 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf41 H SG CYS 202 A CYS 202 1_555 H SG CYS 220 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf42 I SG CYS 21 H CYS 22 1_555 I SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf43 J SG CYS 22 L CYS 23 1_555 J SG CYS 87 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf44 K SG CYS 21 W CYS 22 1_555 K SG CYS 95 W CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf45 L SG CYS 22 V CYS 23 1_555 L SG CYS 87 V CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 C ND2 ASN 134 G ASN 134 1_555 P C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 D ND2 ASN 134 E ASN 134 1_555 Q C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 E ND2 ASN 212 C ASN 212 1_555 M C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale4 F ND2 ASN 134 F ASN 134 1_555 R C1 NAG . F NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 G ND2 ASN 212 B ASN 212 1_555 N C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 H ND2 ASN 212 A ASN 212 1_555 O C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 M O4 NAG . D NAG 1 1_555 M C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 N O4 NAG . I NAG 1 1_555 N C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 O O4 NAG . J NAG 1 1_555 O C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 O O4 NAG . J NAG 2 1_555 O C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 8DER _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 P 7 NAG G 1 501 403 NAG NAG . Q 7 NAG E 1 501 403 NAG NAG . R 7 NAG F 1 501 403 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 7 116.346 128.94 123.521 1 50 ? C1 NAG 501 G 1 HETATM 2 C C2 NAG . . . P 7 116.245 130.424 123.193 1 50 ? C2 NAG 501 G 1 HETATM 3 C C3 NAG . . . P 7 116.69 131.227 124.401 1 50 ? C3 NAG 501 G 1 HETATM 4 C C4 NAG . . . P 7 115.817 130.849 125.586 1 50 ? C4 NAG 501 G 1 HETATM 5 C C5 NAG . . . P 7 115.93 129.35 125.837 1 50 ? C5 NAG 501 G 1 HETATM 6 C C6 NAG . . . P 7 115.031 128.893 126.981 1 50 ? C6 NAG 501 G 1 HETATM 7 C C7 NAG . . . P 7 116.496 130.991 120.85 1 50 ? C7 NAG 501 G 1 HETATM 8 C C8 NAG . . . P 7 116.651 132.383 120.316 1 50 ? C8 NAG 501 G 1 HETATM 9 N N2 NAG . . . P 7 117.051 130.769 122.039 1 50 ? N2 NAG 501 G 1 HETATM 10 O O3 NAG . . . P 7 116.557 132.625 124.126 1 50 ? O3 NAG 501 G 1 HETATM 11 O O4 NAG . . . P 7 116.248 131.587 126.733 1 50 ? O4 NAG 501 G 1 HETATM 12 O O5 NAG . . . P 7 115.535 128.653 124.658 1 50 ? O5 NAG 501 G 1 HETATM 13 O O6 NAG . . . P 7 115.482 129.44 128.225 1 50 ? O6 NAG 501 G 1 HETATM 14 O O7 NAG . . . P 7 115.898 130.126 120.233 1 50 ? O7 NAG 501 G 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 125 _model_server_stats.query_time_ms 554 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #