data_8D21 # _model_server_result.job_id wbUVHP4jh7-kkT1c-06a-Q _model_server_result.datetime_utc '2024-10-20 19:19:23' _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 8d21 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":405}' # _entry.id 8D21 # _exptl.entry_id 8D21 _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 21 _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 8D21 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D21 _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,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N ? 6 V N N ? 6 W N N ? 6 X N N ? 6 Y N N ? 6 Z N N ? 6 AA N N ? 6 BA N N ? 6 CA N N ? 6 DA N N ? 6 EA N N ? 6 FA N N ? 6 GA N N ? 6 HA N N ? 6 IA N N ? 6 JA N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type 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 ? 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 5 n M NAG 1 M 1 NAG B 174 NAG 5 n M NAG 2 M 2 NAG B 175 NAG 5 n M BMA 3 M 3 BMA B 176 BMA 5 n N NAG 1 N 1 NAG C 174 NAG 5 n N NAG 2 N 2 NAG C 175 NAG 5 n N BMA 3 N 3 BMA C 176 BMA 5 n O NAG 1 O 1 NAG G 174 NAG 5 n O NAG 2 O 2 NAG G 175 NAG 5 n O BMA 3 O 3 BMA G 176 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 47 B CYS 47 1_555 J SG CYS 20 I CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 137 B CYS 137 1_555 B SG CYS 4 A CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 144 B CYS 144 1_555 A SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 20 A CYS 30 1_555 E SG CYS 47 C CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 42 A CYS 52 1_555 B SG CYS 274 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 55 A CYS 64 1_555 B SG CYS 67 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 90 A CYS 97 1_555 B SG CYS 135 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 278 A CYS 281 1_555 B SG CYS 302 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 D SG CYS 23 L CYS 23 1_555 D SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf11 E SG CYS 137 C CYS 137 1_555 F SG CYS 4 D CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 E SG CYS 144 C CYS 144 1_555 E SG CYS 148 C CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 F SG CYS 20 D CYS 30 1_555 I SG CYS 47 G CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 F SG CYS 42 D CYS 52 1_555 F SG CYS 274 D CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 F SG CYS 55 D CYS 64 1_555 F SG CYS 67 D CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf16 F SG CYS 90 D CYS 97 1_555 F SG CYS 135 D CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf17 F SG CYS 278 D CYS 281 1_555 F SG CYS 302 D CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf18 G SG CYS 22 E CYS 22 1_555 G SG CYS 96 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 H SG CYS 23 F CYS 23 1_555 H SG CYS 88 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 I SG CYS 137 G CYS 137 1_555 J SG CYS 4 I CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 I SG CYS 144 G CYS 144 1_555 I SG CYS 148 G CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf22 J SG CYS 42 I CYS 52 1_555 J SG CYS 274 I CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf23 J SG CYS 55 I CYS 64 1_555 J SG CYS 67 I CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 J SG CYS 90 I CYS 97 1_555 J SG CYS 135 I CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf25 J SG CYS 278 I CYS 281 1_555 J SG CYS 302 I CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf26 K SG CYS 22 J CYS 22 1_555 K SG CYS 96 J CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf27 L SG CYS 23 K CYS 23 1_555 L SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 154 B ASN 154 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 B ND2 ASN 11 A ASN 21 1_555 P C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 B ND2 ASN 23 A ASN 33 1_555 S C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 B ND2 ASN 54 A ASN 63 1_555 U C1 NAG . A NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 87 A ASN 94 1_555 R C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 125 A ASN 129 1_555 Q C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 159 A ASN 163 1_555 V C1 NAG . A NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 B ND2 ASN 286 A ASN 289 1_555 T C1 NAG . A NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 E ND2 ASN 154 C ASN 154 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 F ND2 ASN 11 D ASN 21 1_555 W C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 F ND2 ASN 23 D ASN 33 1_555 Z C1 NAG . D NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale12 F ND2 ASN 54 D ASN 63 1_555 BA C1 NAG . D NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 F ND2 ASN 87 D ASN 94 1_555 Y C1 NAG . D NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 F ND2 ASN 125 D ASN 129 1_555 X C1 NAG . D NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale15 F ND2 ASN 159 D ASN 163 1_555 CA C1 NAG . D NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale16 F ND2 ASN 286 D ASN 289 1_555 AA C1 NAG . D NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale17 I ND2 ASN 154 G ASN 154 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 J ND2 ASN 11 I ASN 21 1_555 DA C1 NAG . I NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale19 J ND2 ASN 23 I ASN 33 1_555 GA C1 NAG . I NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale20 J ND2 ASN 54 I ASN 63 1_555 IA C1 NAG . I NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale21 J ND2 ASN 87 I ASN 94 1_555 FA C1 NAG . I NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale22 J ND2 ASN 125 I ASN 129 1_555 EA C1 NAG . I NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale23 J ND2 ASN 159 I ASN 163 1_555 JA C1 NAG . I NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale24 J ND2 ASN 286 I ASN 289 1_555 HA C1 NAG . I NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale25 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale26 M O4 NAG . M NAG 2 1_555 M C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale27 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale28 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale29 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale30 O O4 NAG . O NAG 2 1_555 O C1 BMA . O BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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_ _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 8D21 _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 6 NAG A 1 401 504 NAG NAG . Q 6 NAG A 1 402 509 NAG NAG . R 6 NAG A 1 403 510 NAG NAG . S 6 NAG A 1 404 511 NAG NAG . T 6 NAG A 1 405 512 NAG NAG . U 6 NAG A 1 406 514 NAG NAG . V 6 NAG A 1 407 515 NAG NAG . W 6 NAG D 1 401 504 NAG NAG . X 6 NAG D 1 402 509 NAG NAG . Y 6 NAG D 1 403 510 NAG NAG . Z 6 NAG D 1 404 511 NAG NAG . AA 6 NAG D 1 405 512 NAG NAG . BA 6 NAG D 1 406 514 NAG NAG . CA 6 NAG D 1 407 515 NAG NAG . DA 6 NAG I 1 401 504 NAG NAG . EA 6 NAG I 1 402 509 NAG NAG . FA 6 NAG I 1 403 510 NAG NAG . GA 6 NAG I 1 404 511 NAG NAG . HA 6 NAG I 1 405 512 NAG NAG . IA 6 NAG I 1 406 514 NAG NAG . JA 6 NAG I 1 407 515 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 . . . AA 6 191.218 154.226 142.971 1 202.03 ? C1 NAG 405 D 1 HETATM 2 C C2 NAG . . . AA 6 192.72 154.495 142.998 1 202.03 ? C2 NAG 405 D 1 HETATM 3 C C3 NAG . . . AA 6 193.48 153.211 143.314 1 202.03 ? C3 NAG 405 D 1 HETATM 4 C C4 NAG . . . AA 6 192.954 152.588 144.599 1 202.03 ? C4 NAG 405 D 1 HETATM 5 C C5 NAG . . . AA 6 191.442 152.4 144.514 1 202.03 ? C5 NAG 405 D 1 HETATM 6 C C6 NAG . . . AA 6 190.836 151.899 145.804 1 202.03 ? C6 NAG 405 D 1 HETATM 7 C C7 NAG . . . AA 6 193.792 156.238 141.634 1 202.03 ? C7 NAG 405 D 1 HETATM 8 C C8 NAG . . . AA 6 194.182 156.658 140.249 1 202.03 ? C8 NAG 405 D 1 HETATM 9 N N2 NAG . . . AA 6 193.17 155.058 141.734 1 202.03 ? N2 NAG 405 D 1 HETATM 10 O O3 NAG . . . AA 6 194.867 153.502 143.446 1 202.03 ? O3 NAG 405 D 1 HETATM 11 O O4 NAG . . . AA 6 193.572 151.324 144.815 1 202.03 ? O4 NAG 405 D 1 HETATM 12 O O5 NAG . . . AA 6 190.809 153.654 144.219 1 202.03 ? O5 NAG 405 D 1 HETATM 13 O O6 NAG . . . AA 6 189.421 151.802 145.71 1 202.03 ? O6 NAG 405 D 1 HETATM 14 O O7 NAG . . . AA 6 194.028 156.935 142.616 1 202.03 ? O7 NAG 405 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #