data_8DPM # _model_server_result.job_id B2_MUIgyVaJr401p4DrMCQ _model_server_result.datetime_utc '2024-10-19 11:24:43' _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 8dpm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":401}' # _entry.id 8DPM # _exptl.entry_id 8DPM _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 8DPM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DPM _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 pentadecameric _pdbx_struct_assembly.oligomeric_count 15 _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 _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 S N N ? 7 T N N ? 7 U N N # _pdbx_entity_branch.entity_id 6 _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 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 6 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 6 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 6 6 3 MAN BMA C1 O1 . O3 HO3 . 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 6 n P NAG 1 P 1 NAG G 599 NAG 6 n P NAG 2 P 2 NAG G 600 NAG 6 n P BMA 3 P 3 BMA G 601 BMA 6 n P MAN 4 P 4 MAN G 603 MAN 6 n P MAN 5 P 5 MAN G 604 MAN 6 n P MAN 6 P 6 MAN G 602 MAN 6 n Q NAG 1 Q 1 NAG B 599 NAG 6 n Q NAG 2 Q 2 NAG B 600 NAG 6 n Q BMA 3 Q 3 BMA B 601 BMA 6 n Q MAN 4 Q 4 MAN B 603 MAN 6 n Q MAN 5 Q 5 MAN B 604 MAN 6 n Q MAN 6 Q 6 MAN B 602 MAN 6 n R NAG 1 R 1 NAG L 599 NAG 6 n R NAG 2 R 2 NAG L 600 NAG 6 n R BMA 3 R 3 BMA L 601 BMA 6 n R MAN 4 R 4 MAN L 603 MAN 6 n R MAN 5 R 5 MAN L 604 MAN 6 n R MAN 6 R 6 MAN L 602 MAN # 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 76 F CYS 108 1_555 A SG CYS 103 F CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 89 F CYS 121 1_555 A SG CYS 115 F CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 10 G CYS 511 1_555 B SG CYS 55 G CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 C SG CYS 161 H CYS 161 1_555 C SG CYS 226 H CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 D SG CYS 22 I CYS 22 1_555 D SG CYS 98 I CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 E SG CYS 22 J CYS 22 1_555 E SG CYS 90 J CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 F SG CYS 76 A CYS 108 1_555 F SG CYS 103 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 F SG CYS 89 A CYS 121 1_555 F SG CYS 115 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 G SG CYS 10 B CYS 511 1_555 G SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 H SG CYS 22 C CYS 22 1_555 H SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 H SG CYS 161 C CYS 161 1_555 H SG CYS 226 C CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 I SG CYS 22 D CYS 22 1_555 I SG CYS 98 D CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 J SG CYS 22 E CYS 22 1_555 J SG CYS 90 E CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 K SG CYS 76 K CYS 108 1_555 K SG CYS 103 K CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 K SG CYS 89 K CYS 121 1_555 K SG CYS 115 K CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 L SG CYS 10 L CYS 511 1_555 L SG CYS 55 L CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 M SG CYS 22 M CYS 22 1_555 M SG CYS 96 M CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 M SG CYS 161 M CYS 161 1_555 M SG CYS 226 M CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf20 N SG CYS 22 N CYS 22 1_555 N SG CYS 98 N CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 O SG CYS 22 O CYS 22 1_555 O SG CYS 90 O CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 196 F ASN 228 1_555 S C1 NAG . F NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 62 G ASN 563 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 F ND2 ASN 196 A ASN 228 1_555 T C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 G ND2 ASN 62 B ASN 563 1_555 Q C1 NAG . Q NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 K ND2 ASN 196 K ASN 228 1_555 U C1 NAG . K NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 L ND2 ASN 62 L ASN 563 1_555 R C1 NAG . R NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 P O4 NAG . P NAG 2 1_555 P C1 BMA . P BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 P O6 BMA . P BMA 3 1_555 P C1 MAN . P MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 P O3 BMA . P BMA 3 1_555 P C1 MAN . P MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 P O3 MAN . P MAN 4 1_555 P C1 MAN . P MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 Q O4 NAG . Q NAG 2 1_555 Q C1 BMA . Q BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 Q O6 BMA . Q BMA 3 1_555 Q C1 MAN . Q MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 Q O3 BMA . Q BMA 3 1_555 Q C1 MAN . Q MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale16 Q O3 MAN . Q MAN 4 1_555 Q C1 MAN . Q MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale17 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 R O4 NAG . R NAG 2 1_555 R C1 BMA . R BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale19 R O6 BMA . R BMA 3 1_555 R C1 MAN . R MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale20 R O3 BMA . R BMA 3 1_555 R C1 MAN . R MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale21 R O3 MAN . R MAN 4 1_555 R C1 MAN . R MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 8DPM _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 S 7 NAG F 1 401 234 NAG NAG . T 7 NAG A 1 401 234 NAG NAG . U 7 NAG K 1 401 234 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 . . . T 7 222.192 168.299 198.05 1 40.9 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . T 7 222.17 166.775 197.976 1 40.9 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . T 7 223.393 166.198 198.681 1 40.9 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . T 7 224.668 166.819 198.125 1 40.9 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . T 7 224.582 168.343 198.177 1 40.9 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . T 7 225.761 169.029 197.526 1 40.9 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . T 7 220.17 165.353 197.918 1 40.9 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . T 7 218.943 164.908 198.655 1 40.9 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . T 7 220.946 166.239 198.551 1 40.9 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . T 7 223.422 164.786 198.508 1 40.9 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . T 7 225.791 166.39 198.887 1 40.9 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . T 7 223.407 168.789 197.484 1 40.9 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . T 7 225.95 168.594 196.186 1 40.9 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . T 7 220.446 164.929 196.8 1 40.9 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #