data_8V8D # _model_server_result.job_id RxVqkjGwKlylOQKSAbNfLQ _model_server_result.datetime_utc '2024-10-26 02:34:32' _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 8v8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":604}' # _entry.id 8V8D # _exptl.entry_id 8V8D _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 8V8D _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V8D _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 3 K N N ? 3 L N N ? 3 Q N N ? 3 R N N ? 3 V N N ? 3 W N N ? 3 AA N N ? 3 BA N N ? 3 EA N N ? 3 FA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n F NAG 1 F 1 NAG A 513 NAG 2 n F NAG 2 F 2 NAG A 514 NAG 2 n G NAG 1 G 1 NAG B 513 NAG 2 n G NAG 2 G 2 NAG B 514 NAG 2 n H NAG 1 H 1 NAG C 513 NAG 2 n H NAG 2 H 2 NAG C 514 NAG 2 n I NAG 1 I 1 NAG D 513 NAG 2 n I NAG 2 I 2 NAG D 514 NAG 2 n J NAG 1 J 1 NAG E 513 NAG 2 n J NAG 2 J 2 NAG E 514 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 127 A CYS 127 1_555 A SG CYS 141 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 189 A CYS 189 1_555 A SG CYS 190 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 B SG CYS 127 B CYS 127 1_555 B SG CYS 141 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 189 B CYS 189 1_555 B SG CYS 190 B CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 C SG CYS 127 C CYS 127 1_555 C SG CYS 141 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 C SG CYS 189 C CYS 189 1_555 C SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf7 D SG CYS 127 D CYS 127 1_555 D SG CYS 141 D CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 D SG CYS 189 D CYS 189 1_555 D SG CYS 190 D CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf9 E SG CYS 127 E CYS 127 1_555 E SG CYS 141 E CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 E SG CYS 189 E CYS 189 1_555 E SG CYS 190 E CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 23 A ASN 23 1_555 L C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 67 A ASN 67 1_555 K C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 110 A ASN 110 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 B ND2 ASN 23 B ASN 23 1_555 R C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 67 B ASN 67 1_555 Q C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 110 B ASN 110 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 C ND2 ASN 23 C ASN 23 1_555 W C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 C ND2 ASN 67 C ASN 67 1_555 V C1 NAG . C NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 C ND2 ASN 110 C ASN 110 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale10 D ND2 ASN 23 D ASN 23 1_555 BA C1 NAG . D NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 D ND2 ASN 67 D ASN 67 1_555 AA C1 NAG . D NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 D ND2 ASN 110 D ASN 110 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 E ND2 ASN 23 E ASN 23 1_555 FA C1 NAG . E NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 E ND2 ASN 67 E ASN 67 1_555 EA C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 E ND2 ASN 110 E ASN 110 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale17 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale19 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale20 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 B O VAL 42 B VAL 42 1_555 P CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc2 B OE1 GLU 44 B GLU 44 1_555 P CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc3 B OE2 GLU 44 B GLU 44 1_555 P CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.189 ? metalc ? metalc4 C OE2 GLU 172 C GLU 172 1_555 U CA CA . C CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc5 C OH TYR 210 C TYR 210 1_555 U CA CA . C CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc6 D OE1 GLU 44 D GLU 44 1_555 Z CA CA . D CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc7 D OE2 GLU 44 D GLU 44 1_555 Z CA CA . D CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? # _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 300 n n C1 O1 NAG sing 301 n n C1 O5 NAG sing 302 n n C1 H1 NAG sing 303 n n C2 C3 NAG sing 304 n n C2 N2 NAG sing 305 n n C2 H2 NAG sing 306 n n C3 C4 NAG sing 307 n n C3 O3 NAG sing 308 n n C3 H3 NAG sing 309 n n C4 C5 NAG sing 310 n n C4 O4 NAG sing 311 n n C4 H4 NAG sing 312 n n C5 C6 NAG sing 313 n n C5 O5 NAG sing 314 n n C5 H5 NAG sing 315 n n C6 O6 NAG sing 316 n n C6 H61 NAG sing 317 n n C6 H62 NAG sing 318 n n C7 C8 NAG sing 319 n n C7 N2 NAG sing 320 n n C7 O7 NAG doub 321 n n C8 H81 NAG sing 322 n n C8 H82 NAG sing 323 n n C8 H83 NAG sing 324 n n N2 HN2 NAG sing 325 n n O1 HO1 NAG sing 326 n n O3 HO3 NAG sing 327 n n O4 HO4 NAG sing 328 n n O6 HO6 NAG sing 329 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 8V8D _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 3 NAG A 1 601 512 NAG NAG . L 3 NAG A 1 602 510 NAG NAG . M 4 EPJ A 1 603 609 EPJ EPJ . N 5 I34 A 1 604 600 I34 I34 . O 5 I34 B 1 601 600 I34 I34 . P 6 CA B 1 602 504 CA CA . Q 3 NAG B 1 603 512 NAG NAG . R 3 NAG B 1 604 510 NAG NAG . S 4 EPJ B 1 605 609 EPJ EPJ . T 5 I34 C 1 601 600 I34 I34 . U 6 CA C 1 602 504 CA CA . V 3 NAG C 1 603 512 NAG NAG . W 3 NAG C 1 604 510 NAG NAG . X 4 EPJ C 1 605 609 EPJ EPJ . Y 5 I34 D 1 601 600 I34 I34 . Z 6 CA D 1 602 504 CA CA . AA 3 NAG D 1 603 512 NAG NAG . BA 3 NAG D 1 604 510 NAG NAG . CA 4 EPJ D 1 605 609 EPJ EPJ . DA 5 I34 D 1 606 600 I34 I34 . EA 3 NAG E 1 601 512 NAG NAG . FA 3 NAG E 1 602 510 NAG NAG . GA 4 EPJ E 1 603 609 EPJ EPJ . # 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 . . . R 3 116.273 167.098 189.711 1 111.91 ? C1 NAG 604 B 1 HETATM 2 C C2 NAG . . . R 3 115.869 168.02 190.859 1 111.91 ? C2 NAG 604 B 1 HETATM 3 C C3 NAG . . . R 3 114.346 168.073 190.98 1 111.91 ? C3 NAG 604 B 1 HETATM 4 C C4 NAG . . . R 3 113.717 168.417 189.636 1 111.91 ? C4 NAG 604 B 1 HETATM 5 C C5 NAG . . . R 3 114.224 167.451 188.571 1 111.91 ? C5 NAG 604 B 1 HETATM 6 C C6 NAG . . . R 3 113.71 167.768 187.187 1 111.91 ? C6 NAG 604 B 1 HETATM 7 C C7 NAG . . . R 3 117.596 168.093 192.6 1 111.91 ? C7 NAG 604 B 1 HETATM 8 C C8 NAG . . . R 3 118.066 167.522 193.904 1 111.91 ? C8 NAG 604 B 1 HETATM 9 N N2 NAG . . . R 3 116.463 167.581 192.111 1 111.91 ? N2 NAG 604 B 1 HETATM 10 O O3 NAG . . . R 3 113.983 169.049 191.949 1 111.91 ? O3 NAG 604 B 1 HETATM 11 O O4 NAG . . . R 3 112.3 168.316 189.722 1 111.91 ? O4 NAG 604 B 1 HETATM 12 O O5 NAG . . . R 3 115.653 167.535 188.508 1 111.91 ? O5 NAG 604 B 1 HETATM 13 O O6 NAG . . . R 3 114.114 166.785 186.243 1 111.91 ? O6 NAG 604 B 1 HETATM 14 O O7 NAG . . . R 3 118.214 168.977 192.017 1 111.91 ? O7 NAG 604 B 1 HETATM 15 H H2 NAG . . . R 3 116.24 169.021 190.642 1 111.91 ? H2 NAG 604 B 1 HETATM 16 H H3 NAG . . . R 3 113.981 167.096 191.292 1 111.91 ? H3 NAG 604 B 1 HETATM 17 H H4 NAG . . . R 3 113.991 169.436 189.368 1 111.91 ? H4 NAG 604 B 1 HETATM 18 H H5 NAG . . . R 3 113.869 166.462 188.858 1 111.91 ? H5 NAG 604 B 1 HETATM 19 H H61 NAG . . . R 3 112.623 167.829 187.207 1 111.91 ? H61 NAG 604 B 1 HETATM 20 H H62 NAG . . . R 3 114.078 168.745 186.876 1 111.91 ? H62 NAG 604 B 1 HETATM 21 H H81 NAG . . . R 3 117.301 167.69 194.661 1 111.91 ? H81 NAG 604 B 1 HETATM 22 H H82 NAG . . . R 3 118.239 166.454 193.781 1 111.91 ? H82 NAG 604 B 1 HETATM 23 H H83 NAG . . . R 3 118.991 168.017 194.195 1 111.91 ? H83 NAG 604 B 1 HETATM 24 H HN2 NAG . . . R 3 115.994 166.85 192.639 1 111.91 ? HN2 NAG 604 B 1 HETATM 25 H HO3 NAG . . . R 3 113.017 169.084 192.027 1 111.91 ? HO3 NAG 604 B 1 HETATM 26 H HO6 NAG . . . R 3 113.769 167.017 185.367 1 111.91 ? HO6 NAG 604 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 386 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #