data_8PKO # _model_server_result.job_id ZBjLxPhTNmMS_NFGIEc0Vg _model_server_result.datetime_utc '2025-04-24 06:58:31' _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 8pko # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1203}' # _entry.id 8PKO # _exptl.entry_id 8PKO _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 2 _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 8PKO _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PKO _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 _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 x,y,z _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 H N N ? 7 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG 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 3 n C NAG 1 C 1 NAG A 2120 NAG 3 n C NAG 2 C 2 NAG A 2121 NAG 3 n C BMA 3 C 3 BMA A 2122 BMA 3 n C MAN 4 C 4 MAN A 2124 MAN 3 n C MAN 5 C 5 MAN A 2123 MAN 4 n D NAG 1 D 1 NAG A 2390 NAG 4 n D NAG 2 D 2 NAG A 2391 NAG 3 n E NAG 1 E 1 NAG A 2716 NAG 3 n E NAG 2 E 2 NAG A 2717 NAG 3 n E BMA 3 E 3 BMA A 2718 BMA 3 n E MAN 4 E 4 MAN A 2719 MAN 3 n E MAN 5 E 5 MAN A 2720 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 282 A CYS 99 1_555 A SG CYS 741 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 830 A CYS 647 1_555 B SG CYS 368 B CYS 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf3 A SG CYS 902 A CYS 719 1_555 B SG CYS 33 B CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 A SG CYS 1146 A CYS 963 1_555 A SG CYS 1168 A CYS 985 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 B SG CYS 62 B CYS 79 1_555 B SG CYS 69 B CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? covale ? covale1 A ND2 ASN 303 A ASN 120 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale2 A ND2 ASN 573 A ASN 390 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale3 A ND2 ASN 899 A ASN 716 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale4 A ND2 ASN 1096 A ASN 913 1_555 H C1 NAG . A NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 460 B ASN 477 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale14 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 A O THR 791 A THR 608 1_555 F CA CA . A CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc2 A OG1 THR 791 A THR 608 1_555 F CA CA . A CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc3 F CA CA . A CA 1201 1_555 I O3 MAN . A MAN 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc4 F CA CA . A CA 1201 1_555 I O4 MAN . A MAN 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc5 F CA CA . A CA 1201 1_555 K O HOH . A HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc6 F CA CA . A CA 1201 1_555 K O HOH . A HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc7 F CA CA . A CA 1201 1_555 K O HOH . A HOH 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 8PKO _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 F 5 CA A 1 1201 1201 CA CA . G 6 THJ A 1 1202 1203 THJ THJ . H 7 NAG A 1 1203 2913 NAG NAG . I 8 MAN A 1 1204 2914 MAN MAN . J 7 NAG B 1 601 2477 NAG NAG . K 9 HOH A 1 1301 3011 HOH HOH . K 9 HOH A 2 1302 3012 HOH HOH . K 9 HOH A 3 1303 3010 HOH HOH . # 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 . . . H 7 90.005 158.401 142.09 1 313.22 ? C1 NAG 1203 A 1 HETATM 2 C C2 NAG . . . H 7 89.633 159.654 141.297 1 313 ? C2 NAG 1203 A 1 HETATM 3 C C3 NAG . . . H 7 90.881 160.499 141.037 1 312.8 ? C3 NAG 1203 A 1 HETATM 4 C C4 NAG . . . H 7 91.616 160.782 142.34 1 313.01 ? C4 NAG 1203 A 1 HETATM 5 C C5 NAG . . . H 7 91.898 159.477 143.077 1 312.77 ? C5 NAG 1203 A 1 HETATM 6 C C6 NAG . . . H 7 92.533 159.685 144.43 1 312.25 ? C6 NAG 1203 A 1 HETATM 7 C C7 NAG . . . H 7 87.678 159.471 139.806 1 312.04 ? C7 NAG 1203 A 1 HETATM 8 C C8 NAG . . . H 7 86.873 160.058 140.923 1 311.59 ? C8 NAG 1203 A 1 HETATM 9 N N2 NAG . . . H 7 88.984 159.301 140.043 1 312.66 ? N2 NAG 1203 A 1 HETATM 10 O O3 NAG . . . H 7 90.529 161.72 140.396 1 312.46 ? O3 NAG 1203 A 1 HETATM 11 O O4 NAG . . . H 7 92.847 161.444 142.076 1 312.87 ? O4 NAG 1203 A 1 HETATM 12 O O5 NAG . . . H 7 90.667 158.776 143.301 1 313.35 ? O5 NAG 1203 A 1 HETATM 13 O O6 NAG . . . H 7 91.568 160.087 145.392 1 311.83 ? O6 NAG 1203 A 1 HETATM 14 O O7 NAG . . . H 7 87.17 159.162 138.735 1 311.9 ? O7 NAG 1203 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 70 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 23 _model_server_stats.element_count 14 #