data_6C5J # _model_server_result.job_id SpUlnRUr8ho359YrZM-3VA _model_server_result.datetime_utc '2025-07-07 22:19:30' _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 6c5j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6C5J # _exptl.entry_id 6C5J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.31 _cell.angle_gamma 90 _cell.entry_id 6C5J _cell.length_a 116.233 _cell.length_b 45.453 _cell.length_c 75.671 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C5J _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 Z9M GP1 C1 O1 . O6 HO6 . sing 2 ? 3 3 2 KDO Z9M C2 O2 . O6 HO6 . sing 3 ? 3 4 3 KDO KDO C2 O2 . O4 HO4 . sing 4 ? 3 5 4 KDO KDO C2 O2 . O8 HO8 . 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 GP1 1 A 1 GP1 A 1 KDP 3 n C Z9M 2 A 2 Z9M A 1 KDP 3 n C KDO 3 A 3 KDO A 1 KDP 3 n C KDO 4 A 4 KDO A 1 KDP 3 n C KDO 5 A 5 KDO A 1 KDP # 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 22 H CYS 22 1_555 A SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf2 A SG CYS 145 H CYS 140 1_555 A SG CYS 200 H CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 93 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf4 B SG CYS 139 L CYS 134 1_555 B SG CYS 199 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 88 H ASN 85 1_555 D C1 NAG . H NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 C O6 GP1 . A GP1 1 1_555 C C1 Z9M . A Z9M 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale3 C O6 Z9M . A Z9M 2 1_555 C C2 KDO . A KDO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale4 C O4 KDO . A KDO 3 1_555 C C2 KDO . A KDO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 C O8 KDO . A KDO 4 1_555 C C2 KDO . A KDO 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? # _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 297 n n C1 O1 NAG sing 298 n n C1 O5 NAG sing 299 n n C1 H1 NAG sing 300 n n C2 C3 NAG sing 301 n n C2 N2 NAG sing 302 n n C2 H2 NAG sing 303 n n C3 C4 NAG sing 304 n n C3 O3 NAG sing 305 n n C3 H3 NAG sing 306 n n C4 C5 NAG sing 307 n n C4 O4 NAG sing 308 n n C4 H4 NAG sing 309 n n C5 C6 NAG sing 310 n n C5 O5 NAG sing 311 n n C5 H5 NAG sing 312 n n C6 O6 NAG sing 313 n n C6 H61 NAG sing 314 n n C6 H62 NAG sing 315 n n C7 C8 NAG sing 316 n n C7 N2 NAG sing 317 n n C7 O7 NAG doub 318 n n C8 H81 NAG sing 319 n n C8 H82 NAG sing 320 n n C8 H83 NAG sing 321 n n N2 HN2 NAG sing 322 n n O1 HO1 NAG sing 323 n n O3 HO3 NAG sing 324 n n O4 HO4 NAG sing 325 n n O6 HO6 NAG sing 326 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 6C5J _atom_sites.fract_transf_matrix[1][1] 0.008603 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002355 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022001 _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] 0.013701 _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 D 4 NAG H 1 301 400 NAG NAG . E 5 HOH H 1 401 16 HOH HOH . E 5 HOH H 2 402 221 HOH HOH . E 5 HOH H 3 403 216 HOH HOH . E 5 HOH H 4 404 52 HOH HOH . E 5 HOH H 5 405 217 HOH HOH . E 5 HOH H 6 406 13 HOH HOH . E 5 HOH H 7 407 39 HOH HOH . E 5 HOH H 8 408 24 HOH HOH . E 5 HOH H 9 409 206 HOH HOH . E 5 HOH H 10 410 14 HOH HOH . E 5 HOH H 11 411 207 HOH HOH . E 5 HOH H 12 412 218 HOH HOH . E 5 HOH H 13 413 203 HOH HOH . E 5 HOH H 14 414 212 HOH HOH . F 5 HOH L 1 301 220 HOH HOH . F 5 HOH L 2 302 96 HOH HOH . F 5 HOH L 3 303 222 HOH HOH . F 5 HOH L 4 304 215 HOH HOH . F 5 HOH L 5 305 202 HOH HOH . F 5 HOH L 6 306 21 HOH HOH . F 5 HOH L 7 307 214 HOH HOH . F 5 HOH L 8 308 210 HOH HOH . F 5 HOH L 9 309 15 HOH HOH . F 5 HOH L 10 310 8 HOH HOH . F 5 HOH L 11 311 209 HOH HOH . F 5 HOH L 12 312 44 HOH HOH . F 5 HOH L 13 313 211 HOH HOH . F 5 HOH L 14 314 205 HOH HOH . F 5 HOH L 15 315 208 HOH HOH . F 5 HOH L 16 316 31 HOH HOH . F 5 HOH L 17 317 27 HOH HOH . F 5 HOH L 18 318 213 HOH HOH . F 5 HOH L 19 319 219 HOH HOH . F 5 HOH L 20 320 204 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 . . . D 4 133.398 -28.753 32.073 1 85.38 ? C1 NAG 301 H 1 HETATM 2 C C2 NAG . . . D 4 133.95 -27.41 31.576 1 87.72 ? C2 NAG 301 H 1 HETATM 3 C C3 NAG . . . D 4 135.469 -27.369 31.697 1 91.46 ? C3 NAG 301 H 1 HETATM 4 C C4 NAG . . . D 4 135.829 -27.705 33.143 1 94.89 ? C4 NAG 301 H 1 HETATM 5 C C5 NAG . . . D 4 135.317 -29.122 33.45 1 91.87 ? C5 NAG 301 H 1 HETATM 6 C C6 NAG . . . D 4 135.741 -29.669 34.814 1 87.69 ? C6 NAG 301 H 1 HETATM 7 C C7 NAG . . . D 4 132.396 -26.493 29.893 1 85.83 ? C7 NAG 301 H 1 HETATM 8 C C8 NAG . . . D 4 132.024 -26.374 28.445 1 83.36 ? C8 NAG 301 H 1 HETATM 9 N N2 NAG . . . D 4 133.494 -27.202 30.199 1 86.73 ? N2 NAG 301 H 1 HETATM 10 O O3 NAG . . . D 4 135.981 -26.082 31.319 1 88.1 ? O3 NAG 301 H 1 HETATM 11 O O4 NAG . . . D 4 137.24 -27.554 33.348 1 102.29 ? O4 NAG 301 H 1 HETATM 12 O O5 NAG . . . D 4 133.882 -29.083 33.381 1 91.12 ? O5 NAG 301 H 1 HETATM 13 O O6 NAG . . . D 4 135.415 -31.065 34.905 1 84.08 ? O6 NAG 301 H 1 HETATM 14 O O7 NAG . . . D 4 131.706 -25.959 30.744 1 92.37 ? O7 NAG 301 H 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #