data_5N09 # _model_server_result.job_id 5dGud8s1kkOh-cFM7XES0g _model_server_result.datetime_utc '2024-10-10 14:27:48' _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 5n09 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":507}' # _entry.id 5N09 # _exptl.entry_id 5N09 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 90 _cell.angle_gamma 90 _cell.entry_id 5N09 _cell.length_a 58.902 _cell.length_b 180.598 _cell.length_c 205.043 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N09 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 6 1 FUC NAG C1 O1 . O6 HO6 . 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 4 n G NAG 1 C 1 NAG A 501 NAG 4 n G NAG 2 C 2 NAG A 503 NAG 4 n G BMA 3 C 3 BMA A 504 BMA 4 n G MAN 4 C 4 MAN A 506 MAN 4 n G MAN 5 C 5 MAN A 505 MAN 4 n G FUC 6 C 6 FUC A 502 FUC 4 n H NAG 1 D 1 NAG B 501 NAG 4 n H NAG 2 D 2 NAG B 503 NAG 4 n H BMA 3 D 3 BMA B 504 BMA 4 n H MAN 4 D 4 MAN B 506 MAN 4 n H MAN 5 D 5 MAN B 505 MAN 4 n H FUC 6 D 6 FUC B 502 FUC # 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 3 A CYS 3 1_555 A SG CYS 30 A CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 60 A CYS 60 1_555 A SG CYS 121 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 74 A CYS 74 1_555 A SG CYS 105 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 92 A CYS 92 1_555 A SG CYS 116 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 107 A CYS 107 1_555 B SG CYS 313 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 185 A CYS 185 1_555 A SG CYS 285 A CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 302 A CYS 302 1_555 A SG CYS 333 A CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf8 A SG CYS 313 A CYS 313 1_555 B SG CYS 107 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 3 B CYS 3 1_555 B SG CYS 30 B CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf10 B SG CYS 60 B CYS 60 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf11 B SG CYS 74 B CYS 74 1_555 B SG CYS 105 B CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf12 B SG CYS 92 B CYS 92 1_555 B SG CYS 116 B CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 B SG CYS 185 B CYS 185 1_555 B SG CYS 285 B CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf14 B SG CYS 302 B CYS 302 1_555 B SG CYS 333 B CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf15 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf16 C SG CYS 160 H CYS 140 1_555 C SG CYS 216 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 D SG CYS 22 I CYS 22 1_555 D SG CYS 96 I CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf18 D SG CYS 160 I CYS 140 1_555 D SG CYS 216 I CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf19 E SG CYS 24 L CYS 23 1_555 E SG CYS 92 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf20 E SG CYS 140 L CYS 135 1_555 E SG CYS 199 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf21 F SG CYS 24 M CYS 23 1_555 F SG CYS 92 M CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf22 F SG CYS 140 M CYS 135 1_555 F SG CYS 199 M CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 153 A ASN 153 1_555 G C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B ND2 ASN 67 B ASN 67 1_555 I C1 NAG . B NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 B ND2 ASN 153 B ASN 153 1_555 H C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 G O4 NAG . C NAG 1 1_555 G C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale5 G O6 NAG . C NAG 1 1_555 G C1 FUC . C FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 G O4 NAG . C NAG 2 1_555 G C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 G O3 BMA . C BMA 3 1_555 G C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 G O6 BMA . C BMA 3 1_555 G C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 H O4 NAG . D NAG 1 1_555 H C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale10 H O6 NAG . D NAG 1 1_555 H C1 FUC . D FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 H O4 NAG . D NAG 2 1_555 H C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 H O3 BMA . D BMA 3 1_555 H C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 H O6 BMA . D BMA 3 1_555 H C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 308 n n C1 O1 NAG sing 309 n n C1 O5 NAG sing 310 n n C1 H1 NAG sing 311 n n C2 C3 NAG sing 312 n n C2 N2 NAG sing 313 n n C2 H2 NAG sing 314 n n C3 C4 NAG sing 315 n n C3 O3 NAG sing 316 n n C3 H3 NAG sing 317 n n C4 C5 NAG sing 318 n n C4 O4 NAG sing 319 n n C4 H4 NAG sing 320 n n C5 C6 NAG sing 321 n n C5 O5 NAG sing 322 n n C5 H5 NAG sing 323 n n C6 O6 NAG sing 324 n n C6 H61 NAG sing 325 n n C6 H62 NAG sing 326 n n C7 C8 NAG sing 327 n n C7 N2 NAG sing 328 n n C7 O7 NAG doub 329 n n C8 H81 NAG sing 330 n n C8 H82 NAG sing 331 n n C8 H83 NAG sing 332 n n N2 HN2 NAG sing 333 n n O1 HO1 NAG sing 334 n n O3 HO3 NAG sing 335 n n O4 HO4 NAG sing 336 n n O6 HO6 NAG sing 337 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 5N09 _atom_sites.fract_transf_matrix[1][1] 0.016977 _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] 0.005537 _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] 0.004877 _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 I 5 NAG B 1 507 567 NAG NAG . J 6 HOH A 1 601 1 HOH HOH . K 6 HOH H 1 301 2 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 . . . I 5 61.811 33.109 17.094 1 127.05 ? C1 NAG 507 B 1 HETATM 2 C C2 NAG . . . I 5 61.103 33.201 18.448 1 123.01 ? C2 NAG 507 B 1 HETATM 3 C C3 NAG . . . I 5 61.434 34.532 19.125 1 123.44 ? C3 NAG 507 B 1 HETATM 4 C C4 NAG . . . I 5 62.941 34.741 19.19 1 126.62 ? C4 NAG 507 B 1 HETATM 5 C C5 NAG . . . I 5 63.556 34.582 17.802 1 135.05 ? C5 NAG 507 B 1 HETATM 6 C C6 NAG . . . I 5 65.064 34.681 17.803 1 142.74 ? C6 NAG 507 B 1 HETATM 7 C C7 NAG . . . I 5 58.85 32.681 19.28 1 117.74 ? C7 NAG 507 B 1 HETATM 8 C C8 NAG . . . I 5 57.395 32.588 18.934 1 107.22 ? C8 NAG 507 B 1 HETATM 9 N N2 NAG . . . I 5 59.665 33.056 18.289 1 117.11 ? N2 NAG 507 B 1 HETATM 10 O O3 NAG . . . I 5 60.883 34.555 20.437 1 121.4 ? O3 NAG 507 B 1 HETATM 11 O O4 NAG . . . I 5 63.232 36.041 19.69 1 128.3 ? O4 NAG 507 B 1 HETATM 12 O O5 NAG . . . I 5 63.222 33.291 17.273 1 129.67 ? O5 NAG 507 B 1 HETATM 13 O O6 NAG . . . I 5 65.636 33.916 18.855 1 139.43 ? O6 NAG 507 B 1 HETATM 14 O O7 NAG . . . I 5 59.269 32.429 20.406 1 131.71 ? O7 NAG 507 B 1 # _model_server_stats.io_time_ms 138 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #