data_6XSD # _model_server_result.job_id 4WaGPKoRzpWXX8OY-VVlvg _model_server_result.datetime_utc '2024-11-15 10:02:10' _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 6xsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 6XSD # _exptl.entry_id 6XSD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _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 6XSD _cell.length_a 159.463 _cell.length_b 167.566 _cell.length_c 114.161 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 3 D N N ? 3 E 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 B NAG 1 B 1 NAG A 329 NAG 2 n B NAG 2 B 2 NAG A 330 NAG 2 n C NAG 1 C 1 NAG A 333 NAG 2 n C NAG 2 C 2 NAG A 334 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 4 A CYS 4 1_555 A SG CYS 47 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? disulf ? disulf2 A SG CYS 32 A CYS 32 1_555 A SG CYS 60 A CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf3 A SG CYS 65 A CYS 65 1_555 A SG CYS 105 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 A SG CYS 91 A CYS 91 1_555 A SG CYS 118 A CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? disulf ? disulf5 A SG CYS 123 A CYS 123 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf6 A SG CYS 155 A CYS 155 1_555 A SG CYS 181 A CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf7 A SG CYS 186 A CYS 186 1_555 A SG CYS 229 A CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf8 A SG CYS 215 A CYS 215 1_555 A SG CYS 241 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf9 A SG CYS 245 A CYS 245 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf10 A SG CYS 281 A CYS 281 1_555 A SG CYS 306 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf11 A SG CYS 288 A CYS 288 1_555 A SG CYS 326 A CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A ND2 ASN 143 A ASN 143 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 164 A ASN 164 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 174 A ASN 174 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 A ND2 ASN 234 A ASN 234 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 6XSD _atom_sites.fract_transf_matrix[1][1] 0.006271 _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] 0.005968 _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] 0.00876 _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 3 NAG A 1 401 327 NAG NAG . E 3 NAG A 1 402 328 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 . . . E 3 30.819 47.767 88.004 1 112.31 ? C1 NAG 402 A 1 HETATM 2 C C2 NAG . . . E 3 32.362 47.655 87.871 1 131.67 ? C2 NAG 402 A 1 HETATM 3 C C3 NAG . . . E 3 33.123 48.331 89.038 1 137.11 ? C3 NAG 402 A 1 HETATM 4 C C4 NAG . . . E 3 32.504 48.096 90.418 1 135.4 ? C4 NAG 402 A 1 HETATM 5 C C5 NAG . . . E 3 31.01 47.806 90.339 1 127.99 ? C5 NAG 402 A 1 HETATM 6 C C6 NAG . . . E 3 30.238 48.341 91.521 1 120.99 ? C6 NAG 402 A 1 HETATM 7 C C7 NAG . . . E 3 33.456 45.826 86.654 1 134.3 ? C7 NAG 402 A 1 HETATM 8 C C8 NAG . . . E 3 33.819 46.859 85.628 1 128.15 ? C8 NAG 402 A 1 HETATM 9 N N2 NAG . . . E 3 32.77 46.268 87.714 1 137.44 ? N2 NAG 402 A 1 HETATM 10 O O3 NAG . . . E 3 33.267 49.723 88.77 1 137.98 ? O3 NAG 402 A 1 HETATM 11 O O4 NAG . . . E 3 33.18 47.048 91.109 1 134.06 ? O4 NAG 402 A 1 HETATM 12 O O5 NAG . . . E 3 30.485 48.459 89.182 1 125.14 ? O5 NAG 402 A 1 HETATM 13 O O6 NAG . . . E 3 30.376 49.752 91.629 1 117.61 ? O6 NAG 402 A 1 HETATM 14 O O7 NAG . . . E 3 33.778 44.647 86.535 1 135.33 ? O7 NAG 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #