data_5DUQ # _model_server_result.job_id vDhFg7VS-UuIkHqvKUGXvw _model_server_result.datetime_utc '2024-12-26 19:07:32' _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 5duq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5DUQ # _exptl.entry_id 5DUQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method nat _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 103.31 _cell.angle_gamma 90 _cell.entry_id 5DUQ _cell.length_a 112.1 _cell.length_b 197.424 _cell.length_c 56.779 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DUQ _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 F 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 BGC _pdbx_entity_branch_link.comp_id_2 GLC _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 C GLC 1 C 1 GLC D 601 GLC 2 n C BGC 2 C 2 BGC D 602 GLC # 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 covale ? covale1 A ND2 ASN 121 A ASN 216 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 B ND2 ASN 121 B ASN 216 1_555 F C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale3 G S SO3 . B SO3 504 1_555 C O2 GLC . C GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.688 ? covale ? covale4 C O4 GLC . C GLC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _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 5DUQ _atom_sites.fract_transf_matrix[1][1] 0.008921 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00211 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005065 _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] 0.018098 _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 1 501 501 NAG NAG . E 4 GLC A 1 502 601 GLC GLC . F 3 NAG B 1 501 501 NAG NAG . G 5 SO3 B 1 504 603 SO3 SO3 . H 6 HOH A 1 601 6 HOH HOH . H 6 HOH A 2 602 16 HOH HOH . H 6 HOH A 3 603 19 HOH HOH . H 6 HOH A 4 604 26 HOH HOH . H 6 HOH A 5 605 15 HOH HOH . H 6 HOH A 6 606 11 HOH HOH . H 6 HOH A 7 607 1 HOH HOH . H 6 HOH A 8 608 22 HOH HOH . H 6 HOH A 9 609 23 HOH HOH . H 6 HOH A 10 610 12 HOH HOH . H 6 HOH A 11 611 14 HOH HOH . H 6 HOH A 12 612 7 HOH HOH . H 6 HOH A 13 613 8 HOH HOH . I 6 HOH B 1 601 17 HOH HOH . I 6 HOH B 2 602 21 HOH HOH . I 6 HOH B 3 603 10 HOH HOH . I 6 HOH B 4 604 24 HOH HOH . I 6 HOH B 5 605 25 HOH HOH . I 6 HOH B 6 606 5 HOH HOH . I 6 HOH B 7 607 20 HOH HOH . I 6 HOH B 8 608 4 HOH HOH . I 6 HOH B 9 609 18 HOH HOH . I 6 HOH B 10 610 9 HOH HOH . I 6 HOH B 11 611 13 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 3 38.963 25.307 2.908 1 109.83 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . D 3 39.569 26.698 3.112 1 115.22 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . D 3 41.056 26.589 2.769 1 113.62 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . D 3 41.771 25.504 3.601 1 119.18 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . D 3 40.979 24.179 3.743 1 115.62 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . D 3 41.375 23.389 5.006 1 106.3 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . D 3 37.908 28.548 2.642 1 108.51 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . D 3 37.549 29.58 1.613 1 98.08 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . D 3 38.967 27.774 2.306 1 120.6 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . D 3 41.661 27.878 2.96 1 110.12 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . D 3 43.07 25.216 3.027 1 115.41 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . D 3 39.553 24.344 3.782 1 116.02 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . D 3 40.573 23.723 6.157 1 93.34 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . D 3 37.252 28.451 3.674 1 101.47 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #