data_5GQB # _model_server_result.job_id 6Eu2qeNA01jyFo9XoNaKBw _model_server_result.datetime_utc '2024-11-04 22:38:29' _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 5gqb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":610}' # _entry.id 5GQB # _exptl.entry_id 5GQB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method nat _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 5GQB _cell.length_a 49.276 _cell.length_b 114.22 _cell.length_c 123.382 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GQB _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 GCS GCS C1 O1 . O4 HO4 . sing 2 ? 2 3 2 GCS GCS C1 O1 . O4 HO4 . sing 3 ? 2 4 3 GCS GCS C1 O1 . O4 HO4 . sing 4 ? 2 5 4 GCS GCS C1 O1 . O4 HO4 . sing 5 ? 2 6 5 GCS GCS C1 O1 . O4 HO4 . sing 6 ? 2 7 6 GCS GCS C1 O1 . O4 HO4 . sing 7 ? 3 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 2 n B GCS 1 B 1 GCS L 499 GCS 2 n B GCS 2 B 2 GCS L 500 GCS 2 n B GCS 3 B 3 GCS L 501 GCS 2 n B GCS 4 B 4 GCS L 502 GCS 2 n B GCS 5 B 5 GCS L 503 GCS 2 n B GCS 6 B 6 GCS L 504 GCS 2 n B GCS 7 B 7 GCS L 505 GCS 3 n C NAG 1 C 1 NAG L 601 NAG 3 n C NAG 2 C 2 NAG L 602 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 188 A CYS 188 1_555 A SG CYS 211 A CYS 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? covale ? covale1 A ND2 ASN 391 A ASN 391 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 A ND2 ASN 456 A ASN 456 1_555 D C1 NAG . A NAG 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B O4 GCS . B GCS 1 1_555 B C1 GCS . B GCS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale4 B O4 GCS . B GCS 2 1_555 B C1 GCS . B GCS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale5 B O4 GCS . B GCS 3 1_555 B C1 GCS . B GCS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 B O4 GCS . B GCS 4 1_555 B C1 GCS . B GCS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 B O4 GCS . B GCS 5 1_555 B C1 GCS . B GCS 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 B O4 GCS . B GCS 6 1_555 B C1 GCS . B GCS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 262 n n C1 O1 NAG sing 263 n n C1 O5 NAG sing 264 n n C1 H1 NAG sing 265 n n C2 C3 NAG sing 266 n n C2 N2 NAG sing 267 n n C2 H2 NAG sing 268 n n C3 C4 NAG sing 269 n n C3 O3 NAG sing 270 n n C3 H3 NAG sing 271 n n C4 C5 NAG sing 272 n n C4 O4 NAG sing 273 n n C4 H4 NAG sing 274 n n C5 C6 NAG sing 275 n n C5 O5 NAG sing 276 n n C5 H5 NAG sing 277 n n C6 O6 NAG sing 278 n n C6 H61 NAG sing 279 n n C6 H62 NAG sing 280 n n C7 C8 NAG sing 281 n n C7 N2 NAG sing 282 n n C7 O7 NAG doub 283 n n C8 H81 NAG sing 284 n n C8 H82 NAG sing 285 n n C8 H83 NAG sing 286 n n N2 HN2 NAG sing 287 n n O1 HO1 NAG sing 288 n n O3 HO3 NAG sing 289 n n O4 HO4 NAG sing 290 n n O6 HO6 NAG sing 291 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 5GQB _atom_sites.fract_transf_matrix[1][1] 0.020294 _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] 0.008755 _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] 0.008105 _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 A 1 610 603 NAG NAG . E 5 HOH A 1 701 1 HOH HOH . E 5 HOH A 2 702 27 HOH HOH . E 5 HOH A 3 703 22 HOH HOH . E 5 HOH A 4 704 17 HOH HOH . E 5 HOH A 5 705 26 HOH HOH . E 5 HOH A 6 706 8 HOH HOH . E 5 HOH A 7 707 23 HOH HOH . E 5 HOH A 8 708 16 HOH HOH . E 5 HOH A 9 709 37 HOH HOH . E 5 HOH A 10 710 2 HOH HOH . E 5 HOH A 11 711 12 HOH HOH . E 5 HOH A 12 712 32 HOH HOH . E 5 HOH A 13 713 11 HOH HOH . E 5 HOH A 14 714 44 HOH HOH . E 5 HOH A 15 715 20 HOH HOH . E 5 HOH A 16 716 6 HOH HOH . E 5 HOH A 17 717 36 HOH HOH . E 5 HOH A 18 718 5 HOH HOH . E 5 HOH A 19 719 19 HOH HOH . E 5 HOH A 20 720 13 HOH HOH . E 5 HOH A 21 721 15 HOH HOH . E 5 HOH A 22 722 9 HOH HOH . E 5 HOH A 23 723 28 HOH HOH . E 5 HOH A 24 724 30 HOH HOH . E 5 HOH A 25 725 25 HOH HOH . E 5 HOH A 26 726 53 HOH HOH . E 5 HOH A 27 727 4 HOH HOH . E 5 HOH A 28 728 24 HOH HOH . E 5 HOH A 29 729 3 HOH HOH . E 5 HOH A 30 730 10 HOH HOH . E 5 HOH A 31 731 41 HOH HOH . E 5 HOH A 32 732 14 HOH HOH . E 5 HOH A 33 733 50 HOH HOH . E 5 HOH A 34 734 47 HOH HOH . E 5 HOH A 35 735 34 HOH HOH . E 5 HOH A 36 736 33 HOH HOH . E 5 HOH A 37 737 49 HOH HOH . E 5 HOH A 38 738 39 HOH HOH . E 5 HOH A 39 739 42 HOH HOH . E 5 HOH A 40 740 18 HOH HOH . E 5 HOH A 41 741 31 HOH HOH . E 5 HOH A 42 742 43 HOH HOH . E 5 HOH A 43 743 51 HOH HOH . E 5 HOH A 44 744 52 HOH HOH . E 5 HOH A 45 745 38 HOH HOH . E 5 HOH A 46 746 40 HOH HOH . E 5 HOH A 47 747 46 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 11.684 40.165 -0.332 1 59.09 ? C1 NAG 610 A 1 HETATM 2 C C2 NAG . . . D 4 11.874 40.275 -1.847 1 61.19 ? C2 NAG 610 A 1 HETATM 3 C C3 NAG . . . D 4 10.536 40.536 -2.541 1 68.54 ? C3 NAG 610 A 1 HETATM 4 C C4 NAG . . . D 4 9.493 39.515 -2.109 1 62.88 ? C4 NAG 610 A 1 HETATM 5 C C5 NAG . . . D 4 9.4 39.498 -0.589 1 60.14 ? C5 NAG 610 A 1 HETATM 6 C C6 NAG . . . D 4 8.445 38.451 -0.061 1 63.35 ? C6 NAG 610 A 1 HETATM 7 C C7 NAG . . . D 4 14.044 41.084 -2.667 1 70.15 ? C7 NAG 610 A 1 HETATM 8 C C8 NAG . . . D 4 14.885 42.292 -2.962 1 66.21 ? C8 NAG 610 A 1 HETATM 9 N N2 NAG . . . D 4 12.824 41.325 -2.175 1 64.62 ? N2 NAG 610 A 1 HETATM 10 O O3 NAG . . . D 4 10.706 40.477 -3.954 1 72.23 ? O3 NAG 610 A 1 HETATM 11 O O4 NAG . . . D 4 8.228 39.847 -2.675 1 60.84 ? O4 NAG 610 A 1 HETATM 12 O O5 NAG . . . D 4 10.69 39.191 -0.044 1 57.69 ? O5 NAG 610 A 1 HETATM 13 O O6 NAG . . . D 4 7.336 38.262 -0.929 1 70.74 ? O6 NAG 610 A 1 HETATM 14 O O7 NAG . . . D 4 14.452 39.944 -2.863 1 68.47 ? O7 NAG 610 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #