data_5WZR # _model_server_result.job_id uHWL9wKi5h9RchWHtzBHnw _model_server_result.datetime_utc '2024-11-16 12:26:16' _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 5wzr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 5WZR # _exptl.entry_id 5WZR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 204.224 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide _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 5WZR _cell.length_a 64.628 _cell.length_b 128.478 _cell.length_c 176.885 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WZR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 G N N # 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 metalc ? metalc1 A OD1 ASP 322 A ASP 322 1_555 E CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc2 A OD2 ASP 322 A ASP 322 1_555 E CA CA . A CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc3 A SG CYS 407 A CYS 407 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc4 A SG CYS 445 A CYS 445 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 A O HIS 450 A HIS 450 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc6 A ND1 HIS 450 A HIS 450 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc7 E CA CA . A CA 703 1_555 I O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc8 B OD1 ASP 322 B ASP 322 1_555 H CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc9 B OD2 ASP 322 B ASP 322 1_555 H CA CA . B CA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc10 B SG CYS 407 B CYS 407 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc11 B SG CYS 445 B CYS 445 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc12 B O HIS 450 B HIS 450 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc13 B ND1 HIS 450 B HIS 450 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc14 H CA CA . B CA 703 1_555 J O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc15 H CA CA . B CA 703 1_555 J O HOH . B HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? # _chem_comp.formula 'C8 H16 N2 O4' _chem_comp.formula_weight 204.224 _chem_comp.id DJN _chem_comp.mon_nstd_flag . _chem_comp.name N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-acetamido-1,2-dideoxy-D-galacto-nojirimycin;DGJNAc # 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 O4 C4 DJN sing 83 n n O3 C3 DJN sing 84 n n C4 C3 DJN sing 85 n n C4 C5 DJN sing 86 n n C6 C5 DJN sing 87 n n C6 O6 DJN sing 88 n n C3 C2 DJN sing 89 n n C5 N5 DJN sing 90 n n O7 C7 DJN doub 91 n n C2 N2 DJN sing 92 n n C2 C1 DJN sing 93 n n N5 C1 DJN sing 94 n n C7 N2 DJN sing 95 n n C7 C8 DJN sing 96 n n C8 H1 DJN sing 97 n n C8 H2 DJN sing 98 n n C8 H3 DJN sing 99 n n N2 H4 DJN sing 100 n n C2 H5 DJN sing 101 n n C3 H6 DJN sing 102 n n O3 H7 DJN sing 103 n n C4 H8 DJN sing 104 n n O4 H9 DJN sing 105 n n C5 H10 DJN sing 106 n n C6 H11 DJN sing 107 n n C6 H12 DJN sing 108 n n O6 H13 DJN sing 109 n n N5 H14 DJN sing 110 n n C1 H16 DJN sing 111 n n C1 H17 DJN sing 112 n n # _atom_sites.entry_id 5WZR _atom_sites.fract_transf_matrix[1][1] 0.015473 _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] 0.007783 _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] 0.005653 _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 C 2 ZN A 1 701 3 ZN ZN . D 3 DJN A 1 702 1 DJN NDJ . E 4 CA A 1 703 1 CA CA . F 2 ZN B 1 701 4 ZN ZN . G 3 DJN B 1 702 1 DJN NDJ . H 4 CA B 1 703 2 CA CA . I 5 HOH A 1 801 2 HOH HOH . I 5 HOH A 2 802 1 HOH HOH . J 5 HOH B 1 801 4 HOH HOH . J 5 HOH B 2 802 3 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 O O7 DJN . . . D 3 18.505 3.374 57.165 1 58.71 ? O7 DJN 702 A 1 HETATM 2 C C7 DJN . . . D 3 18.321 4.572 57.371 1 58.43 ? C7 DJN 702 A 1 HETATM 3 C C8 DJN . . . D 3 16.888 5.065 57.362 1 59.86 ? C8 DJN 702 A 1 HETATM 4 N N2 DJN . . . D 3 19.289 5.517 57.602 1 53.98 ? N2 DJN 702 A 1 HETATM 5 C C2 DJN . . . D 3 20.739 5.199 57.659 1 50.91 ? C2 DJN 702 A 1 HETATM 6 C C3 DJN . . . D 3 21.341 5.589 58.991 1 46.41 ? C3 DJN 702 A 1 HETATM 7 O O3 DJN . . . D 3 20.628 4.968 60.037 1 46.16 ? O3 DJN 702 A 1 HETATM 8 C C4 DJN . . . D 3 22.799 5.145 59.053 1 46.63 ? C4 DJN 702 A 1 HETATM 9 O O4 DJN . . . D 3 22.916 3.678 58.959 1 43.99 ? O4 DJN 702 A 1 HETATM 10 C C5 DJN . . . D 3 23.526 5.867 57.921 1 45.44 ? C5 DJN 702 A 1 HETATM 11 C C6 DJN . . . D 3 24.941 5.393 57.782 1 46.33 ? C6 DJN 702 A 1 HETATM 12 O O6 DJN . . . D 3 25.392 5.873 56.486 1 50.86 ? O6 DJN 702 A 1 HETATM 13 N N5 DJN . . . D 3 22.883 5.604 56.642 1 47.87 ? N5 DJN 702 A 1 HETATM 14 C C1 DJN . . . D 3 21.446 5.946 56.604 1 50.23 ? C1 DJN 702 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #