data_3KIF # _model_server_result.job_id u3meNiLqXZ3j6u7QaeWKKA _model_server_result.datetime_utc '2024-10-15 12:20:44' _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 3kif # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":110}' # _entry.id 3KIF # _exptl.entry_id 3KIF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 219.192 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone _entity.pdbx_number_of_molecules 9 _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 120 _cell.entry_id 3KIF _cell.length_a 80.558 _cell.length_b 80.558 _cell.length_c 170.681 _cell.Z_PDB 30 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KIF _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? decameric 10 author_defined_assembly 1 PISA pentameric 5 software_defined_assembly 2 PISA pentameric 5 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA 1 1 A,B,C,D,E,K,L,M,N,O,P,V,W,X,Y,Z 2 1 F,G,H,I,J,Q,R,S,T,U,AA,BA,CA,DA,EA 3 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 ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N # _chem_comp.formula 'C8 H13 N O6' _chem_comp.formula_weight 219.192 _chem_comp.id GDL _chem_comp.mon_nstd_flag . _chem_comp.name 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE # 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 GDL sing 70 n n C1 O1 GDL doub 71 n n C1 O5 GDL sing 72 n n C2 C3 GDL sing 73 n n C2 N2 GDL sing 74 n n C2 H2 GDL sing 75 n n C3 C4 GDL sing 76 n n C3 O3 GDL sing 77 n n C3 H3 GDL sing 78 n n C4 C5 GDL sing 79 n n C4 O4 GDL sing 80 n n C4 H4 GDL sing 81 n n C5 C6 GDL sing 82 n n C5 O5 GDL sing 83 n n C5 H5 GDL sing 84 n n C6 O6 GDL sing 85 n n C6 H61 GDL sing 86 n n C6 H62 GDL sing 87 n n C7 C8 GDL sing 88 n n C7 N2 GDL sing 89 n n C7 O7 GDL doub 90 n n C8 H81 GDL sing 91 n n C8 H82 GDL sing 92 n n C8 H83 GDL sing 93 n n N2 HN2 GDL sing 94 n n O3 HO3 GDL sing 95 n n O4 HO4 GDL sing 96 n n O6 HO6 GDL sing 97 n n # _atom_sites.entry_id 3KIF _atom_sites.fract_transf_matrix[1][1] 0.012413 _atom_sites.fract_transf_matrix[1][2] 0.007167 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014334 _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] 0.005859 _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 K 2 GDL A 1 110 110 GDL NDG . L 2 GDL B 1 110 110 GDL NDG . M 2 GDL D 1 241 241 GDL NDG . N 2 GDL D 1 238 238 GDL NDG . O 2 GDL E 1 110 110 GDL NDG . P 3 SO4 E 1 107 1 SO4 SO4 . Q 2 GDL F 1 110 110 GDL NDG . R 2 GDL G 1 110 110 GDL NDG . S 2 GDL I 1 110 110 GDL NDG . T 2 GDL J 1 110 110 GDL NDG . U 3 SO4 J 1 107 2 SO4 SO4 . V 4 HOH A 1 107 2 HOH HOH . V 4 HOH A 2 108 35 HOH HOH . W 4 HOH B 1 107 34 HOH HOH . W 4 HOH B 2 108 58 HOH HOH . W 4 HOH B 3 109 8 HOH HOH . X 4 HOH C 1 107 4 HOH HOH . X 4 HOH C 2 108 44 HOH HOH . Y 4 HOH D 1 107 10 HOH HOH . Y 4 HOH D 2 109 24 HOH HOH . Y 4 HOH D 3 110 26 HOH HOH . Y 4 HOH D 4 111 28 HOH HOH . Y 4 HOH D 5 112 39 HOH HOH . Y 4 HOH D 6 113 50 HOH HOH . Y 4 HOH D 7 114 69 HOH HOH . Z 4 HOH E 1 108 12 HOH HOH . Z 4 HOH E 2 109 47 HOH HOH . Z 4 HOH E 3 111 62 HOH HOH . AA 4 HOH F 1 107 37 HOH HOH . AA 4 HOH F 2 108 53 HOH HOH . AA 4 HOH F 3 109 75 HOH HOH . BA 4 HOH G 1 107 45 HOH HOH . BA 4 HOH G 2 108 13 HOH HOH . BA 4 HOH G 3 109 56 HOH HOH . BA 4 HOH G 4 111 65 HOH HOH . BA 4 HOH G 5 112 73 HOH HOH . BA 4 HOH G 6 113 54 HOH HOH . CA 4 HOH H 1 107 7 HOH HOH . CA 4 HOH H 2 108 74 HOH HOH . CA 4 HOH H 3 109 77 HOH HOH . DA 4 HOH I 1 108 9 HOH HOH . DA 4 HOH I 2 109 15 HOH HOH . DA 4 HOH I 3 111 23 HOH HOH . DA 4 HOH I 4 112 25 HOH HOH . DA 4 HOH I 5 113 27 HOH HOH . EA 4 HOH J 1 108 5 HOH HOH . EA 4 HOH J 2 109 19 HOH HOH . EA 4 HOH J 3 111 20 HOH HOH . EA 4 HOH J 4 112 21 HOH HOH . EA 4 HOH J 5 113 33 HOH HOH . EA 4 HOH J 6 114 36 HOH HOH . EA 4 HOH J 7 115 38 HOH HOH . EA 4 HOH J 8 116 57 HOH HOH . EA 4 HOH J 9 117 64 HOH HOH . EA 4 HOH J 10 118 67 HOH HOH . EA 4 HOH J 11 119 78 HOH HOH . EA 4 HOH J 12 120 79 HOH HOH . EA 4 HOH J 13 121 80 HOH HOH . EA 4 HOH J 14 122 81 HOH HOH . EA 4 HOH J 15 123 82 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 GDL . . . T 2 -52.29 -65.787 -2.9 1 54.5 ? C1 GDL 110 J 1 HETATM 2 C C2 GDL . . . T 2 -51.6 -67.034 -3.098 1 54.2 ? C2 GDL 110 J 1 HETATM 3 C C3 GDL . . . T 2 -51.065 -67.009 -4.538 1 52.38 ? C3 GDL 110 J 1 HETATM 4 C C4 GDL . . . T 2 -51.418 -65.889 -5.533 1 55.46 ? C4 GDL 110 J 1 HETATM 5 C C5 GDL . . . T 2 -52.139 -64.661 -4.857 1 54.07 ? C5 GDL 110 J 1 HETATM 6 C C6 GDL . . . T 2 -53.146 -63.733 -5.524 1 50.5 ? C6 GDL 110 J 1 HETATM 7 C C7 GDL . . . T 2 -49.394 -67.131 -2.195 1 52.7 ? C7 GDL 110 J 1 HETATM 8 C C8 GDL . . . T 2 -48.544 -66.795 -0.987 1 46.84 ? C8 GDL 110 J 1 HETATM 9 N N2 GDL . . . T 2 -50.636 -66.789 -2.056 1 53.93 ? N2 GDL 110 J 1 HETATM 10 O O1 GDL . . . T 2 -52.122 -65.225 -1.85 1 52.64 ? O1 GDL 110 J 1 HETATM 11 O O3 GDL . . . T 2 -51.767 -67.996 -5.253 1 52.52 ? O3 GDL 110 J 1 HETATM 12 O O4 GDL . . . T 2 -50.226 -65.762 -6.436 1 55.17 ? O4 GDL 110 J 1 HETATM 13 O O5 GDL . . . T 2 -53.061 -65.299 -4.017 1 54.18 ? O5 GDL 110 J 1 HETATM 14 O O6 GDL . . . T 2 -54.427 -64.388 -5.353 1 49.08 ? O6 GDL 110 J 1 HETATM 15 O O7 GDL . . . T 2 -49.1 -67.687 -3.259 1 52.05 ? O7 GDL 110 J 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #