data_1DIR # _model_server_result.job_id amTVgT4bNTv-KchewezPbg _model_server_result.datetime_utc '2025-02-27 02:16:28' _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 1dir # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":241}' # _entry.id 1DIR # _exptl.entry_id 1DIR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.1 _cell.angle_gamma 90 _cell.entry_id 1DIR _cell.length_a 222.2 _cell.length_b 46.5 _cell.length_c 94.3 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DIR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 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 1 1 C,D,G,H,K,L 2 1 A,B,E,F,I,J 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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PA O1A NAD doub 237 n n PA O2A NAD sing 238 n n PA O5B NAD sing 239 n n PA O3 NAD sing 240 n n O2A HOA2 NAD sing 241 n n O5B C5B NAD sing 242 n n C5B C4B NAD sing 243 n n C5B H51A NAD sing 244 n n C5B H52A NAD sing 245 n n C4B O4B NAD sing 246 n n C4B C3B NAD sing 247 n n C4B H4B NAD sing 248 n n O4B C1B NAD sing 249 n n C3B O3B NAD sing 250 n n C3B C2B NAD sing 251 n n C3B H3B NAD sing 252 n n O3B HO3A NAD sing 253 n n C2B O2B NAD sing 254 n n C2B C1B NAD sing 255 n n C2B H2B NAD sing 256 n n O2B HO2A NAD sing 257 n n C1B N9A NAD sing 258 n n C1B H1B NAD sing 259 n n N9A C8A NAD sing 260 n y N9A C4A NAD sing 261 n y C8A N7A NAD doub 262 n y C8A H8A NAD sing 263 n n N7A C5A NAD sing 264 n y C5A C6A NAD sing 265 n y C5A C4A NAD doub 266 n y C6A N6A NAD sing 267 n n C6A N1A NAD doub 268 n y N6A H61A NAD sing 269 n n N6A H62A NAD sing 270 n n N1A C2A NAD sing 271 n y C2A N3A NAD doub 272 n y C2A H2A NAD sing 273 n n N3A C4A NAD sing 274 n y O3 PN NAD sing 275 n n PN O1N NAD doub 276 n n PN O2N NAD sing 277 n n PN O5D NAD sing 278 n n O5D C5D NAD sing 279 n n C5D C4D NAD sing 280 n n C5D H51N NAD sing 281 n n C5D H52N NAD sing 282 n n C4D O4D NAD sing 283 n n C4D C3D NAD sing 284 n n C4D H4D NAD sing 285 n n O4D C1D NAD sing 286 n n C3D O3D NAD sing 287 n n C3D C2D NAD sing 288 n n C3D H3D NAD sing 289 n n O3D HO3N NAD sing 290 n n C2D O2D NAD sing 291 n n C2D C1D NAD sing 292 n n C2D H2D NAD sing 293 n n O2D HO2N NAD sing 294 n n C1D N1N NAD sing 295 n n C1D H1D NAD sing 296 n n N1N C2N NAD sing 297 n y N1N C6N NAD doub 298 n y C2N C3N NAD doub 299 n y C2N H2N NAD sing 300 n n C3N C7N NAD sing 301 n n C3N C4N NAD sing 302 n y C7N O7N NAD doub 303 n n C7N N7N NAD sing 304 n n N7N H71N NAD sing 305 n n N7N H72N NAD sing 306 n n C4N C5N NAD doub 307 n y C4N H4N NAD sing 308 n n C5N C6N NAD sing 309 n y C5N H5N NAD sing 310 n n C6N H6N NAD sing 311 n n # _atom_sites.entry_id 1DIR _atom_sites.fract_transf_matrix[1][1] 0.0045 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000883 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021505 _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] 0.010807 _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 E 2 NAD A 1 241 241 NAD NAD . F 2 NAD B 1 241 241 NAD NAD . G 2 NAD C 1 241 241 NAD NAD . H 2 NAD D 1 241 241 NAD NAD . I 3 HOH A 1 953 953 HOH HOH . I 3 HOH A 2 954 964 HOH HOH . I 3 HOH A 3 955 965 HOH HOH . I 3 HOH A 4 956 967 HOH HOH . I 3 HOH A 5 957 968 HOH HOH . I 3 HOH A 6 958 969 HOH HOH . I 3 HOH A 7 959 978 HOH HOH . I 3 HOH A 8 960 979 HOH HOH . I 3 HOH A 9 961 988 HOH HOH . I 3 HOH A 10 962 991 HOH HOH . I 3 HOH A 11 963 992 HOH HOH . I 3 HOH A 12 964 995 HOH HOH . I 3 HOH A 13 965 4 HOH HOH . I 3 HOH A 14 966 5 HOH HOH . I 3 HOH A 15 967 10 HOH HOH . I 3 HOH A 16 968 15 HOH HOH . I 3 HOH A 17 969 16 HOH HOH . I 3 HOH A 18 970 19 HOH HOH . I 3 HOH A 19 971 25 HOH HOH . I 3 HOH A 20 972 26 HOH HOH . I 3 HOH A 21 973 29 HOH HOH . I 3 HOH A 22 974 39 HOH HOH . I 3 HOH A 23 975 41 HOH HOH . I 3 HOH A 24 976 46 HOH HOH . I 3 HOH A 25 977 47 HOH HOH . I 3 HOH A 26 978 49 HOH HOH . I 3 HOH A 27 979 55 HOH HOH . I 3 HOH A 28 980 57 HOH HOH . I 3 HOH A 29 981 60 HOH HOH . I 3 HOH A 30 982 77 HOH HOH . I 3 HOH A 31 983 78 HOH HOH . I 3 HOH A 32 984 81 HOH HOH . I 3 HOH A 33 985 85 HOH HOH . I 3 HOH A 34 986 90 HOH HOH . I 3 HOH A 35 987 99 HOH HOH . I 3 HOH A 36 988 103 HOH HOH . I 3 HOH A 37 989 107 HOH HOH . I 3 HOH A 38 990 110 HOH HOH . J 3 HOH B 1 954 954 HOH HOH . J 3 HOH B 2 955 959 HOH HOH . J 3 HOH B 3 956 962 HOH HOH . J 3 HOH B 4 957 970 HOH HOH . J 3 HOH B 5 958 976 HOH HOH . J 3 HOH B 6 959 981 HOH HOH . J 3 HOH B 7 960 983 HOH HOH . J 3 HOH B 8 961 984 HOH HOH . J 3 HOH B 9 962 986 HOH HOH . J 3 HOH B 10 963 996 HOH HOH . J 3 HOH B 11 964 997 HOH HOH . J 3 HOH B 12 965 998 HOH HOH . J 3 HOH B 13 966 1000 HOH HOH . J 3 HOH B 14 967 2 HOH HOH . J 3 HOH B 15 968 9 HOH HOH . J 3 HOH B 16 969 11 HOH HOH . J 3 HOH B 17 970 12 HOH HOH . J 3 HOH B 18 971 14 HOH HOH . J 3 HOH B 19 972 21 HOH HOH . J 3 HOH B 20 973 30 HOH HOH . J 3 HOH B 21 974 31 HOH HOH . J 3 HOH B 22 975 38 HOH HOH . J 3 HOH B 23 976 44 HOH HOH . J 3 HOH B 24 977 45 HOH HOH . J 3 HOH B 25 978 48 HOH HOH . J 3 HOH B 26 979 52 HOH HOH . J 3 HOH B 27 980 59 HOH HOH . J 3 HOH B 28 981 62 HOH HOH . J 3 HOH B 29 982 63 HOH HOH . J 3 HOH B 30 983 68 HOH HOH . J 3 HOH B 31 984 69 HOH HOH . J 3 HOH B 32 985 92 HOH HOH . J 3 HOH B 33 986 95 HOH HOH . J 3 HOH B 34 987 97 HOH HOH . J 3 HOH B 35 988 102 HOH HOH . J 3 HOH B 36 989 105 HOH HOH . K 3 HOH C 1 956 956 HOH HOH . K 3 HOH C 2 957 958 HOH HOH . K 3 HOH C 3 958 963 HOH HOH . K 3 HOH C 4 959 966 HOH HOH . K 3 HOH C 5 960 972 HOH HOH . K 3 HOH C 6 961 974 HOH HOH . K 3 HOH C 7 962 975 HOH HOH . K 3 HOH C 8 963 987 HOH HOH . K 3 HOH C 9 964 989 HOH HOH . K 3 HOH C 10 965 994 HOH HOH . K 3 HOH C 11 966 999 HOH HOH . K 3 HOH C 12 967 1 HOH HOH . K 3 HOH C 13 968 6 HOH HOH . K 3 HOH C 14 969 8 HOH HOH . K 3 HOH C 15 970 17 HOH HOH . K 3 HOH C 16 971 18 HOH HOH . K 3 HOH C 17 972 22 HOH HOH . K 3 HOH C 18 973 27 HOH HOH . K 3 HOH C 19 974 32 HOH HOH . K 3 HOH C 20 975 35 HOH HOH . K 3 HOH C 21 976 42 HOH HOH . K 3 HOH C 22 977 56 HOH HOH . K 3 HOH C 23 978 61 HOH HOH . K 3 HOH C 24 979 64 HOH HOH . K 3 HOH C 25 980 65 HOH HOH . K 3 HOH C 26 981 70 HOH HOH . K 3 HOH C 27 982 71 HOH HOH . K 3 HOH C 28 983 72 HOH HOH . K 3 HOH C 29 984 75 HOH HOH . K 3 HOH C 30 985 79 HOH HOH . K 3 HOH C 31 986 83 HOH HOH . K 3 HOH C 32 987 84 HOH HOH . K 3 HOH C 33 988 87 HOH HOH . K 3 HOH C 34 989 88 HOH HOH . K 3 HOH C 35 990 91 HOH HOH . K 3 HOH C 36 991 94 HOH HOH . K 3 HOH C 37 992 100 HOH HOH . K 3 HOH C 38 993 101 HOH HOH . K 3 HOH C 39 994 104 HOH HOH . L 3 HOH D 1 957 957 HOH HOH . L 3 HOH D 2 958 960 HOH HOH . L 3 HOH D 3 959 971 HOH HOH . L 3 HOH D 4 960 973 HOH HOH . L 3 HOH D 5 961 977 HOH HOH . L 3 HOH D 6 962 990 HOH HOH . L 3 HOH D 7 963 993 HOH HOH . L 3 HOH D 8 964 7 HOH HOH . L 3 HOH D 9 965 20 HOH HOH . L 3 HOH D 10 966 23 HOH HOH . L 3 HOH D 11 967 33 HOH HOH . L 3 HOH D 12 968 34 HOH HOH . L 3 HOH D 13 969 36 HOH HOH . L 3 HOH D 14 970 37 HOH HOH . L 3 HOH D 15 971 43 HOH HOH . L 3 HOH D 16 972 50 HOH HOH . L 3 HOH D 17 973 51 HOH HOH . L 3 HOH D 18 974 53 HOH HOH . L 3 HOH D 19 975 58 HOH HOH . L 3 HOH D 20 976 66 HOH HOH . L 3 HOH D 21 977 73 HOH HOH . L 3 HOH D 22 978 74 HOH HOH . L 3 HOH D 23 979 76 HOH HOH . L 3 HOH D 24 980 80 HOH HOH . L 3 HOH D 25 981 82 HOH HOH . L 3 HOH D 26 982 86 HOH HOH . L 3 HOH D 27 983 89 HOH HOH . L 3 HOH D 28 984 96 HOH HOH . L 3 HOH D 29 985 98 HOH HOH . L 3 HOH D 30 986 106 HOH HOH . L 3 HOH D 31 987 108 HOH HOH . L 3 HOH D 32 988 109 HOH HOH . L 3 HOH D 33 989 111 HOH HOH . L 3 HOH D 34 990 112 HOH HOH . L 3 HOH D 35 991 114 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 P PA NAD . . . E 2 77.596 21.825 -1.265 1 48 ? PA NAD 241 A 1 HETATM 2 O O1A NAD . . . E 2 77.259 20.467 -0.758 1 47.83 ? O1A NAD 241 A 1 HETATM 3 O O2A NAD . . . E 2 77.265 21.873 -2.717 1 42.63 ? O2A NAD 241 A 1 HETATM 4 O O5B NAD . . . E 2 79.242 22.019 -1.069 1 48.18 ? O5B NAD 241 A 1 HETATM 5 C C5B NAD . . . E 2 79.741 21.496 0.203 1 45.17 ? C5B NAD 241 A 1 HETATM 6 C C4B NAD . . . E 2 80.863 20.446 0.024 1 41.4 ? C4B NAD 241 A 1 HETATM 7 O O4B NAD . . . E 2 81.306 20.06 1.326 1 44.8 ? O4B NAD 241 A 1 HETATM 8 C C3B NAD . . . E 2 80.354 19.171 -0.632 1 39.26 ? C3B NAD 241 A 1 HETATM 9 O O3B NAD . . . E 2 80.948 19.065 -1.916 1 36.9 ? O3B NAD 241 A 1 HETATM 10 C C2B NAD . . . E 2 80.816 18.019 0.275 1 40.54 ? C2B NAD 241 A 1 HETATM 11 O O2B NAD . . . E 2 81.542 17.044 -0.477 1 36.46 ? O2B NAD 241 A 1 HETATM 12 C C1B NAD . . . E 2 81.74 18.684 1.296 1 43.23 ? C1B NAD 241 A 1 HETATM 13 N N9A NAD . . . E 2 81.623 18.203 2.612 1 44.31 ? N9A NAD 241 A 1 HETATM 14 C C8A NAD . . . E 2 80.627 17.298 2.994 1 45.1 ? C8A NAD 241 A 1 HETATM 15 N N7A NAD . . . E 2 81.155 16.522 4.061 1 45.49 ? N7A NAD 241 A 1 HETATM 16 C C5A NAD . . . E 2 82.442 16.947 4.195 1 43.75 ? C5A NAD 241 A 1 HETATM 17 C C6A NAD . . . E 2 83.347 16.487 5.078 1 44.72 ? C6A NAD 241 A 1 HETATM 18 N N6A NAD . . . E 2 83.021 15.501 6.015 1 41.4 ? N6A NAD 241 A 1 HETATM 19 N N1A NAD . . . E 2 84.622 17.012 5.043 1 43.41 ? N1A NAD 241 A 1 HETATM 20 C C2A NAD . . . E 2 84.909 18.037 4.126 1 42.17 ? C2A NAD 241 A 1 HETATM 21 N N3A NAD . . . E 2 83.943 18.51 3.246 1 40.67 ? N3A NAD 241 A 1 HETATM 22 C C4A NAD . . . E 2 82.731 17.9 3.34 1 43.66 ? C4A NAD 241 A 1 HETATM 23 O O3 NAD . . . E 2 76.746 22.933 -0.362 1 42.36 ? O3 NAD 241 A 1 HETATM 24 P PN NAD . . . E 2 76.353 24.409 -0.988 1 40.03 ? PN NAD 241 A 1 HETATM 25 O O1N NAD . . . E 2 75.044 24.265 -1.669 1 38.69 ? O1N NAD 241 A 1 HETATM 26 O O2N NAD . . . E 2 77.358 24.891 -1.955 1 30.55 ? O2N NAD 241 A 1 HETATM 27 O O5D NAD . . . E 2 76.149 25.513 0.194 1 39.77 ? O5D NAD 241 A 1 HETATM 28 C C5D NAD . . . E 2 77.195 25.797 1.133 1 36.99 ? C5D NAD 241 A 1 HETATM 29 C C4D NAD . . . E 2 76.621 25.91 2.553 1 40 ? C4D NAD 241 A 1 HETATM 30 O O4D NAD . . . E 2 75.35 26.662 2.617 1 40.05 ? O4D NAD 241 A 1 HETATM 31 C C3D NAD . . . E 2 76.366 24.53 3.13 1 43.07 ? C3D NAD 241 A 1 HETATM 32 O O3D NAD . . . E 2 76.75 24.591 4.51 1 43.41 ? O3D NAD 241 A 1 HETATM 33 C C2D NAD . . . E 2 74.846 24.422 2.945 1 44.02 ? C2D NAD 241 A 1 HETATM 34 O O2D NAD . . . E 2 74.225 23.464 3.795 1 41.13 ? O2D NAD 241 A 1 HETATM 35 C C1D NAD . . . E 2 74.328 25.825 3.213 1 40.74 ? C1D NAD 241 A 1 HETATM 36 N N1N NAD . . . E 2 73.09 25.995 2.589 1 40.95 ? N1N NAD 241 A 1 HETATM 37 C C2N NAD . . . E 2 72.922 25.646 1.265 1 40.14 ? C2N NAD 241 A 1 HETATM 38 C C3N NAD . . . E 2 71.698 25.926 0.677 1 42.34 ? C3N NAD 241 A 1 HETATM 39 C C7N NAD . . . E 2 71.386 25.437 -0.585 1 42.31 ? C7N NAD 241 A 1 HETATM 40 O O7N NAD . . . E 2 72.266 24.611 -1.275 1 46.75 ? O7N NAD 241 A 1 HETATM 41 N N7N NAD . . . E 2 70.199 25.763 -1.167 1 39.62 ? N7N NAD 241 A 1 HETATM 42 C C4N NAD . . . E 2 70.73 26.592 1.413 1 39.02 ? C4N NAD 241 A 1 HETATM 43 C C5N NAD . . . E 2 70.943 26.914 2.72 1 39.13 ? C5N NAD 241 A 1 HETATM 44 C C6N NAD . . . E 2 72.133 26.603 3.322 1 40.81 ? C6N NAD 241 A 1 HETATM 45 H HO3A NAD . . . E 2 80.295 18.756 -2.55 1 0 ? HO3A NAD 241 A 1 HETATM 46 H HO2A NAD . . . E 2 82.435 17.347 -0.61 1 0 ? HO2A NAD 241 A 1 HETATM 47 H H61A NAD . . . E 2 82.102 15.091 6.014 1 0 ? H61A NAD 241 A 1 HETATM 48 H H62A NAD . . . E 2 83.731 15.137 6.64 1 0 ? H62A NAD 241 A 1 HETATM 49 H HO3N NAD . . . E 2 76.616 23.726 4.883 1 0 ? HO3N NAD 241 A 1 HETATM 50 H HO2N NAD . . . E 2 73.388 23.198 3.415 1 0 ? HO2N NAD 241 A 1 HETATM 51 H H71N NAD . . . E 2 69.554 26.396 -0.711 1 0 ? H71N NAD 241 A 1 HETATM 52 H H72N NAD . . . E 2 69.876 25.232 -1.941 1 0 ? H72N NAD 241 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 405 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 52 #