data_1DIR # _model_server_result.job_id vvVQsXBTbN3-LWbiXkAdMQ _model_server_result.datetime_utc '2025-02-27 02:37:57' _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":"H","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 . . . H 2 -0.895 23.856 26.686 1 28.8 ? PA NAD 241 D 1 HETATM 2 O O1A NAD . . . H 2 -0.075 25.087 26.814 1 22.54 ? O1A NAD 241 D 1 HETATM 3 O O2A NAD . . . H 2 -2.203 24.233 26.094 1 29.74 ? O2A NAD 241 D 1 HETATM 4 O O5B NAD . . . H 2 -1.184 23.202 28.138 1 24.76 ? O5B NAD 241 D 1 HETATM 5 C C5B NAD . . . H 2 -0.035 22.803 28.911 1 24.28 ? C5B NAD 241 D 1 HETATM 6 C C4B NAD . . . H 2 -0.385 22.772 30.407 1 27.28 ? C4B NAD 241 D 1 HETATM 7 O O4B NAD . . . H 2 0.749 22.408 31.161 1 27.29 ? O4B NAD 241 D 1 HETATM 8 C C3B NAD . . . H 2 -0.824 24.136 30.947 1 28.23 ? C3B NAD 241 D 1 HETATM 9 O O3B NAD . . . H 2 -1.885 23.92 31.885 1 32.33 ? O3B NAD 241 D 1 HETATM 10 C C2B NAD . . . H 2 0.339 24.613 31.743 1 25.36 ? C2B NAD 241 D 1 HETATM 11 O O2B NAD . . . H 2 -0.15 25.405 32.831 1 22.36 ? O2B NAD 241 D 1 HETATM 12 C C1B NAD . . . H 2 0.842 23.287 32.258 1 24.07 ? C1B NAD 241 D 1 HETATM 13 N N9A NAD . . . H 2 2.154 23.263 32.588 1 24.35 ? N9A NAD 241 D 1 HETATM 14 C C8A NAD . . . H 2 2.933 24.409 32.352 1 23.53 ? C8A NAD 241 D 1 HETATM 15 N N7A NAD . . . H 2 3.695 24.655 33.509 1 25.02 ? N7A NAD 241 D 1 HETATM 16 C C5A NAD . . . H 2 3.288 23.675 34.397 1 26.67 ? C5A NAD 241 D 1 HETATM 17 C C6A NAD . . . H 2 3.759 23.461 35.635 1 23.27 ? C6A NAD 241 D 1 HETATM 18 N N6A NAD . . . H 2 4.792 24.229 36.115 1 24.18 ? N6A NAD 241 D 1 HETATM 19 N N1A NAD . . . H 2 3.261 22.438 36.393 1 24.27 ? N1A NAD 241 D 1 HETATM 20 C C2A NAD . . . H 2 2.269 21.619 35.832 1 24.87 ? C2A NAD 241 D 1 HETATM 21 N N3A NAD . . . H 2 1.824 21.839 34.538 1 26.37 ? N3A NAD 241 D 1 HETATM 22 C C4A NAD . . . H 2 2.396 22.896 33.878 1 25.91 ? C4A NAD 241 D 1 HETATM 23 O O3 NAD . . . H 2 -0.08 22.707 25.779 1 29.29 ? O3 NAD 241 D 1 HETATM 24 P PN NAD . . . H 2 -0.853 21.675 24.706 1 31.88 ? PN NAD 241 D 1 HETATM 25 O O1N NAD . . . H 2 -1.145 22.501 23.519 1 24.82 ? O1N NAD 241 D 1 HETATM 26 O O2N NAD . . . H 2 -2.131 21.145 25.234 1 30.94 ? O2N NAD 241 D 1 HETATM 27 O O5D NAD . . . H 2 -0.04 20.325 24.257 1 31.67 ? O5D NAD 241 D 1 HETATM 28 C C5D NAD . . . H 2 0.553 19.535 25.304 1 33.33 ? C5D NAD 241 D 1 HETATM 29 C C4D NAD . . . H 2 2.085 19.412 25.105 1 36.62 ? C4D NAD 241 D 1 HETATM 30 O O4D NAD . . . H 2 2.406 18.97 23.752 1 37.81 ? O4D NAD 241 D 1 HETATM 31 C C3D NAD . . . H 2 2.781 20.766 25.328 1 38.85 ? C3D NAD 241 D 1 HETATM 32 O O3D NAD . . . H 2 3.913 20.583 26.175 1 38.56 ? O3D NAD 241 D 1 HETATM 33 C C2D NAD . . . H 2 3.198 21.223 23.928 1 37.38 ? C2D NAD 241 D 1 HETATM 34 O O2D NAD . . . H 2 4.403 21.979 23.937 1 34.92 ? O2D NAD 241 D 1 HETATM 35 C C1D NAD . . . H 2 3.35 19.91 23.139 1 37.21 ? C1D NAD 241 D 1 HETATM 36 N N1N NAD . . . H 2 3.024 20.072 21.779 1 38.15 ? N1N NAD 241 D 1 HETATM 37 C C2N NAD . . . H 2 1.879 20.8 21.475 1 37.47 ? C2N NAD 241 D 1 HETATM 38 C C3N NAD . . . H 2 1.757 21.382 20.237 1 35.93 ? C3N NAD 241 D 1 HETATM 39 C C7N NAD . . . H 2 0.63 22.163 19.904 1 33.18 ? C7N NAD 241 D 1 HETATM 40 O O7N NAD . . . H 2 -0.517 22.132 20.647 1 30.62 ? O7N NAD 241 D 1 HETATM 41 N N7N NAD . . . H 2 0.636 22.985 18.821 1 33.11 ? N7N NAD 241 D 1 HETATM 42 C C4N NAD . . . H 2 2.797 21.2 19.334 1 39.21 ? C4N NAD 241 D 1 HETATM 43 C C5N NAD . . . H 2 3.931 20.483 19.668 1 37.92 ? C5N NAD 241 D 1 HETATM 44 C C6N NAD . . . H 2 4.054 19.923 20.907 1 36.46 ? C6N NAD 241 D 1 HETATM 45 H HO3A NAD . . . H 2 -1.543 23.948 32.774 1 0 ? HO3A NAD 241 D 1 HETATM 46 H HO2A NAD . . . H 2 0.388 26.192 32.921 1 0 ? HO2A NAD 241 D 1 HETATM 47 H H61A NAD . . . H 2 5.187 24.956 35.534 1 0 ? H61A NAD 241 D 1 HETATM 48 H H62A NAD . . . H 2 5.122 24.099 37.059 1 0 ? H62A NAD 241 D 1 HETATM 49 H HO3N NAD . . . H 2 4.416 19.817 25.889 1 0 ? HO3N NAD 241 D 1 HETATM 50 H HO2N NAD . . . H 2 5.152 21.38 23.995 1 0 ? HO2N NAD 241 D 1 HETATM 51 H H71N NAD . . . H 2 1.449 23.037 18.223 1 0 ? H71N NAD 241 D 1 HETATM 52 H H72N NAD . . . H 2 -0.199 23.488 18.57 1 0 ? H72N NAD 241 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 442 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 52 #