data_6NKK # _model_server_result.job_id G-VinBxJm_DdfEX8FIZX9Q _model_server_result.datetime_utc '2024-11-23 03:56:32' _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 6nkk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":801}' # _entry.id 6NKK # _exptl.entry_id 6NKK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.96 _cell.angle_gamma 90 _cell.entry_id 6NKK _cell.length_a 209.586 _cell.length_b 117.248 _cell.length_c 64.809 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NKK _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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,G,H,I,J,K,L,M,N,S,T,U,V 1 1 E,O,P,W 2 1,3 F,Q,R 2 2,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_545 x,y-1,z 1 0 0 0 1 0 0 0 1 0 -117.248 0 3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -19.984047 0 61.650988 4 'crystal symmetry operation' 2_546 -x,y-1,-z+1 -1 0 0 0 1 0 0 0 -1 -19.984047 -117.248 61.650988 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 NAP doub 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 6NKK _atom_sites.fract_transf_matrix[1][1] 0.004771 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001546 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008529 _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] 0.01622 _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 G 2 NAP A 1 801 801 NAP NAP . H 3 PM7 A 1 802 901 PM7 PM7 . I 2 NAP B 1 801 801 NAP NAP . J 3 PM7 B 1 802 901 PM7 PM7 . K 2 NAP C 1 801 801 NAP NAP . L 3 PM7 C 1 802 901 PM7 PM7 . M 2 NAP D 1 801 801 NAP NAP . N 3 PM7 D 1 802 901 PM7 PM7 . O 2 NAP E 1 801 801 NAP NAP . P 3 PM7 E 1 802 901 PM7 PM7 . Q 2 NAP F 1 801 801 NAP NAP . R 3 PM7 F 1 802 901 PM7 PM7 . S 4 HOH A 1 901 53 HOH HOH . S 4 HOH A 2 902 15 HOH HOH . S 4 HOH A 3 903 58 HOH HOH . S 4 HOH A 4 904 33 HOH HOH . S 4 HOH A 5 905 34 HOH HOH . S 4 HOH A 6 906 64 HOH HOH . S 4 HOH A 7 907 60 HOH HOH . S 4 HOH A 8 908 107 HOH HOH . S 4 HOH A 9 909 37 HOH HOH . S 4 HOH A 10 910 76 HOH HOH . S 4 HOH A 11 911 31 HOH HOH . S 4 HOH A 12 912 6 HOH HOH . S 4 HOH A 13 913 12 HOH HOH . S 4 HOH A 14 914 92 HOH HOH . S 4 HOH A 15 915 24 HOH HOH . S 4 HOH A 16 916 19 HOH HOH . S 4 HOH A 17 917 23 HOH HOH . S 4 HOH A 18 918 103 HOH HOH . S 4 HOH A 19 919 20 HOH HOH . S 4 HOH A 20 920 59 HOH HOH . S 4 HOH A 21 921 32 HOH HOH . S 4 HOH A 22 922 77 HOH HOH . S 4 HOH A 23 923 26 HOH HOH . S 4 HOH A 24 924 38 HOH HOH . S 4 HOH A 25 925 96 HOH HOH . S 4 HOH A 26 926 7 HOH HOH . S 4 HOH A 27 927 83 HOH HOH . S 4 HOH A 28 928 25 HOH HOH . S 4 HOH A 29 929 87 HOH HOH . S 4 HOH A 30 930 106 HOH HOH . S 4 HOH A 31 931 100 HOH HOH . S 4 HOH A 32 932 78 HOH HOH . T 4 HOH B 1 901 14 HOH HOH . T 4 HOH B 2 902 94 HOH HOH . T 4 HOH B 3 903 97 HOH HOH . T 4 HOH B 4 904 108 HOH HOH . T 4 HOH B 5 905 4 HOH HOH . T 4 HOH B 6 906 51 HOH HOH . T 4 HOH B 7 907 70 HOH HOH . T 4 HOH B 8 908 81 HOH HOH . T 4 HOH B 9 909 28 HOH HOH . T 4 HOH B 10 910 13 HOH HOH . T 4 HOH B 11 911 30 HOH HOH . T 4 HOH B 12 912 109 HOH HOH . T 4 HOH B 13 913 18 HOH HOH . T 4 HOH B 14 914 52 HOH HOH . T 4 HOH B 15 915 65 HOH HOH . T 4 HOH B 16 916 72 HOH HOH . T 4 HOH B 17 917 27 HOH HOH . T 4 HOH B 18 918 49 HOH HOH . T 4 HOH B 19 919 68 HOH HOH . T 4 HOH B 20 920 67 HOH HOH . T 4 HOH B 21 921 3 HOH HOH . T 4 HOH B 22 922 75 HOH HOH . T 4 HOH B 23 923 1 HOH HOH . T 4 HOH B 24 924 48 HOH HOH . T 4 HOH B 25 925 50 HOH HOH . T 4 HOH B 26 926 71 HOH HOH . T 4 HOH B 27 927 66 HOH HOH . T 4 HOH B 28 928 29 HOH HOH . T 4 HOH B 29 929 95 HOH HOH . T 4 HOH B 30 930 69 HOH HOH . T 4 HOH B 31 931 73 HOH HOH . T 4 HOH B 32 932 74 HOH HOH . T 4 HOH B 33 933 5 HOH HOH . T 4 HOH B 34 934 93 HOH HOH . T 4 HOH B 35 935 101 HOH HOH . T 4 HOH B 36 936 91 HOH HOH . U 4 HOH C 1 901 45 HOH HOH . U 4 HOH C 2 902 98 HOH HOH . U 4 HOH C 3 903 10 HOH HOH . U 4 HOH C 4 904 47 HOH HOH . U 4 HOH C 5 905 42 HOH HOH . U 4 HOH C 6 906 89 HOH HOH . U 4 HOH C 7 907 57 HOH HOH . U 4 HOH C 8 908 8 HOH HOH . U 4 HOH C 9 909 56 HOH HOH . U 4 HOH C 10 910 102 HOH HOH . U 4 HOH C 11 911 88 HOH HOH . U 4 HOH C 12 912 105 HOH HOH . U 4 HOH C 13 913 9 HOH HOH . U 4 HOH C 14 914 2 HOH HOH . U 4 HOH C 15 915 90 HOH HOH . U 4 HOH C 16 916 46 HOH HOH . U 4 HOH C 17 917 16 HOH HOH . U 4 HOH C 18 918 17 HOH HOH . U 4 HOH C 19 919 85 HOH HOH . U 4 HOH C 20 920 43 HOH HOH . U 4 HOH C 21 921 44 HOH HOH . U 4 HOH C 22 922 84 HOH HOH . V 4 HOH D 1 901 35 HOH HOH . V 4 HOH D 2 902 41 HOH HOH . V 4 HOH D 3 903 21 HOH HOH . V 4 HOH D 4 904 39 HOH HOH . V 4 HOH D 5 905 99 HOH HOH . V 4 HOH D 6 906 86 HOH HOH . V 4 HOH D 7 907 22 HOH HOH . V 4 HOH D 8 908 82 HOH HOH . V 4 HOH D 9 909 104 HOH HOH . V 4 HOH D 10 910 36 HOH HOH . V 4 HOH D 11 911 63 HOH HOH . V 4 HOH D 12 912 80 HOH HOH . V 4 HOH D 13 913 54 HOH HOH . V 4 HOH D 14 914 40 HOH HOH . V 4 HOH D 15 915 79 HOH HOH . V 4 HOH D 16 916 62 HOH HOH . V 4 HOH D 17 917 61 HOH HOH . V 4 HOH D 18 918 55 HOH HOH . W 4 HOH E 1 901 11 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 NAP . . . M 2 33.091 46.002 65.451 1 61.9 ? PA NAP 801 D 1 HETATM 2 O O1A NAP . . . M 2 32.532 45.388 66.712 1 61.77 -1 O1A NAP 801 D 1 HETATM 3 O O2A NAP . . . M 2 33.842 47.267 65.787 1 68.24 ? O2A NAP 801 D 1 HETATM 4 O O5B NAP . . . M 2 34.118 44.938 64.721 1 60.52 ? O5B NAP 801 D 1 HETATM 5 C C5B NAP . . . M 2 35.413 45.393 64.441 1 63.41 ? C5B NAP 801 D 1 HETATM 6 C C4B NAP . . . M 2 36.453 44.272 64.69 1 68.27 ? C4B NAP 801 D 1 HETATM 7 O O4B NAP . . . M 2 37.551 44.502 64.016 1 71.99 ? O4B NAP 801 D 1 HETATM 8 C C3B NAP . . . M 2 36.87 44.397 66.162 1 73.04 ? C3B NAP 801 D 1 HETATM 9 O O3B NAP . . . M 2 37.409 43.238 66.618 1 74.77 ? O3B NAP 801 D 1 HETATM 10 C C2B NAP . . . M 2 37.944 45.491 66.097 1 73.59 ? C2B NAP 801 D 1 HETATM 11 O O2B NAP . . . M 2 38.713 45.434 67.379 1 75.29 ? O2B NAP 801 D 1 HETATM 12 C C1B NAP . . . M 2 38.634 45.159 65.035 1 72.1 ? C1B NAP 801 D 1 HETATM 13 N N9A NAP . . . M 2 39.24 46.324 64.431 1 72.67 ? N9A NAP 801 D 1 HETATM 14 C C8A NAP . . . M 2 38.812 47.558 64.145 1 71.55 ? C8A NAP 801 D 1 HETATM 15 N N7A NAP . . . M 2 39.821 48.229 63.582 1 73.33 ? N7A NAP 801 D 1 HETATM 16 C C5A NAP . . . M 2 40.88 47.411 63.515 1 73.6 ? C5A NAP 801 D 1 HETATM 17 C C6A NAP . . . M 2 42.158 47.592 63.033 1 74.44 ? C6A NAP 801 D 1 HETATM 18 N N6A NAP . . . M 2 42.871 48.695 62.411 1 76.24 ? N6A NAP 801 D 1 HETATM 19 N N1A NAP . . . M 2 43.036 46.605 63.076 1 76.94 ? N1A NAP 801 D 1 HETATM 20 C C2A NAP . . . M 2 42.676 45.413 63.607 1 77.71 ? C2A NAP 801 D 1 HETATM 21 N N3A NAP . . . M 2 41.422 45.231 64.084 1 77.15 ? N3A NAP 801 D 1 HETATM 22 C C4A NAP . . . M 2 40.524 46.234 64.037 1 74.49 ? C4A NAP 801 D 1 HETATM 23 O O3 NAP . . . M 2 31.85 46.368 64.43 1 66.26 ? O3 NAP 801 D 1 HETATM 24 P PN NAP . . . M 2 30.855 45.272 63.711 1 59.71 ? PN NAP 801 D 1 HETATM 25 O O1N NAP . . . M 2 29.437 45.788 63.775 1 62.52 -1 O1N NAP 801 D 1 HETATM 26 O O2N NAP . . . M 2 30.957 43.943 64.419 1 66 ? O2N NAP 801 D 1 HETATM 27 O O5D NAP . . . M 2 31.306 45.106 62.136 1 53.29 ? O5D NAP 801 D 1 HETATM 28 C C5D NAP . . . M 2 31.782 43.877 61.668 1 47.64 ? C5D NAP 801 D 1 HETATM 29 C C4D NAP . . . M 2 31.827 43.9 60.114 1 49.92 ? C4D NAP 801 D 1 HETATM 30 O O4D NAP . . . M 2 30.619 43.861 59.607 1 54.5 ? O4D NAP 801 D 1 HETATM 31 C C3D NAP . . . M 2 32.452 45.22 59.61 1 48.57 ? C3D NAP 801 D 1 HETATM 32 O O3D NAP . . . M 2 33.237 44.98 58.529 1 42.73 ? O3D NAP 801 D 1 HETATM 33 C C2D NAP . . . M 2 31.244 46.071 59.186 1 52.88 ? C2D NAP 801 D 1 HETATM 34 O O2D NAP . . . M 2 31.692 47.064 58.164 1 56.34 ? O2D NAP 801 D 1 HETATM 35 C C1D NAP . . . M 2 30.431 45.177 58.684 1 54.04 ? C1D NAP 801 D 1 HETATM 36 N N1N NAP . . . M 2 29.05 45.588 58.74 1 53.13 ? N1N NAP 801 D 1 HETATM 37 C C2N NAP . . . M 2 28.416 45.701 59.932 1 53.88 ? C2N NAP 801 D 1 HETATM 38 C C3N NAP . . . M 2 27.085 46.087 59.975 1 55.41 ? C3N NAP 801 D 1 HETATM 39 C C7N NAP . . . M 2 26.358 46.225 61.31 1 57.93 ? C7N NAP 801 D 1 HETATM 40 O O7N NAP . . . M 2 25.233 46.595 61.329 1 61.43 ? O7N NAP 801 D 1 HETATM 41 N N7N NAP . . . M 2 27.038 45.906 62.553 1 58.32 ? N7N NAP 801 D 1 HETATM 42 C C4N NAP . . . M 2 26.418 46.347 58.825 1 55.53 ? C4N NAP 801 D 1 HETATM 43 C C5N NAP . . . M 2 27.05 46.23 57.634 1 55.3 ? C5N NAP 801 D 1 HETATM 44 C C6N NAP . . . M 2 28.38 45.842 57.593 1 53.77 ? C6N NAP 801 D 1 HETATM 45 P P2B NAP . . . M 2 39.366 46.807 68.015 1 69.17 ? P2B NAP 801 D 1 HETATM 46 O O1X NAP . . . M 2 39.415 47.919 66.994 1 69.2 ? O1X NAP 801 D 1 HETATM 47 O O2X NAP . . . M 2 38.54 47.245 69.199 1 70.47 -1 O2X NAP 801 D 1 HETATM 48 O O3X NAP . . . M 2 40.762 46.5 68.492 1 77.14 ? O3X NAP 801 D 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 48 #