data_2D38 # _model_server_result.job_id NDCw2587T6mDJOH9Ckesrw _model_server_result.datetime_utc '2025-03-06 08:52:19' _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 2d38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 2D38 # _exptl.entry_id 2D38 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _entity.pdbx_number_of_molecules 1 _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 2D38 _cell.length_a 86.617 _cell.length_b 86.617 _cell.length_c 49.122 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D38 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 32.748 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 291 n n PA O2A NAP sing 292 n n PA O5B NAP sing 293 n n PA O3 NAP sing 294 n n O2A HOA2 NAP sing 295 n n O5B C5B NAP sing 296 n n C5B C4B NAP sing 297 n n C5B H51A NAP sing 298 n n C5B H52A NAP sing 299 n n C4B O4B NAP sing 300 n n C4B C3B NAP sing 301 n n C4B H4B NAP sing 302 n n O4B C1B NAP sing 303 n n C3B O3B NAP sing 304 n n C3B C2B NAP sing 305 n n C3B H3B NAP sing 306 n n O3B HO3A NAP sing 307 n n C2B O2B NAP sing 308 n n C2B C1B NAP sing 309 n n C2B H2B NAP sing 310 n n O2B P2B NAP sing 311 n n C1B N9A NAP sing 312 n n C1B H1B NAP sing 313 n n N9A C8A NAP sing 314 n y N9A C4A NAP sing 315 n y C8A N7A NAP doub 316 n y C8A H8A NAP sing 317 n n N7A C5A NAP sing 318 n y C5A C6A NAP sing 319 n y C5A C4A NAP doub 320 n y C6A N6A NAP sing 321 n n C6A N1A NAP doub 322 n y N6A H61A NAP sing 323 n n N6A H62A NAP sing 324 n n N1A C2A NAP sing 325 n y C2A N3A NAP doub 326 n y C2A H2A NAP sing 327 n n N3A C4A NAP sing 328 n y O3 PN NAP sing 329 n n PN O1N NAP doub 330 n n PN O2N NAP sing 331 n n PN O5D NAP sing 332 n n O5D C5D NAP sing 333 n n C5D C4D NAP sing 334 n n C5D H51N NAP sing 335 n n C5D H52N NAP sing 336 n n C4D O4D NAP sing 337 n n C4D C3D NAP sing 338 n n C4D H4D NAP sing 339 n n O4D C1D NAP sing 340 n n C3D O3D NAP sing 341 n n C3D C2D NAP sing 342 n n C3D H3D NAP sing 343 n n O3D HO3N NAP sing 344 n n C2D O2D NAP sing 345 n n C2D C1D NAP sing 346 n n C2D H2D NAP sing 347 n n O2D HO2N NAP sing 348 n n C1D N1N NAP sing 349 n n C1D H1D NAP sing 350 n n N1N C2N NAP sing 351 n y N1N C6N NAP doub 352 n y C2N C3N NAP doub 353 n y C2N H2N NAP sing 354 n n C3N C7N NAP sing 355 n n C3N C4N NAP sing 356 n y C7N O7N NAP doub 357 n n C7N N7N NAP sing 358 n n N7N H71N NAP sing 359 n n N7N H72N NAP sing 360 n n C4N C5N NAP doub 361 n y C4N H4N NAP sing 362 n n C5N C6N NAP sing 363 n y C5N H5N NAP sing 364 n n C6N H6N NAP sing 365 n n P2B O1X NAP doub 366 n n P2B O2X NAP sing 367 n n P2B O3X NAP sing 368 n n O2X HOP2 NAP sing 369 n n O3X HOP3 NAP sing 370 n n # _atom_sites.entry_id 2D38 _atom_sites.fract_transf_matrix[1][1] 0.011545 _atom_sites.fract_transf_matrix[1][2] 0.006666 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013331 _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] 0.020357 _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 B 2 FMN A 1 200 200 FMN FMN . C 3 NAP A 1 300 300 NAP NAP . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 51 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 53 HOH HOH . D 4 HOH A 54 354 54 HOH HOH . D 4 HOH A 55 355 55 HOH HOH . D 4 HOH A 56 356 56 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 . . . C 3 42.932 11.919 24.093 1 28.91 ? PA NAP 300 A 1 HETATM 2 O O1A NAP . . . C 3 43.738 10.747 23.699 1 29.79 ? O1A NAP 300 A 1 HETATM 3 O O2A NAP . . . C 3 43.788 13.015 24.766 1 29.94 ? O2A NAP 300 A 1 HETATM 4 O O5B NAP . . . C 3 42.232 12.522 22.766 1 31.29 ? O5B NAP 300 A 1 HETATM 5 C C5B NAP . . . C 3 42.132 13.928 22.547 1 32.27 ? C5B NAP 300 A 1 HETATM 6 C C4B NAP . . . C 3 40.667 14.326 22.383 1 33.31 ? C4B NAP 300 A 1 HETATM 7 O O4B NAP . . . C 3 39.934 13.735 21.334 1 33.8 ? O4B NAP 300 A 1 HETATM 8 C C3B NAP . . . C 3 39.958 13.967 23.68 1 35.14 ? C3B NAP 300 A 1 HETATM 9 O O3B NAP . . . C 3 40.248 14.998 24.618 1 37.18 ? O3B NAP 300 A 1 HETATM 10 C C2B NAP . . . C 3 38.553 13.618 23.28 1 34.86 ? C2B NAP 300 A 1 HETATM 11 O O2B NAP . . . C 3 37.658 14.66 23.548 1 39.33 ? O2B NAP 300 A 1 HETATM 12 C C1B NAP . . . C 3 38.65 13.38 21.783 1 32.7 ? C1B NAP 300 A 1 HETATM 13 N N9A NAP . . . C 3 38.394 11.963 21.53 1 29.48 ? N9A NAP 300 A 1 HETATM 14 C C8A NAP . . . C 3 39.287 10.919 21.489 1 28.75 ? C8A NAP 300 A 1 HETATM 15 N N7A NAP . . . C 3 38.592 9.786 21.242 1 26.94 ? N7A NAP 300 A 1 HETATM 16 C C5A NAP . . . C 3 37.274 10.096 21.144 1 28.6 ? C5A NAP 300 A 1 HETATM 17 C C6A NAP . . . C 3 36.125 9.342 20.901 1 28.28 ? C6A NAP 300 A 1 HETATM 18 N N6A NAP . . . C 3 36.157 8.011 20.896 1 29.32 ? N6A NAP 300 A 1 HETATM 19 N N1A NAP . . . C 3 34.905 9.979 20.853 1 28.03 ? N1A NAP 300 A 1 HETATM 20 C C2A NAP . . . C 3 34.808 11.337 21.048 1 27.41 ? C2A NAP 300 A 1 HETATM 21 N N3A NAP . . . C 3 35.941 12.086 21.288 1 28.56 ? N3A NAP 300 A 1 HETATM 22 C C4A NAP . . . C 3 37.148 11.466 21.33 1 28.13 ? C4A NAP 300 A 1 HETATM 23 O O3 NAP . . . C 3 41.66 11.501 24.977 1 30.66 ? O3 NAP 300 A 1 HETATM 24 P PN NAP . . . C 3 41.662 11.386 26.58 1 29.33 ? PN NAP 300 A 1 HETATM 25 O O1N NAP . . . C 3 40.638 12.325 27.091 1 30.56 ? O1N NAP 300 A 1 HETATM 26 O O2N NAP . . . C 3 43.051 11.422 27.053 1 30.07 ? O2N NAP 300 A 1 HETATM 27 O O5D NAP . . . C 3 41.134 9.871 26.729 1 28.11 ? O5D NAP 300 A 1 HETATM 28 C C5D NAP . . . C 3 41.956 8.796 26.3 1 26.02 ? C5D NAP 300 A 1 HETATM 29 C C4D NAP . . . C 3 41.136 7.79 25.499 1 25.13 ? C4D NAP 300 A 1 HETATM 30 O O4D NAP . . . C 3 39.849 7.479 25.978 1 24.93 ? O4D NAP 300 A 1 HETATM 31 C C3D NAP . . . C 3 40.916 8.212 24.039 1 25.87 ? C3D NAP 300 A 1 HETATM 32 O O3D NAP . . . C 3 42.111 8.05 23.302 1 28.83 ? O3D NAP 300 A 1 HETATM 33 C C2D NAP . . . C 3 39.693 7.448 23.621 1 25.55 ? C2D NAP 300 A 1 HETATM 34 O O2D NAP . . . C 3 40.03 6.194 23.069 1 27.2 ? O2D NAP 300 A 1 HETATM 35 C C1D NAP . . . C 3 38.928 7.257 24.925 1 25.42 ? C1D NAP 300 A 1 HETATM 36 N N1N NAP . . . C 3 37.752 8.199 24.952 1 26.39 ? N1N NAP 300 A 1 HETATM 37 C C2N NAP . . . C 3 36.593 7.619 24.544 1 26.75 ? C2N NAP 300 A 1 HETATM 38 C C3N NAP . . . C 3 35.44 8.337 24.476 1 27.51 ? C3N NAP 300 A 1 HETATM 39 C C7N NAP . . . C 3 34.173 7.662 24.092 1 28.09 ? C7N NAP 300 A 1 HETATM 40 O O7N NAP . . . C 3 32.964 8.37 24.188 1 32.39 ? O7N NAP 300 A 1 HETATM 41 N N7N NAP . . . C 3 34.201 6.397 23.681 1 29.59 ? N7N NAP 300 A 1 HETATM 42 C C4N NAP . . . C 3 35.508 9.665 24.825 1 25.9 ? C4N NAP 300 A 1 HETATM 43 C C5N NAP . . . C 3 36.73 10.204 25.204 1 26.03 ? C5N NAP 300 A 1 HETATM 44 C C6N NAP . . . C 3 37.984 9.545 25.309 1 25.64 ? C6N NAP 300 A 1 HETATM 45 P P2B NAP . . . C 3 37.176 15.005 25.049 1 43.23 ? P2B NAP 300 A 1 HETATM 46 O O1X NAP . . . C 3 36.353 16.237 24.938 1 42.04 ? O1X NAP 300 A 1 HETATM 47 O O2X NAP . . . C 3 36.34 13.855 25.649 1 42.32 ? O2X NAP 300 A 1 HETATM 48 O O3X NAP . . . C 3 38.404 15.277 25.948 1 41.68 ? O3X NAP 300 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 48 #