data_5PGU # _model_server_result.job_id TyQa9d_yZ6XKKIMKjecAfA _model_server_result.datetime_utc '2024-11-21 17:12:32' _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 5pgu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5PGU # _exptl.entry_id 5PGU _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 4 _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 90 _cell.entry_id 5PGU _cell.length_a 74.3 _cell.length_b 93.8 _cell.length_c 168.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5PGU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 G N N ? 2 I N N ? 2 K 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 295 n n PA O2A NAP sing 296 n n PA O5B NAP sing 297 n n PA O3 NAP sing 298 n n O2A HOA2 NAP sing 299 n n O5B C5B NAP sing 300 n n C5B C4B NAP sing 301 n n C5B H51A NAP sing 302 n n C5B H52A NAP sing 303 n n C4B O4B NAP sing 304 n n C4B C3B NAP sing 305 n n C4B H4B NAP sing 306 n n O4B C1B NAP sing 307 n n C3B O3B NAP sing 308 n n C3B C2B NAP sing 309 n n C3B H3B NAP sing 310 n n O3B HO3A NAP sing 311 n n C2B O2B NAP sing 312 n n C2B C1B NAP sing 313 n n C2B H2B NAP sing 314 n n O2B P2B NAP sing 315 n n C1B N9A NAP sing 316 n n C1B H1B NAP sing 317 n n N9A C8A NAP sing 318 n y N9A C4A NAP sing 319 n y C8A N7A NAP doub 320 n y C8A H8A NAP sing 321 n n N7A C5A NAP sing 322 n y C5A C6A NAP sing 323 n y C5A C4A NAP doub 324 n y C6A N6A NAP sing 325 n n C6A N1A NAP doub 326 n y N6A H61A NAP sing 327 n n N6A H62A NAP sing 328 n n N1A C2A NAP sing 329 n y C2A N3A NAP doub 330 n y C2A H2A NAP sing 331 n n N3A C4A NAP sing 332 n y O3 PN NAP sing 333 n n PN O1N NAP doub 334 n n PN O2N NAP sing 335 n n PN O5D NAP sing 336 n n O5D C5D NAP sing 337 n n C5D C4D NAP sing 338 n n C5D H51N NAP sing 339 n n C5D H52N NAP sing 340 n n C4D O4D NAP sing 341 n n C4D C3D NAP sing 342 n n C4D H4D NAP sing 343 n n O4D C1D NAP sing 344 n n C3D O3D NAP sing 345 n n C3D C2D NAP sing 346 n n C3D H3D NAP sing 347 n n O3D HO3N NAP sing 348 n n C2D O2D NAP sing 349 n n C2D C1D NAP sing 350 n n C2D H2D NAP sing 351 n n O2D HO2N NAP sing 352 n n C1D N1N NAP sing 353 n n C1D H1D NAP sing 354 n n N1N C2N NAP sing 355 n y N1N C6N NAP doub 356 n y C2N C3N NAP doub 357 n y C2N H2N NAP sing 358 n n C3N C7N NAP sing 359 n n C3N C4N NAP sing 360 n y C7N O7N NAP doub 361 n n C7N N7N NAP sing 362 n n N7N H71N NAP sing 363 n n N7N H72N NAP sing 364 n n C4N C5N NAP doub 365 n y C4N H4N NAP sing 366 n n C5N C6N NAP sing 367 n y C5N H5N NAP sing 368 n n C6N H6N NAP sing 369 n n P2B O1X NAP doub 370 n n P2B O2X NAP sing 371 n n P2B O3X NAP sing 372 n n O2X HOP2 NAP sing 373 n n O3X HOP3 NAP sing 374 n n # _atom_sites.entry_id 5PGU _atom_sites.fract_transf_matrix[1][1] 0.013459 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010661 _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] 0.005949 _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 NAP A 1 301 301 NAP NAP . F 3 8K4 A 1 302 302 8K4 LG1 . G 2 NAP B 1 301 301 NAP NAP . H 3 8K4 B 1 302 302 8K4 LG1 . I 2 NAP D 1 301 301 NAP NAP . J 3 8K4 D 1 302 302 8K4 LG1 . K 2 NAP E 1 301 301 NAP NAP . L 3 8K4 E 1 302 302 8K4 LG1 . M 4 HOH A 1 401 66 HOH HOH . M 4 HOH A 2 402 87 HOH HOH . M 4 HOH A 3 403 56 HOH HOH . M 4 HOH A 4 404 7 HOH HOH . M 4 HOH A 5 405 81 HOH HOH . M 4 HOH A 6 406 84 HOH HOH . M 4 HOH A 7 407 47 HOH HOH . M 4 HOH A 8 408 19 HOH HOH . M 4 HOH A 9 409 80 HOH HOH . M 4 HOH A 10 410 83 HOH HOH . M 4 HOH A 11 411 88 HOH HOH . M 4 HOH A 12 412 2 HOH HOH . M 4 HOH A 13 413 51 HOH HOH . M 4 HOH A 14 414 78 HOH HOH . M 4 HOH A 15 415 68 HOH HOH . M 4 HOH A 16 416 70 HOH HOH . M 4 HOH A 17 417 27 HOH HOH . M 4 HOH A 18 418 49 HOH HOH . M 4 HOH A 19 419 62 HOH HOH . M 4 HOH A 20 420 44 HOH HOH . M 4 HOH A 21 421 12 HOH HOH . M 4 HOH A 22 422 39 HOH HOH . M 4 HOH A 23 423 32 HOH HOH . M 4 HOH A 24 424 43 HOH HOH . M 4 HOH A 25 425 24 HOH HOH . M 4 HOH A 26 426 25 HOH HOH . M 4 HOH A 27 427 8 HOH HOH . M 4 HOH A 28 428 57 HOH HOH . M 4 HOH A 29 429 37 HOH HOH . N 4 HOH B 1 401 67 HOH HOH . N 4 HOH B 2 402 71 HOH HOH . N 4 HOH B 3 403 14 HOH HOH . N 4 HOH B 4 404 31 HOH HOH . N 4 HOH B 5 405 69 HOH HOH . N 4 HOH B 6 406 1 HOH HOH . N 4 HOH B 7 407 55 HOH HOH . N 4 HOH B 8 408 6 HOH HOH . N 4 HOH B 9 409 76 HOH HOH . N 4 HOH B 10 410 26 HOH HOH . N 4 HOH B 11 411 17 HOH HOH . N 4 HOH B 12 412 22 HOH HOH . N 4 HOH B 13 413 18 HOH HOH . N 4 HOH B 14 414 72 HOH HOH . N 4 HOH B 15 415 60 HOH HOH . N 4 HOH B 16 416 29 HOH HOH . N 4 HOH B 17 417 42 HOH HOH . N 4 HOH B 18 418 36 HOH HOH . N 4 HOH B 19 419 50 HOH HOH . N 4 HOH B 20 420 53 HOH HOH . N 4 HOH B 21 421 65 HOH HOH . N 4 HOH B 22 422 75 HOH HOH . N 4 HOH B 23 423 79 HOH HOH . N 4 HOH B 24 424 23 HOH HOH . N 4 HOH B 25 425 73 HOH HOH . N 4 HOH B 26 426 59 HOH HOH . N 4 HOH B 27 427 11 HOH HOH . N 4 HOH B 28 428 10 HOH HOH . N 4 HOH B 29 429 52 HOH HOH . N 4 HOH B 30 430 35 HOH HOH . N 4 HOH B 31 431 4 HOH HOH . N 4 HOH B 32 432 40 HOH HOH . N 4 HOH B 33 433 9 HOH HOH . N 4 HOH B 34 434 46 HOH HOH . N 4 HOH B 35 435 5 HOH HOH . N 4 HOH B 36 436 38 HOH HOH . N 4 HOH B 37 437 21 HOH HOH . N 4 HOH B 38 438 3 HOH HOH . O 4 HOH D 1 401 64 HOH HOH . O 4 HOH D 2 402 54 HOH HOH . O 4 HOH D 3 403 82 HOH HOH . O 4 HOH D 4 404 48 HOH HOH . O 4 HOH D 5 405 34 HOH HOH . O 4 HOH D 6 406 58 HOH HOH . O 4 HOH D 7 407 45 HOH HOH . O 4 HOH D 8 408 33 HOH HOH . O 4 HOH D 9 409 15 HOH HOH . O 4 HOH D 10 410 85 HOH HOH . O 4 HOH D 11 411 13 HOH HOH . O 4 HOH D 12 412 77 HOH HOH . O 4 HOH D 13 413 28 HOH HOH . O 4 HOH D 14 414 63 HOH HOH . O 4 HOH D 15 415 20 HOH HOH . O 4 HOH D 16 416 61 HOH HOH . O 4 HOH D 17 417 74 HOH HOH . P 4 HOH E 1 401 86 HOH HOH . P 4 HOH E 2 402 30 HOH HOH . P 4 HOH E 3 403 41 HOH HOH . P 4 HOH E 4 404 16 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 . . . E 2 53.827 59.125 78.357 1 27.31 ? PA NAP 301 A 1 HETATM 2 O O1A NAP . . . E 2 54.615 60.371 78.459 1 32.15 ? O1A NAP 301 A 1 HETATM 3 O O2A NAP . . . E 2 52.956 59.04 77.117 1 25.74 ? O2A NAP 301 A 1 HETATM 4 O O5B NAP . . . E 2 54.833 57.894 78.181 1 28.82 ? O5B NAP 301 A 1 HETATM 5 C C5B NAP . . . E 2 54.418 56.52 78.057 1 30.49 ? C5B NAP 301 A 1 HETATM 6 C C4B NAP . . . E 2 55.645 55.708 77.737 1 32.36 ? C4B NAP 301 A 1 HETATM 7 O O4B NAP . . . E 2 55.263 54.392 77.265 1 30.16 ? O4B NAP 301 A 1 HETATM 8 C C3B NAP . . . E 2 56.564 56.309 76.672 1 32.07 ? C3B NAP 301 A 1 HETATM 9 O O3B NAP . . . E 2 57.922 56.248 77.099 1 33.12 ? O3B NAP 301 A 1 HETATM 10 C C2B NAP . . . E 2 56.33 55.436 75.447 1 31.11 ? C2B NAP 301 A 1 HETATM 11 O O2B NAP . . . E 2 57.55 55.359 74.684 1 30.27 ? O2B NAP 301 A 1 HETATM 12 C C1B NAP . . . E 2 55.949 54.092 76.067 1 30.38 ? C1B NAP 301 A 1 HETATM 13 N N9A NAP . . . E 2 55.122 53.208 75.243 1 26.8 ? N9A NAP 301 A 1 HETATM 14 C C8A NAP . . . E 2 54.039 53.552 74.478 1 23.68 ? C8A NAP 301 A 1 HETATM 15 N N7A NAP . . . E 2 53.581 52.579 73.729 1 23.92 ? N7A NAP 301 A 1 HETATM 16 C C5A NAP . . . E 2 54.419 51.512 74.026 1 25.54 ? C5A NAP 301 A 1 HETATM 17 C C6A NAP . . . E 2 54.481 50.182 73.55 1 24.72 ? C6A NAP 301 A 1 HETATM 18 N N6A NAP . . . E 2 53.61 49.649 72.679 1 23.52 ? N6A NAP 301 A 1 HETATM 19 N N1A NAP . . . E 2 55.462 49.389 74.037 1 25.17 ? N1A NAP 301 A 1 HETATM 20 C C2A NAP . . . E 2 56.3 49.886 74.951 1 22.37 ? C2A NAP 301 A 1 HETATM 21 N N3A NAP . . . E 2 56.331 51.111 75.48 1 24.4 ? N3A NAP 301 A 1 HETATM 22 C C4A NAP . . . E 2 55.367 51.885 74.966 1 25.78 ? C4A NAP 301 A 1 HETATM 23 O O3 NAP . . . E 2 53.001 58.653 79.651 1 28.45 ? O3 NAP 301 A 1 HETATM 24 P PN NAP . . . E 2 52.792 59.096 81.179 1 29.67 ? PN NAP 301 A 1 HETATM 25 O O1N NAP . . . E 2 51.752 60.148 81.204 1 28.04 ? O1N NAP 301 A 1 HETATM 26 O O2N NAP . . . E 2 54.101 59.372 81.816 1 32.8 ? O2N NAP 301 A 1 HETATM 27 O O5D NAP . . . E 2 52.158 57.788 81.81 1 27.71 ? O5D NAP 301 A 1 HETATM 28 C C5D NAP . . . E 2 52.973 56.759 82.411 1 27.09 ? C5D NAP 301 A 1 HETATM 29 C C4D NAP . . . E 2 52.105 55.954 83.347 1 27.67 ? C4D NAP 301 A 1 HETATM 30 O O4D NAP . . . E 2 51.417 56.835 84.263 1 27.51 ? O4D NAP 301 A 1 HETATM 31 C C3D NAP . . . E 2 51.014 55.138 82.671 1 27.5 ? C3D NAP 301 A 1 HETATM 32 O O3D NAP . . . E 2 50.917 53.843 83.255 1 29.62 ? O3D NAP 301 A 1 HETATM 33 C C2D NAP . . . E 2 49.779 55.997 82.917 1 27.83 ? C2D NAP 301 A 1 HETATM 34 O O2D NAP . . . E 2 48.587 55.223 82.984 1 25.83 ? O2D NAP 301 A 1 HETATM 35 C C1D NAP . . . E 2 50.062 56.529 84.341 1 28.29 ? C1D NAP 301 A 1 HETATM 36 N N1N NAP . . . E 2 49.264 57.822 84.598 1 28.55 ? N1N NAP 301 A 1 HETATM 37 C C2N NAP . . . E 2 49.597 59.006 83.957 1 27.97 ? C2N NAP 301 A 1 HETATM 38 C C3N NAP . . . E 2 48.814 60.135 84.132 1 31.3 ? C3N NAP 301 A 1 HETATM 39 C C7N NAP . . . E 2 49.114 61.472 83.515 1 35.23 ? C7N NAP 301 A 1 HETATM 40 O O7N NAP . . . E 2 48.237 62.367 83.539 1 38.07 ? O7N NAP 301 A 1 HETATM 41 N N7N NAP . . . E 2 50.3 61.639 82.889 1 32.72 ? N7N NAP 301 A 1 HETATM 42 C C4N NAP . . . E 2 47.709 60.053 84.97 1 29.41 ? C4N NAP 301 A 1 HETATM 43 C C5N NAP . . . E 2 47.405 58.867 85.611 1 28.75 ? C5N NAP 301 A 1 HETATM 44 C C6N NAP . . . E 2 48.193 57.761 85.411 1 28.52 ? C6N NAP 301 A 1 HETATM 45 P P2B NAP . . . E 2 57.623 54.953 73.143 1 28.89 ? P2B NAP 301 A 1 HETATM 46 O O1X NAP . . . E 2 57.419 53.518 73.057 1 30.34 ? O1X NAP 301 A 1 HETATM 47 O O2X NAP . . . E 2 56.533 55.785 72.484 1 32.61 ? O2X NAP 301 A 1 HETATM 48 O O3X NAP . . . E 2 58.938 55.457 72.581 1 28.64 ? O3X NAP 301 A 1 HETATM 49 H HOA2 NAP . . . E 2 52.129 58.523 76.931 0 25.79 ? HOA2 NAP 301 A 1 HETATM 50 H H51A NAP . . . E 2 54.037 56.253 79.041 0 30.49 ? H51A NAP 301 A 1 HETATM 51 H H52A NAP . . . E 2 53.616 56.395 77.331 0 30.49 ? H52A NAP 301 A 1 HETATM 52 H H4B NAP . . . E 2 56.177 55.486 78.659 0 32.37 ? H4B NAP 301 A 1 HETATM 53 H H3B NAP . . . E 2 56.284 57.335 76.447 0 32.09 ? H3B NAP 301 A 1 HETATM 54 H HO3A NAP . . . E 2 57.991 56.85 77.886 0 33.15 ? HO3A NAP 301 A 1 HETATM 55 H H2B NAP . . . E 2 55.531 55.881 74.856 0 31.13 ? H2B NAP 301 A 1 HETATM 56 H H1B NAP . . . E 2 56.83 53.519 76.355 0 30.42 ? H1B NAP 301 A 1 HETATM 57 H H8A NAP . . . E 2 53.613 54.554 74.47 0 23.66 ? H8A NAP 301 A 1 HETATM 58 H H61A NAP . . . E 2 52.84 50.2 72.314 0 23.52 ? H61A NAP 301 A 1 HETATM 59 H H62A NAP . . . E 2 53.69 48.688 72.362 0 23.52 ? H62A NAP 301 A 1 HETATM 60 H H2A NAP . . . E 2 57.061 49.203 75.321 0 22.33 ? H2A NAP 301 A 1 HETATM 61 H H51N NAP . . . E 2 53.868 57.108 82.925 0 27.08 ? H51N NAP 301 A 1 HETATM 62 H H52N NAP . . . E 2 53.319 56.166 81.566 0 27.08 ? H52N NAP 301 A 1 HETATM 63 H H4D NAP . . . E 2 52.721 55.314 83.974 0 27.67 ? H4D NAP 301 A 1 HETATM 64 H H3D NAP . . . E 2 51.17 55.047 81.598 0 27.5 ? H3D NAP 301 A 1 HETATM 65 H HO3N NAP . . . E 2 50.793 53.95 84.234 0 29.66 ? HO3N NAP 301 A 1 HETATM 66 H H2D NAP . . . E 2 49.669 56.791 82.182 0 27.81 ? H2D NAP 301 A 1 HETATM 67 H HO2N NAP . . . E 2 48.228 55.109 82.067 0 25.81 ? HO2N NAP 301 A 1 HETATM 68 H H1D NAP . . . E 2 49.863 55.855 85.171 0 28.34 ? H1D NAP 301 A 1 HETATM 69 H H2N NAP . . . E 2 50.463 59.005 83.299 0 27.95 ? H2N NAP 301 A 1 HETATM 70 H H71N NAP . . . E 2 50.537 62.532 82.469 0 32.75 ? H71N NAP 301 A 1 HETATM 71 H H72N NAP . . . E 2 51.034 60.944 82.814 0 32.75 ? H72N NAP 301 A 1 HETATM 72 H H4N NAP . . . E 2 47.038 60.897 85.121 0 29.42 ? H4N NAP 301 A 1 HETATM 73 H H5N NAP . . . E 2 46.524 58.779 86.243 0 28.73 ? H5N NAP 301 A 1 HETATM 74 H H6N NAP . . . E 2 47.909 56.816 85.865 0 28.53 ? H6N NAP 301 A 1 HETATM 75 H HOP2 NAP . . . E 2 56.519 56.759 72.678 0 32.73 ? HOP2 NAP 301 A 1 HETATM 76 H HOP3 NAP . . . E 2 59.503 56.151 73.011 0 28.68 ? HOP3 NAP 301 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 76 #