data_5PGU # _model_server_result.job_id HayjO6wk4GTHciYE3pbAwg _model_server_result.datetime_utc '2024-11-21 17:18:17' _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":"I","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 . . . I 2 39.469 51.835 138.684 1 34.22 ? PA NAP 301 D 1 HETATM 2 O O1A NAP . . . I 2 40.538 50.846 138.938 1 34.35 ? O1A NAP 301 D 1 HETATM 3 O O2A NAP . . . I 2 38.128 51.55 139.348 1 34.63 ? O2A NAP 301 D 1 HETATM 4 O O5B NAP . . . I 2 39.871 53.276 139.243 1 33.39 ? O5B NAP 301 D 1 HETATM 5 C C5B NAP . . . I 2 39.002 54.428 139.189 1 33.16 ? C5B NAP 301 D 1 HETATM 6 C C4B NAP . . . I 2 39.769 55.554 139.824 1 35.41 ? C4B NAP 301 D 1 HETATM 7 O O4B NAP . . . I 2 38.936 56.736 139.885 1 33.75 ? O4B NAP 301 D 1 HETATM 8 C C3B NAP . . . I 2 40.247 55.275 141.254 1 35.4 ? C3B NAP 301 D 1 HETATM 9 O O3B NAP . . . I 2 41.557 55.788 141.48 1 35.15 ? O3B NAP 301 D 1 HETATM 10 C C2B NAP . . . I 2 39.216 56.004 142.104 1 34.65 ? C2B NAP 301 D 1 HETATM 11 O O2B NAP . . . I 2 39.812 56.402 143.355 1 37.69 ? O2B NAP 301 D 1 HETATM 12 C C1B NAP . . . I 2 38.87 57.2 141.22 1 33.32 ? C1B NAP 301 D 1 HETATM 13 N N9A NAP . . . I 2 37.564 57.817 141.45 1 29.6 ? N9A NAP 301 D 1 HETATM 14 C C8A NAP . . . I 2 36.36 57.185 141.627 1 29.37 ? C8A NAP 301 D 1 HETATM 15 N N7A NAP . . . I 2 35.373 57.989 141.944 1 29.42 ? N7A NAP 301 D 1 HETATM 16 C C5A NAP . . . I 2 35.97 59.241 141.983 1 29.16 ? C5A NAP 301 D 1 HETATM 17 C C6A NAP . . . I 2 35.48 60.52 142.326 1 28.96 ? C6A NAP 301 D 1 HETATM 18 N N6A NAP . . . I 2 34.216 60.765 142.689 1 26.69 ? N6A NAP 301 D 1 HETATM 19 N N1A NAP . . . I 2 36.354 61.551 142.308 1 32.59 ? N1A NAP 301 D 1 HETATM 20 C C2A NAP . . . I 2 37.63 61.312 141.983 1 30.63 ? C2A NAP 301 D 1 HETATM 21 N N3A NAP . . . I 2 38.208 60.155 141.651 1 27.62 ? N3A NAP 301 D 1 HETATM 22 C C4A NAP . . . I 2 37.318 59.151 141.667 1 28.5 ? C4A NAP 301 D 1 HETATM 23 O O3 NAP . . . I 2 39.199 52.202 137.146 1 36.95 ? O3 NAP 301 D 1 HETATM 24 P PN NAP . . . I 2 39.94 51.712 135.816 1 37.52 ? PN NAP 301 D 1 HETATM 25 O O1N NAP . . . I 2 39.396 50.379 135.477 1 38.25 ? O1N NAP 301 D 1 HETATM 26 O O2N NAP . . . I 2 41.406 51.852 135.978 1 38.39 ? O2N NAP 301 D 1 HETATM 27 O O5D NAP . . . I 2 39.416 52.783 134.759 1 39.35 ? O5D NAP 301 D 1 HETATM 28 C C5D NAP . . . I 2 40.126 54.02 134.498 1 36.3 ? C5D NAP 301 D 1 HETATM 29 C C4D NAP . . . I 2 39.611 54.647 133.224 1 34.26 ? C4D NAP 301 D 1 HETATM 30 O O4D NAP . . . I 2 39.698 53.703 132.132 1 33.51 ? O4D NAP 301 D 1 HETATM 31 C C3D NAP . . . I 2 38.161 55.119 133.237 1 33.22 ? C3D NAP 301 D 1 HETATM 32 O O3D NAP . . . I 2 38.031 56.343 132.519 1 34.83 ? O3D NAP 301 D 1 HETATM 33 C C2D NAP . . . I 2 37.448 53.988 132.499 1 28.86 ? C2D NAP 301 D 1 HETATM 34 O O2D NAP . . . I 2 36.287 54.445 131.813 1 21.6 ? O2D NAP 301 D 1 HETATM 35 C C1D NAP . . . I 2 38.496 53.655 131.418 1 31.93 ? C1D NAP 301 D 1 HETATM 36 N N1N NAP . . . I 2 38.259 52.226 130.909 1 30.99 ? N1N NAP 301 D 1 HETATM 37 C C2N NAP . . . I 2 38.574 51.126 131.703 1 29.68 ? C2N NAP 301 D 1 HETATM 38 C C3N NAP . . . I 2 38.244 49.85 131.275 1 31.7 ? C3N NAP 301 D 1 HETATM 39 C C7N NAP . . . I 2 38.51 48.599 132.076 1 34.1 ? C7N NAP 301 D 1 HETATM 40 O O7N NAP . . . I 2 37.963 47.548 131.751 1 34.47 ? O7N NAP 301 D 1 HETATM 41 N N7N NAP . . . I 2 39.251 48.698 133.175 1 37.03 ? N7N NAP 301 D 1 HETATM 42 C C4N NAP . . . I 2 37.64 49.702 130.031 1 29.15 ? C4N NAP 301 D 1 HETATM 43 C C5N NAP . . . I 2 37.343 50.81 129.26 1 28 ? C5N NAP 301 D 1 HETATM 44 C C6N NAP . . . I 2 37.655 52.065 129.716 1 29.51 ? C6N NAP 301 D 1 HETATM 45 P P2B NAP . . . I 2 38.992 56.904 144.629 1 33.91 ? P2B NAP 301 D 1 HETATM 46 O O1X NAP . . . I 2 38.456 58.205 144.389 1 31.85 ? O1X NAP 301 D 1 HETATM 47 O O2X NAP . . . I 2 37.907 55.825 144.94 1 34.35 ? O2X NAP 301 D 1 HETATM 48 O O3X NAP . . . I 2 40.092 56.87 145.68 1 36.02 ? O3X NAP 301 D 1 HETATM 49 H HOA2 NAP . . . I 2 37.238 51.975 139.233 0 34.68 ? HOA2 NAP 301 D 1 HETATM 50 H H51A NAP . . . I 2 38.85 54.626 138.13 0 33.18 ? H51A NAP 301 D 1 HETATM 51 H H52A NAP . . . I 2 38.035 54.243 139.653 0 33.18 ? H52A NAP 301 D 1 HETATM 52 H H4B NAP . . . I 2 40.585 55.864 139.174 0 35.48 ? H4B NAP 301 D 1 HETATM 53 H H3B NAP . . . I 2 40.237 54.208 141.47 0 35.44 ? H3B NAP 301 D 1 HETATM 54 H HO3A NAP . . . I 2 42.165 55.262 140.898 0 35.14 ? HO3A NAP 301 D 1 HETATM 55 H H2B NAP . . . I 2 38.371 55.342 142.285 0 34.66 ? H2B NAP 301 D 1 HETATM 56 H H1B NAP . . . I 2 39.613 57.992 141.306 0 33.31 ? H1B NAP 301 D 1 HETATM 57 H H8A NAP . . . I 2 36.232 56.109 141.514 0 29.42 ? H8A NAP 301 D 1 HETATM 58 H H61A NAP . . . I 2 33.534 60.014 142.732 0 26.66 ? H61A NAP 301 D 1 HETATM 59 H H62A NAP . . . I 2 33.9 61.699 142.932 0 26.66 ? H62A NAP 301 D 1 HETATM 60 H H2A NAP . . . I 2 38.284 62.181 141.96 0 30.65 ? H2A NAP 301 D 1 HETATM 61 H H51N NAP . . . I 2 41.211 53.926 134.461 0 36.32 ? H51N NAP 301 D 1 HETATM 62 H H52N NAP . . . I 2 39.908 54.634 135.37 0 36.32 ? H52N NAP 301 D 1 HETATM 63 H H4D NAP . . . I 2 40.263 55.466 132.929 0 34.29 ? H4D NAP 301 D 1 HETATM 64 H H3D NAP . . . I 2 37.745 55.219 134.238 0 33.24 ? H3D NAP 301 D 1 HETATM 65 H HO3N NAP . . . I 2 38.045 57.06 133.205 0 34.89 ? HO3N NAP 301 D 1 HETATM 66 H H2D NAP . . . I 2 37.205 53.144 133.142 0 28.86 ? H2D NAP 301 D 1 HETATM 67 H HO2N NAP . . . I 2 35.536 54.471 132.461 0 21.54 ? HO2N NAP 301 D 1 HETATM 68 H H1D NAP . . . I 2 38.537 54.313 130.553 0 31.97 ? H1D NAP 301 D 1 HETATM 69 H H2N NAP . . . I 2 39.057 51.306 132.661 0 29.69 ? H2N NAP 301 D 1 HETATM 70 H H71N NAP . . . I 2 39.456 47.872 133.727 0 37.02 ? H71N NAP 301 D 1 HETATM 71 H H72N NAP . . . I 2 39.676 49.545 133.536 0 37.02 ? H72N NAP 301 D 1 HETATM 72 H H4N NAP . . . I 2 37.392 48.722 129.628 0 29.06 ? H4N NAP 301 D 1 HETATM 73 H H5N NAP . . . I 2 36.85 50.701 128.296 0 28 ? H5N NAP 301 D 1 HETATM 74 H H6N NAP . . . I 2 37.374 52.938 129.133 0 29.55 ? H6N NAP 301 D 1 HETATM 75 H HOP2 NAP . . . I 2 38.128 54.88 144.731 0 34.32 ? HOP2 NAP 301 D 1 HETATM 76 H HOP3 NAP . . . I 2 40.38 56.054 146.166 0 36.05 ? HOP3 NAP 301 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 76 #