data_5DXV # _model_server_result.job_id bvZsRfdMQgYpBiN_5lrQcQ _model_server_result.datetime_utc '2024-11-05 00:22:18' _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 5dxv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5DXV # _exptl.entry_id 5DXV _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 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 90 _cell.entry_id 5DXV _cell.length_a 44.817 _cell.length_b 120.054 _cell.length_c 111.187 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DXV _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,F,J 1 1 B,G,H,I,K 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C TYR 140 A TYR 139 1_555 A N CME 141 A CME 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale2 A C CME 141 A CME 140 1_555 A N PHE 142 A PHE 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale3 B C TYR 140 B TYR 139 1_555 B N CME 141 B CME 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? covale ? covale4 B C CME 141 B CME 140 1_555 B N PHE 142 B PHE 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? # _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" # _atom_sites.entry_id 5DXV _atom_sites.fract_transf_matrix[1][1] 0.022313 _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] 0.00833 _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] 0.008994 _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 C 2 NAP A 1 201 201 NAP NAP . D 3 PEG A 1 202 301 PEG PEG . E 4 EDO A 1 203 302 EDO EDO . F 5 CL A 1 204 401 CL CL . G 3 PEG B 1 301 301 PEG PEG . H 4 EDO B 1 302 302 EDO EDO . I 5 CL B 1 303 401 CL CL . J 6 HOH A 1 301 109 HOH HOH . J 6 HOH A 2 302 151 HOH HOH . J 6 HOH A 3 303 146 HOH HOH . J 6 HOH A 4 304 145 HOH HOH . J 6 HOH A 5 305 39 HOH HOH . J 6 HOH A 6 306 95 HOH HOH . J 6 HOH A 7 307 94 HOH HOH . J 6 HOH A 8 308 124 HOH HOH . J 6 HOH A 9 309 112 HOH HOH . J 6 HOH A 10 310 91 HOH HOH . J 6 HOH A 11 311 67 HOH HOH . J 6 HOH A 12 312 8 HOH HOH . J 6 HOH A 13 313 40 HOH HOH . J 6 HOH A 14 314 14 HOH HOH . J 6 HOH A 15 315 82 HOH HOH . J 6 HOH A 16 316 78 HOH HOH . J 6 HOH A 17 317 87 HOH HOH . J 6 HOH A 18 318 129 HOH HOH . J 6 HOH A 19 319 34 HOH HOH . J 6 HOH A 20 320 62 HOH HOH . J 6 HOH A 21 321 16 HOH HOH . J 6 HOH A 22 322 117 HOH HOH . J 6 HOH A 23 323 68 HOH HOH . J 6 HOH A 24 324 121 HOH HOH . J 6 HOH A 25 325 21 HOH HOH . J 6 HOH A 26 326 92 HOH HOH . J 6 HOH A 27 327 122 HOH HOH . J 6 HOH A 28 328 69 HOH HOH . J 6 HOH A 29 329 93 HOH HOH . J 6 HOH A 30 330 85 HOH HOH . J 6 HOH A 31 331 2 HOH HOH . J 6 HOH A 32 332 140 HOH HOH . J 6 HOH A 33 333 22 HOH HOH . J 6 HOH A 34 334 89 HOH HOH . J 6 HOH A 35 335 128 HOH HOH . J 6 HOH A 36 336 17 HOH HOH . J 6 HOH A 37 337 63 HOH HOH . J 6 HOH A 38 338 97 HOH HOH . J 6 HOH A 39 339 103 HOH HOH . J 6 HOH A 40 340 18 HOH HOH . J 6 HOH A 41 341 120 HOH HOH . J 6 HOH A 42 342 98 HOH HOH . J 6 HOH A 43 343 81 HOH HOH . J 6 HOH A 44 344 102 HOH HOH . J 6 HOH A 45 345 84 HOH HOH . J 6 HOH A 46 346 79 HOH HOH . J 6 HOH A 47 347 33 HOH HOH . J 6 HOH A 48 348 20 HOH HOH . J 6 HOH A 49 349 77 HOH HOH . J 6 HOH A 50 350 64 HOH HOH . J 6 HOH A 51 351 118 HOH HOH . J 6 HOH A 52 352 54 HOH HOH . J 6 HOH A 53 353 53 HOH HOH . J 6 HOH A 54 354 138 HOH HOH . J 6 HOH A 55 355 113 HOH HOH . J 6 HOH A 56 356 43 HOH HOH . J 6 HOH A 57 357 73 HOH HOH . J 6 HOH A 58 358 74 HOH HOH . J 6 HOH A 59 359 32 HOH HOH . J 6 HOH A 60 360 27 HOH HOH . J 6 HOH A 61 361 75 HOH HOH . J 6 HOH A 62 362 107 HOH HOH . J 6 HOH A 63 363 7 HOH HOH . J 6 HOH A 64 364 41 HOH HOH . J 6 HOH A 65 365 3 HOH HOH . J 6 HOH A 66 366 131 HOH HOH . J 6 HOH A 67 367 50 HOH HOH . J 6 HOH A 68 368 42 HOH HOH . J 6 HOH A 69 369 12 HOH HOH . J 6 HOH A 70 370 143 HOH HOH . J 6 HOH A 71 371 66 HOH HOH . J 6 HOH A 72 372 30 HOH HOH . J 6 HOH A 73 373 45 HOH HOH . J 6 HOH A 74 374 147 HOH HOH . J 6 HOH A 75 375 126 HOH HOH . J 6 HOH A 76 376 149 HOH HOH . J 6 HOH A 77 377 153 HOH HOH . J 6 HOH A 78 378 114 HOH HOH . J 6 HOH A 79 379 31 HOH HOH . J 6 HOH A 80 380 47 HOH HOH . J 6 HOH A 81 381 123 HOH HOH . J 6 HOH A 82 382 110 HOH HOH . J 6 HOH A 83 383 5 HOH HOH . J 6 HOH A 84 384 133 HOH HOH . J 6 HOH A 85 385 48 HOH HOH . J 6 HOH A 86 386 119 HOH HOH . J 6 HOH A 87 387 44 HOH HOH . K 6 HOH B 1 401 111 HOH HOH . K 6 HOH B 2 402 108 HOH HOH . K 6 HOH B 3 403 150 HOH HOH . K 6 HOH B 4 404 139 HOH HOH . K 6 HOH B 5 405 127 HOH HOH . K 6 HOH B 6 406 26 HOH HOH . K 6 HOH B 7 407 134 HOH HOH . K 6 HOH B 8 408 58 HOH HOH . K 6 HOH B 9 409 152 HOH HOH . K 6 HOH B 10 410 52 HOH HOH . K 6 HOH B 11 411 24 HOH HOH . K 6 HOH B 12 412 96 HOH HOH . K 6 HOH B 13 413 99 HOH HOH . K 6 HOH B 14 414 51 HOH HOH . K 6 HOH B 15 415 37 HOH HOH . K 6 HOH B 16 416 144 HOH HOH . K 6 HOH B 17 417 104 HOH HOH . K 6 HOH B 18 418 106 HOH HOH . K 6 HOH B 19 419 59 HOH HOH . K 6 HOH B 20 420 6 HOH HOH . K 6 HOH B 21 421 25 HOH HOH . K 6 HOH B 22 422 19 HOH HOH . K 6 HOH B 23 423 15 HOH HOH . K 6 HOH B 24 424 101 HOH HOH . K 6 HOH B 25 425 4 HOH HOH . K 6 HOH B 26 426 60 HOH HOH . K 6 HOH B 27 427 116 HOH HOH . K 6 HOH B 28 428 141 HOH HOH . K 6 HOH B 29 429 55 HOH HOH . K 6 HOH B 30 430 1 HOH HOH . K 6 HOH B 31 431 148 HOH HOH . K 6 HOH B 32 432 38 HOH HOH . K 6 HOH B 33 433 65 HOH HOH . K 6 HOH B 34 434 36 HOH HOH . K 6 HOH B 35 435 56 HOH HOH . K 6 HOH B 36 436 61 HOH HOH . K 6 HOH B 37 437 70 HOH HOH . K 6 HOH B 38 438 90 HOH HOH . K 6 HOH B 39 439 76 HOH HOH . K 6 HOH B 40 440 35 HOH HOH . K 6 HOH B 41 441 88 HOH HOH . K 6 HOH B 42 442 130 HOH HOH . K 6 HOH B 43 443 135 HOH HOH . K 6 HOH B 44 444 72 HOH HOH . K 6 HOH B 45 445 100 HOH HOH . K 6 HOH B 46 446 83 HOH HOH . K 6 HOH B 47 447 86 HOH HOH . K 6 HOH B 48 448 28 HOH HOH . K 6 HOH B 49 449 115 HOH HOH . K 6 HOH B 50 450 23 HOH HOH . K 6 HOH B 51 451 46 HOH HOH . K 6 HOH B 52 452 125 HOH HOH . K 6 HOH B 53 453 13 HOH HOH . K 6 HOH B 54 454 9 HOH HOH . K 6 HOH B 55 455 137 HOH HOH . K 6 HOH B 56 456 142 HOH HOH . K 6 HOH B 57 457 57 HOH HOH . K 6 HOH B 58 458 105 HOH HOH . K 6 HOH B 59 459 136 HOH HOH . K 6 HOH B 60 460 29 HOH HOH . K 6 HOH B 61 461 80 HOH HOH . K 6 HOH B 62 462 132 HOH HOH . K 6 HOH B 63 463 11 HOH HOH . K 6 HOH B 64 464 49 HOH HOH . K 6 HOH B 65 465 10 HOH HOH . K 6 HOH B 66 466 71 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 2 10.12 -53.494 -5.932 1 25.97 ? PA NAP 201 A 1 HETATM 2 O O1A NAP . . . C 2 11.308 -54.372 -5.697 1 23.42 ? O1A NAP 201 A 1 HETATM 3 O O2A NAP . . . C 2 9.596 -52.881 -7.223 1 21.53 ? O2A NAP 201 A 1 HETATM 4 O O5B NAP . . . C 2 8.803 -54.378 -5.515 1 27.11 ? O5B NAP 201 A 1 HETATM 5 C C5B NAP . . . C 2 8.686 -55.112 -4.27 1 28.06 ? C5B NAP 201 A 1 HETATM 6 C C4B NAP . . . C 2 7.429 -55.952 -4.313 1 27.79 ? C4B NAP 201 A 1 HETATM 7 O O4B NAP . . . C 2 7.628 -57.068 -5.211 1 28.53 ? O4B NAP 201 A 1 HETATM 8 C C3B NAP . . . C 2 7.19 -56.656 -2.984 1 28.49 ? C3B NAP 201 A 1 HETATM 9 O O3B NAP . . . C 2 6.45 -55.819 -2.066 1 33.25 ? O3B NAP 201 A 1 HETATM 10 C C2B NAP . . . C 2 6.47 -57.931 -3.364 1 26.96 ? C2B NAP 201 A 1 HETATM 11 O O2B NAP . . . C 2 5.183 -57.559 -3.694 1 29.99 ? O2B NAP 201 A 1 HETATM 12 C C1B NAP . . . C 2 7.136 -58.297 -4.715 1 27.32 ? C1B NAP 201 A 1 HETATM 13 N N9A NAP . . . C 2 8.253 -59.245 -4.472 1 29.39 ? N9A NAP 201 A 1 HETATM 14 C C8A NAP . . . C 2 9.613 -58.984 -4.328 1 30.61 ? C8A NAP 201 A 1 HETATM 15 N N7A NAP . . . C 2 10.297 -60.104 -4.065 1 32.7 ? N7A NAP 201 A 1 HETATM 16 C C5A NAP . . . C 2 9.364 -61.12 -4.033 1 30.36 ? C5A NAP 201 A 1 HETATM 17 C C6A NAP . . . C 2 9.432 -62.577 -3.838 1 34.8 ? C6A NAP 201 A 1 HETATM 18 N N6A NAP . . . C 2 10.588 -63.195 -3.598 1 31.17 ? N6A NAP 201 A 1 HETATM 19 N N1A NAP . . . C 2 8.254 -63.186 -3.847 1 29.36 ? N1A NAP 201 A 1 HETATM 20 C C2A NAP . . . C 2 7.162 -62.554 -4.115 1 27.82 ? C2A NAP 201 A 1 HETATM 21 N N3A NAP . . . C 2 6.953 -61.267 -4.321 1 31.21 ? N3A NAP 201 A 1 HETATM 22 C C4A NAP . . . C 2 8.059 -60.511 -4.259 1 30.84 ? C4A NAP 201 A 1 HETATM 23 O O3 NAP . . . C 2 10.029 -52.422 -4.642 1 27.03 ? O3 NAP 201 A 1 HETATM 24 P PN NAP . . . C 2 11.108 -51.577 -3.916 1 26.78 ? PN NAP 201 A 1 HETATM 25 O O1N NAP . . . C 2 12.147 -52.359 -3.266 1 26.74 ? O1N NAP 201 A 1 HETATM 26 O O2N NAP . . . C 2 10.139 -50.855 -2.956 1 27.19 ? O2N NAP 201 A 1 HETATM 27 O O5D NAP . . . C 2 11.747 -50.608 -4.972 1 26.32 ? O5D NAP 201 A 1 HETATM 28 C C5D NAP . . . C 2 10.868 -49.832 -5.77 1 27.46 ? C5D NAP 201 A 1 HETATM 29 C C4D NAP . . . C 2 11.576 -48.591 -6.109 1 30.58 ? C4D NAP 201 A 1 HETATM 30 O O4D NAP . . . C 2 12.675 -49.007 -6.961 1 32.02 ? O4D NAP 201 A 1 HETATM 31 C C3D NAP . . . C 2 10.802 -47.622 -6.973 1 36.34 ? C3D NAP 201 A 1 HETATM 32 O O3D NAP . . . C 2 10.134 -46.652 -6.14 1 37.88 ? O3D NAP 201 A 1 HETATM 33 C C2D NAP . . . C 2 11.857 -47.002 -7.868 1 37.21 ? C2D NAP 201 A 1 HETATM 34 O O2D NAP . . . C 2 12.021 -45.655 -7.462 1 38.67 ? O2D NAP 201 A 1 HETATM 35 C C1D NAP . . . C 2 13.11 -47.868 -7.69 1 36.33 ? C1D NAP 201 A 1 HETATM 36 N N1N NAP . . . C 2 13.726 -48.245 -9.014 1 28.96 ? N1N NAP 201 A 1 HETATM 37 C C2N NAP . . . C 2 14.938 -47.797 -9.319 1 28.67 ? C2N NAP 201 A 1 HETATM 38 C C3N NAP . . . C 2 15.463 -48.126 -10.591 1 25.86 ? C3N NAP 201 A 1 HETATM 39 C C7N NAP . . . C 2 16.84 -47.673 -11.035 1 28.05 ? C7N NAP 201 A 1 HETATM 40 O O7N NAP . . . C 2 17.071 -47.569 -12.224 1 30.46 ? O7N NAP 201 A 1 HETATM 41 N N7N NAP . . . C 2 17.744 -47.267 -10.179 1 28.47 ? N7N NAP 201 A 1 HETATM 42 C C4N NAP . . . C 2 14.694 -48.919 -11.462 1 25.41 ? C4N NAP 201 A 1 HETATM 43 C C5N NAP . . . C 2 13.417 -49.323 -11.095 1 26.78 ? C5N NAP 201 A 1 HETATM 44 C C6N NAP . . . C 2 12.958 -48.953 -9.851 1 29.43 ? C6N NAP 201 A 1 HETATM 45 P P2B NAP . . . C 2 3.831 -57.907 -2.739 1 31.92 ? P2B NAP 201 A 1 HETATM 46 O O1X NAP . . . C 2 2.803 -57.741 -3.782 1 31.25 ? O1X NAP 201 A 1 HETATM 47 O O2X NAP . . . C 2 4.025 -59.338 -2.188 1 32.51 ? O2X NAP 201 A 1 HETATM 48 O O3X NAP . . . C 2 4.009 -56.801 -1.703 1 34.35 ? O3X NAP 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #