data_1RX9 # _model_server_result.job_id NYinVpLRus2flhOaOhNf7Q _model_server_result.datetime_utc '2025-02-17 09:27:03' _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 1rx9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":164}' # _entry.id 1RX9 # _exptl.entry_id 1RX9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 4 _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 1RX9 _cell.length_a 34.409 _cell.length_b 45.512 _cell.length_c 99.199 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RX9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 4 _struct_asym.id D _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 metalc ? metalc1 A O ASP 116 A ASP 116 1_455 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 A ND1 HIS 149 A HIS 149 1_455 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc3 A OXT ARG 159 A ARG 159 1_555 B CA CA . A CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc4 B CA CA . A CA 300 1_555 E O HOH . A HOH 310 3_645 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc5 B CA CA . A CA 300 1_555 E O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 B CA CA . A CA 300 1_555 E O HOH . A HOH 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc7 B CA CA . A CA 300 1_555 E O HOH . A HOH 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? # _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 246 n n PA O2A NAP sing 247 n n PA O5B NAP sing 248 n n PA O3 NAP sing 249 n n O2A HOA2 NAP sing 250 n n O5B C5B NAP sing 251 n n C5B C4B NAP sing 252 n n C5B H51A NAP sing 253 n n C5B H52A NAP sing 254 n n C4B O4B NAP sing 255 n n C4B C3B NAP sing 256 n n C4B H4B NAP sing 257 n n O4B C1B NAP sing 258 n n C3B O3B NAP sing 259 n n C3B C2B NAP sing 260 n n C3B H3B NAP sing 261 n n O3B HO3A NAP sing 262 n n C2B O2B NAP sing 263 n n C2B C1B NAP sing 264 n n C2B H2B NAP sing 265 n n O2B P2B NAP sing 266 n n C1B N9A NAP sing 267 n n C1B H1B NAP sing 268 n n N9A C8A NAP sing 269 n y N9A C4A NAP sing 270 n y C8A N7A NAP doub 271 n y C8A H8A NAP sing 272 n n N7A C5A NAP sing 273 n y C5A C6A NAP sing 274 n y C5A C4A NAP doub 275 n y C6A N6A NAP sing 276 n n C6A N1A NAP doub 277 n y N6A H61A NAP sing 278 n n N6A H62A NAP sing 279 n n N1A C2A NAP sing 280 n y C2A N3A NAP doub 281 n y C2A H2A NAP sing 282 n n N3A C4A NAP sing 283 n y O3 PN NAP sing 284 n n PN O1N NAP doub 285 n n PN O2N NAP sing 286 n n PN O5D NAP sing 287 n n O5D C5D NAP sing 288 n n C5D C4D NAP sing 289 n n C5D H51N NAP sing 290 n n C5D H52N NAP sing 291 n n C4D O4D NAP sing 292 n n C4D C3D NAP sing 293 n n C4D H4D NAP sing 294 n n O4D C1D NAP sing 295 n n C3D O3D NAP sing 296 n n C3D C2D NAP sing 297 n n C3D H3D NAP sing 298 n n O3D HO3N NAP sing 299 n n C2D O2D NAP sing 300 n n C2D C1D NAP sing 301 n n C2D H2D NAP sing 302 n n O2D HO2N NAP sing 303 n n C1D N1N NAP sing 304 n n C1D H1D NAP sing 305 n n N1N C2N NAP sing 306 n y N1N C6N NAP doub 307 n y C2N C3N NAP doub 308 n y C2N H2N NAP sing 309 n n C3N C7N NAP sing 310 n n C3N C4N NAP sing 311 n y C7N O7N NAP doub 312 n n C7N N7N NAP sing 313 n n N7N H71N NAP sing 314 n n N7N H72N NAP sing 315 n n C4N C5N NAP doub 316 n y C4N H4N NAP sing 317 n n C5N C6N NAP sing 318 n y C5N H5N NAP sing 319 n n C6N H6N NAP sing 320 n n P2B O1X NAP doub 321 n n P2B O2X NAP sing 322 n n P2B O3X NAP sing 323 n n O2X HOP2 NAP sing 324 n n O3X HOP3 NAP sing 325 n n # _atom_sites.entry_id 1RX9 _atom_sites.fract_transf_matrix[1][1] 0.029062 _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] 0.021972 _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] 0.010081 _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 CA A 1 300 300 CA CA . C 3 BME A 1 162 162 BME BME . D 4 NAP A 1 164 164 NAP NAP . E 5 HOH A 1 301 301 HOH HOH . E 5 HOH A 2 302 302 HOH HOH . E 5 HOH A 3 303 303 HOH HOH . E 5 HOH A 4 304 304 HOH HOH . E 5 HOH A 5 305 305 HOH HOH . E 5 HOH A 6 307 307 HOH HOH . E 5 HOH A 7 309 309 HOH HOH . E 5 HOH A 8 310 310 HOH HOH . E 5 HOH A 9 314 314 HOH HOH . E 5 HOH A 10 316 316 HOH HOH . E 5 HOH A 11 317 317 HOH HOH . E 5 HOH A 12 319 319 HOH HOH . E 5 HOH A 13 320 320 HOH HOH . E 5 HOH A 14 321 321 HOH HOH . E 5 HOH A 15 322 322 HOH HOH . E 5 HOH A 16 323 323 HOH HOH . E 5 HOH A 17 324 324 HOH HOH . E 5 HOH A 18 325 325 HOH HOH . E 5 HOH A 19 326 326 HOH HOH . E 5 HOH A 20 327 327 HOH HOH . E 5 HOH A 21 328 328 HOH HOH . E 5 HOH A 22 329 329 HOH HOH . E 5 HOH A 23 332 332 HOH HOH . E 5 HOH A 24 333 333 HOH HOH . E 5 HOH A 25 334 334 HOH HOH . E 5 HOH A 26 335 335 HOH HOH . E 5 HOH A 27 336 336 HOH HOH . E 5 HOH A 28 340 340 HOH HOH . E 5 HOH A 29 341 341 HOH HOH . E 5 HOH A 30 343 343 HOH HOH . E 5 HOH A 31 344 344 HOH HOH . E 5 HOH A 32 345 345 HOH HOH . E 5 HOH A 33 346 346 HOH HOH . E 5 HOH A 34 347 347 HOH HOH . E 5 HOH A 35 348 348 HOH HOH . E 5 HOH A 36 349 349 HOH HOH . E 5 HOH A 37 350 350 HOH HOH . E 5 HOH A 38 354 354 HOH HOH . E 5 HOH A 39 356 356 HOH HOH . E 5 HOH A 40 357 357 HOH HOH . E 5 HOH A 41 358 358 HOH HOH . E 5 HOH A 42 361 361 HOH HOH . E 5 HOH A 43 362 362 HOH HOH . E 5 HOH A 44 363 363 HOH HOH . E 5 HOH A 45 364 364 HOH HOH . E 5 HOH A 46 365 365 HOH HOH . E 5 HOH A 47 366 366 HOH HOH . E 5 HOH A 48 368 368 HOH HOH . E 5 HOH A 49 370 370 HOH HOH . E 5 HOH A 50 371 371 HOH HOH . E 5 HOH A 51 372 372 HOH HOH . E 5 HOH A 52 373 373 HOH HOH . E 5 HOH A 53 374 374 HOH HOH . E 5 HOH A 54 375 375 HOH HOH . E 5 HOH A 55 376 376 HOH HOH . E 5 HOH A 56 377 377 HOH HOH . E 5 HOH A 57 378 378 HOH HOH . E 5 HOH A 58 379 379 HOH HOH . E 5 HOH A 59 380 380 HOH HOH . E 5 HOH A 60 381 381 HOH HOH . E 5 HOH A 61 382 382 HOH HOH . E 5 HOH A 62 383 383 HOH HOH . E 5 HOH A 63 384 384 HOH HOH . E 5 HOH A 64 385 385 HOH HOH . E 5 HOH A 65 386 386 HOH HOH . E 5 HOH A 66 387 387 HOH HOH . E 5 HOH A 67 388 388 HOH HOH . E 5 HOH A 68 389 389 HOH HOH . E 5 HOH A 69 390 390 HOH HOH . E 5 HOH A 70 391 391 HOH HOH . E 5 HOH A 71 392 392 HOH HOH . E 5 HOH A 72 393 393 HOH HOH . E 5 HOH A 73 395 395 HOH HOH . E 5 HOH A 74 396 396 HOH HOH . E 5 HOH A 75 397 397 HOH HOH . E 5 HOH A 76 398 398 HOH HOH . E 5 HOH A 77 399 399 HOH HOH . E 5 HOH A 78 401 401 HOH HOH . E 5 HOH A 79 402 402 HOH HOH . E 5 HOH A 80 403 403 HOH HOH . E 5 HOH A 81 404 404 HOH HOH . E 5 HOH A 82 405 405 HOH HOH . E 5 HOH A 83 406 406 HOH HOH . E 5 HOH A 84 407 407 HOH HOH . E 5 HOH A 85 408 408 HOH HOH . E 5 HOH A 86 409 409 HOH HOH . E 5 HOH A 87 410 410 HOH HOH . E 5 HOH A 88 411 411 HOH HOH . E 5 HOH A 89 412 412 HOH HOH . E 5 HOH A 90 413 413 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 . . . D 4 29.65 54.155 15.052 1 30.15 ? PA NAP 164 A 1 HETATM 2 O O1A NAP . . . D 4 28.518 53.603 15.863 1 12.64 ? O1A NAP 164 A 1 HETATM 3 O O2A NAP . . . D 4 30.213 53.541 13.827 1 12.51 ? O2A NAP 164 A 1 HETATM 4 O O5B NAP . . . D 4 29.262 55.637 14.577 1 41.67 ? O5B NAP 164 A 1 HETATM 5 C C5B NAP . . . D 4 28.561 56.627 15.371 1 28.74 ? C5B NAP 164 A 1 HETATM 6 C C4B NAP . . . D 4 28.191 57.866 14.592 1 23.88 ? C4B NAP 164 A 1 HETATM 7 O O4B NAP . . . D 4 26.981 57.591 13.87 1 14.8 ? O4B NAP 164 A 1 HETATM 8 C C3B NAP . . . D 4 27.743 58.995 15.503 1 25.12 ? C3B NAP 164 A 1 HETATM 9 O O3B NAP . . . D 4 28.861 59.776 15.856 1 26.89 ? O3B NAP 164 A 1 HETATM 10 C C2B NAP . . . D 4 26.78 59.85 14.665 1 25 ? C2B NAP 164 A 1 HETATM 11 O O2B NAP . . . D 4 27.592 60.518 13.726 1 30.54 ? O2B NAP 164 A 1 HETATM 12 C C1B NAP . . . D 4 26.146 58.723 13.865 1 21.14 ? C1B NAP 164 A 1 HETATM 13 N N9A NAP . . . D 4 24.973 58.33 14.63 1 22.29 ? N9A NAP 164 A 1 HETATM 14 C C8A NAP . . . D 4 24.833 57.338 15.559 1 19.07 ? C8A NAP 164 A 1 HETATM 15 N N7A NAP . . . D 4 23.598 57.289 16.042 1 24.93 ? N7A NAP 164 A 1 HETATM 16 C C5A NAP . . . D 4 22.929 58.375 15.395 1 18.57 ? C5A NAP 164 A 1 HETATM 17 C C6A NAP . . . D 4 21.607 58.87 15.408 1 22.47 ? C6A NAP 164 A 1 HETATM 18 N N6A NAP . . . D 4 20.626 58.38 16.2 1 28.77 ? N6A NAP 164 A 1 HETATM 19 N N1A NAP . . . D 4 21.31 59.949 14.596 1 13.05 ? N1A NAP 164 A 1 HETATM 20 C C2A NAP . . . D 4 22.262 60.436 13.834 1 15.34 ? C2A NAP 164 A 1 HETATM 21 N N3A NAP . . . D 4 23.561 60.044 13.713 1 25.29 ? N3A NAP 164 A 1 HETATM 22 C C4A NAP . . . D 4 23.801 59.011 14.508 1 22.14 ? C4A NAP 164 A 1 HETATM 23 O O3 NAP . . . D 4 30.925 54.421 15.995 1 36.17 ? O3 NAP 164 A 1 HETATM 24 P PN NAP . . . D 4 31.464 53.795 17.408 1 30.81 ? PN NAP 164 A 1 HETATM 25 O O1N NAP . 2 . D 4 30.379 54.023 18.431 0.5 18.07 ? O1N NAP 164 A 1 HETATM 26 O O5D NAP . 1 . D 4 32.808 54.574 17.727 0.5 35.81 ? O5D NAP 164 A 1 HETATM 27 O O5D NAP . 2 . D 4 31.924 52.4 17.222 0.5 34.64 ? O5D NAP 164 A 1 HETATM 28 C C5D NAP . 1 . D 4 32.95 56.071 17.782 0.5 62.11 ? C5D NAP 164 A 1 HETATM 29 C C5D NAP . 2 . D 4 33.13 52.051 16.402 0.5 62.11 ? C5D NAP 164 A 1 HETATM 30 C C4D NAP . 1 . D 4 34.503 56.397 17.853 0.5 78.43 ? C4D NAP 164 A 1 HETATM 31 C C4D NAP . 2 . D 4 34.278 51.045 16.619 0.5 63.14 ? C4D NAP 164 A 1 HETATM 32 O O4D NAP . 1 . D 4 34.938 56.868 19.175 0.5 86.86 ? O4D NAP 164 A 1 HETATM 33 O O4D NAP . 2 . D 4 33.438 49.836 16.561 0.5 64.12 ? O4D NAP 164 A 1 HETATM 34 C C3D NAP . 1 . D 4 35.414 55.148 17.651 0.5 76.89 ? C3D NAP 164 A 1 HETATM 35 C C3D NAP . 2 . D 4 35.634 50.563 15.995 0.5 59.84 ? C3D NAP 164 A 1 HETATM 36 O O3D NAP . 1 . D 4 36.404 55.407 16.74 0.5 76.51 ? O3D NAP 164 A 1 HETATM 37 O O3D NAP . 2 . D 4 36.556 50.373 16.991 0.5 55.71 ? O3D NAP 164 A 1 HETATM 38 C C2D NAP . 1 . D 4 36.072 54.89 19.046 0.5 83.9 ? C2D NAP 164 A 1 HETATM 39 C C2D NAP . 2 . D 4 35.241 49.337 15.102 0.5 63.27 ? C2D NAP 164 A 1 HETATM 40 O O2D NAP . 1 . D 4 37.414 55.098 18.856 0.5 88 ? O2D NAP 164 A 1 HETATM 41 O O2D NAP . 2 . D 4 36.26 48.563 14.598 0.5 56.58 ? O2D NAP 164 A 1 HETATM 42 C C1D NAP . 1 . D 4 35.369 55.724 19.989 0.5 86.12 ? C1D NAP 164 A 1 HETATM 43 C C1D NAP . 2 . D 4 34.083 48.784 15.765 0.5 65.86 ? C1D NAP 164 A 1 HETATM 44 N N1N NAP . 2 . D 4 33.072 47.788 15.152 0.5 61.88 ? N1N NAP 164 A 1 HETATM 45 C C2N NAP . 2 . D 4 33.229 46.413 15.37 0.5 62.97 ? C2N NAP 164 A 1 HETATM 46 C C3N NAP . 2 . D 4 32.384 45.532 14.877 0.5 57.06 ? C3N NAP 164 A 1 HETATM 47 C C7N NAP . 2 . D 4 32.641 44.127 15.18 0.5 41.8 ? C7N NAP 164 A 1 HETATM 48 O O7N NAP . 2 . D 4 31.818 43.267 14.756 0.5 18.98 ? O7N NAP 164 A 1 HETATM 49 N N7N NAP . 2 . D 4 33.616 43.749 15.999 0.5 40.47 ? N7N NAP 164 A 1 HETATM 50 C C4N NAP . 2 . D 4 31.145 45.944 14.016 0.5 54.44 ? C4N NAP 164 A 1 HETATM 51 C C5N NAP . 2 . D 4 31.113 47.466 13.868 0.5 51.92 ? C5N NAP 164 A 1 HETATM 52 C C6N NAP . 2 . D 4 31.999 48.218 14.402 0.5 54.92 ? C6N NAP 164 A 1 HETATM 53 P P2B NAP . . . D 4 27.67 62.105 13.669 1 27.35 ? P2B NAP 164 A 1 HETATM 54 O O1X NAP . . . D 4 28.018 62.369 12.161 1 24.63 ? O1X NAP 164 A 1 HETATM 55 O O2X NAP . . . D 4 26.354 62.539 14.264 1 21.15 ? O2X NAP 164 A 1 HETATM 56 O O3X NAP . . . D 4 28.95 62.285 14.46 1 33.26 ? O3X NAP 164 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 499 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 56 #