data_3LUT # _model_server_result.job_id bglawghebgwb6LEFuLkFiQ _model_server_result.datetime_utc '2025-01-13 12:47:47' _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 3lut # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":368}' # _entry.id 3LUT # _exptl.entry_id 3LUT _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 90 _cell.entry_id 3LUT _cell.length_a 113.605 _cell.length_b 113.605 _cell.length_c 260.473 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LUT _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_775 -x+2,-y+2,z -1 0 0 0 -1 0 0 0 1 227.21 227.21 0 3 'crystal symmetry operation' 3_755 -y+2,x,z 0 -1 0 1 0 0 0 0 1 227.21 0 0 4 'crystal symmetry operation' 4_575 y,-x+2,z 0 1 0 -1 0 0 0 0 1 0 227.21 0 # _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 # 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 B OG1 THR 374 B THR 374 1_555 D K K . B K 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc2 B O THR 374 B THR 374 1_555 D K K . B K 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.285 ? metalc ? metalc3 B O THR 374 B THR 374 1_555 E K K . B K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc4 B O VAL 375 B VAL 375 1_555 F K K . B K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.132 ? metalc ? metalc5 B O GLY 376 B GLY 376 1_555 F K K . B K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.193 ? metalc ? metalc6 B O GLY 376 B GLY 376 1_555 G K K . B K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.201 ? # _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 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 3LUT _atom_sites.fract_transf_matrix[1][1] 0.008802 _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] 0.008802 _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] 0.003839 _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 3 NAP A 1 368 1 NAP NAP . D 4 K B 1 500 1 K K . E 4 K B 1 501 2 K K . F 4 K B 1 502 3 K K . G 4 K B 1 503 4 K K . H 4 K B 1 504 5 K K . I 4 K B 1 505 6 K K . J 5 HOH A 1 369 2 HOH HOH . J 5 HOH A 2 370 3 HOH HOH . J 5 HOH A 3 371 4 HOH HOH . J 5 HOH A 4 372 5 HOH HOH . J 5 HOH A 5 373 6 HOH HOH . J 5 HOH A 6 374 7 HOH HOH . J 5 HOH A 7 375 8 HOH HOH . J 5 HOH A 8 376 10 HOH HOH . J 5 HOH A 9 377 11 HOH HOH . J 5 HOH A 10 378 12 HOH HOH . J 5 HOH A 11 379 14 HOH HOH . J 5 HOH A 12 380 15 HOH HOH . J 5 HOH A 13 381 16 HOH HOH . J 5 HOH A 14 382 17 HOH HOH . J 5 HOH A 15 383 18 HOH HOH . J 5 HOH A 16 384 19 HOH HOH . J 5 HOH A 17 385 20 HOH HOH . J 5 HOH A 18 386 21 HOH HOH . J 5 HOH A 19 387 22 HOH HOH . J 5 HOH A 20 388 24 HOH HOH . J 5 HOH A 21 389 25 HOH HOH . J 5 HOH A 22 390 26 HOH HOH . J 5 HOH A 23 391 27 HOH HOH . J 5 HOH A 24 392 28 HOH HOH . J 5 HOH A 25 393 29 HOH HOH . J 5 HOH A 26 394 30 HOH HOH . J 5 HOH A 27 395 32 HOH HOH . J 5 HOH A 28 396 33 HOH HOH . J 5 HOH A 29 397 34 HOH HOH . J 5 HOH A 30 398 36 HOH HOH . J 5 HOH A 31 399 37 HOH HOH . J 5 HOH A 32 400 40 HOH HOH . J 5 HOH A 33 401 41 HOH HOH . J 5 HOH A 34 402 42 HOH HOH . J 5 HOH A 35 403 43 HOH HOH . J 5 HOH A 36 404 44 HOH HOH . J 5 HOH A 37 405 45 HOH HOH . J 5 HOH A 38 406 46 HOH HOH . J 5 HOH A 39 407 47 HOH HOH . J 5 HOH A 40 408 48 HOH HOH . J 5 HOH A 41 409 49 HOH HOH . J 5 HOH A 42 410 50 HOH HOH . J 5 HOH A 43 411 51 HOH HOH . J 5 HOH A 44 412 52 HOH HOH . J 5 HOH A 45 413 53 HOH HOH . J 5 HOH A 46 414 54 HOH HOH . J 5 HOH A 47 415 56 HOH HOH . J 5 HOH A 48 416 57 HOH HOH . J 5 HOH A 49 417 58 HOH HOH . J 5 HOH A 50 418 61 HOH HOH . J 5 HOH A 51 419 62 HOH HOH . J 5 HOH A 52 420 64 HOH HOH . J 5 HOH A 53 421 65 HOH HOH . J 5 HOH A 54 422 66 HOH HOH . J 5 HOH A 55 423 67 HOH HOH . J 5 HOH A 56 424 69 HOH HOH . J 5 HOH A 57 425 70 HOH HOH . J 5 HOH A 58 426 72 HOH HOH . J 5 HOH A 59 427 73 HOH HOH . J 5 HOH A 60 428 74 HOH HOH . J 5 HOH A 61 429 75 HOH HOH . J 5 HOH A 62 430 77 HOH HOH . J 5 HOH A 63 431 78 HOH HOH . J 5 HOH A 64 432 79 HOH HOH . J 5 HOH A 65 433 80 HOH HOH . J 5 HOH A 66 434 81 HOH HOH . J 5 HOH A 67 435 82 HOH HOH . J 5 HOH A 68 436 83 HOH HOH . J 5 HOH A 69 437 84 HOH HOH . J 5 HOH A 70 438 85 HOH HOH . J 5 HOH A 71 439 86 HOH HOH . J 5 HOH A 72 440 87 HOH HOH . K 5 HOH B 1 506 9 HOH HOH . K 5 HOH B 2 507 13 HOH HOH . K 5 HOH B 3 508 23 HOH HOH . K 5 HOH B 4 509 31 HOH HOH . K 5 HOH B 5 510 35 HOH HOH . K 5 HOH B 6 511 38 HOH HOH . K 5 HOH B 7 512 39 HOH HOH . K 5 HOH B 8 513 55 HOH HOH . K 5 HOH B 9 514 59 HOH HOH . K 5 HOH B 10 515 60 HOH HOH . K 5 HOH B 11 516 63 HOH HOH . K 5 HOH B 12 517 68 HOH HOH . K 5 HOH B 13 518 71 HOH HOH . K 5 HOH B 14 519 76 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 74.573 105.336 9.316 1 42.63 ? PA NAP 368 A 1 HETATM 2 O O1A NAP . . . C 3 74.13 106.054 8.096 1 41.24 ? O1A NAP 368 A 1 HETATM 3 O O2A NAP . . . C 3 74.706 103.883 9.06 1 41.95 ? O2A NAP 368 A 1 HETATM 4 O O5B NAP . . . C 3 73.593 105.642 10.547 1 42.77 ? O5B NAP 368 A 1 HETATM 5 C C5B NAP . . . C 3 73.962 105.294 11.861 1 44.39 ? C5B NAP 368 A 1 HETATM 6 C C4B NAP . . . C 3 72.914 105.88 12.799 1 46.41 ? C4B NAP 368 A 1 HETATM 7 O O4B NAP . . . C 3 71.615 105.354 12.518 1 47.47 ? O4B NAP 368 A 1 HETATM 8 C C3B NAP . . . C 3 73.265 105.54 14.233 1 47.21 ? C3B NAP 368 A 1 HETATM 9 O O3B NAP . . . C 3 73.699 106.682 14.936 1 47.6 ? O3B NAP 368 A 1 HETATM 10 C C2B NAP . . . C 3 71.98 104.957 14.808 1 48.53 ? C2B NAP 368 A 1 HETATM 11 O O2B NAP . . . C 3 71.492 105.762 15.889 1 49.79 ? O2B NAP 368 A 1 HETATM 12 C C1B NAP . . . C 3 71.07 104.647 13.615 1 48.56 ? C1B NAP 368 A 1 HETATM 13 N N9A NAP . . . C 3 71.16 103.167 13.439 1 49.56 ? N9A NAP 368 A 1 HETATM 14 C C8A NAP . . . C 3 72.323 102.444 13.306 1 49.54 ? C8A NAP 368 A 1 HETATM 15 N N7A NAP . . . C 3 72.048 101.124 13.202 1 49.71 ? N7A NAP 368 A 1 HETATM 16 C C5A NAP . . . C 3 70.714 100.965 13.276 1 50.25 ? C5A NAP 368 A 1 HETATM 17 C C6A NAP . . . C 3 69.91 99.827 13.227 1 50.93 ? C6A NAP 368 A 1 HETATM 18 N N6A NAP . . . C 3 70.448 98.617 13.077 1 51.3 ? N6A NAP 368 A 1 HETATM 19 N N1A NAP . . . C 3 68.538 99.96 13.333 1 51.64 ? N1A NAP 368 A 1 HETATM 20 C C2A NAP . . . C 3 67.979 101.215 13.496 1 51.16 ? C2A NAP 368 A 1 HETATM 21 N N3A NAP . . . C 3 68.785 102.337 13.539 1 50.14 ? N3A NAP 368 A 1 HETATM 22 C C4A NAP . . . C 3 70.138 102.231 13.428 1 50.05 ? C4A NAP 368 A 1 HETATM 23 O O3 NAP . . . C 3 75.971 105.878 9.905 1 42.51 ? O3 NAP 368 A 1 HETATM 24 P PN NAP . . . C 3 76.685 107.32 9.978 1 42.2 ? PN NAP 368 A 1 HETATM 25 O O1N NAP . . . C 3 76.23 108.114 11.138 1 42.49 ? O1N NAP 368 A 1 HETATM 26 O O2N NAP . . . C 3 76.699 107.911 8.627 1 42.44 ? O2N NAP 368 A 1 HETATM 27 O O5D NAP . . . C 3 78.148 106.814 10.356 1 41.84 ? O5D NAP 368 A 1 HETATM 28 C C5D NAP . . . C 3 79.048 106.483 9.342 1 40.27 ? C5D NAP 368 A 1 HETATM 29 C C4D NAP . . . C 3 80.446 106.819 9.828 1 39.12 ? C4D NAP 368 A 1 HETATM 30 O O4D NAP . . . C 3 81.095 107.329 8.689 1 39.84 ? O4D NAP 368 A 1 HETATM 31 C C3D NAP . . . C 3 80.528 107.92 10.884 1 38.64 ? C3D NAP 368 A 1 HETATM 32 O O3D NAP . . . C 3 80.608 107.432 12.206 1 37.39 ? O3D NAP 368 A 1 HETATM 33 C C2D NAP . . . C 3 81.769 108.694 10.487 1 38.86 ? C2D NAP 368 A 1 HETATM 34 O O2D NAP . . . C 3 82.933 108.163 11.072 1 39.68 ? O2D NAP 368 A 1 HETATM 35 C C1D NAP . . . C 3 81.896 108.444 8.996 1 39.43 ? C1D NAP 368 A 1 HETATM 36 N N1N NAP . . . C 3 81.455 109.627 8.234 1 39.11 ? N1N NAP 368 A 1 HETATM 37 C C2N NAP . . . C 3 82.34 110.2 7.366 1 39.09 ? C2N NAP 368 A 1 HETATM 38 C C3N NAP . . . C 3 81.977 111.33 6.637 1 39.63 ? C3N NAP 368 A 1 HETATM 39 C C7N NAP . . . C 3 82.958 111.954 5.686 1 39.58 ? C7N NAP 368 A 1 HETATM 40 O O7N NAP . . . C 3 82.77 113.301 5.306 1 38.14 ? O7N NAP 368 A 1 HETATM 41 N N7N NAP . . . C 3 83.98 111.222 5.224 1 38.77 ? N7N NAP 368 A 1 HETATM 42 C C4N NAP . . . C 3 80.708 111.887 6.798 1 40.26 ? C4N NAP 368 A 1 HETATM 43 C C5N NAP . . . C 3 79.808 111.301 7.69 1 40.51 ? C5N NAP 368 A 1 HETATM 44 C C6N NAP . . . C 3 80.197 110.162 8.4 1 39.84 ? C6N NAP 368 A 1 HETATM 45 P P2B NAP . . . C 3 70.183 106.7 16.071 1 49.34 ? P2B NAP 368 A 1 HETATM 46 O O1X NAP . . . C 3 69.471 106.909 14.75 1 50.15 ? O1X NAP 368 A 1 HETATM 47 O O2X NAP . . . C 3 69.291 105.997 17.064 1 49.85 ? O2X NAP 368 A 1 HETATM 48 O O3X NAP . . . C 3 70.586 108.025 16.691 1 48.29 ? O3X NAP 368 A 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 48 #