0.019545 0.000000 0.000000 0.000000 0.016866 0.000000 0.000000 0.000000 0.016290 0.000000 0.000000 0.000000 Prabu-Jeyabalan, M. King, N.M. Schiffer, C.A. Nalivaika, E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 51.164 59.291 61.389 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C38 H50 N6 O5 670.841 (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide Fortovase; SAQUINAVIR; RO 31-8959 peptide-like C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N N N 128 N C N 129 N C N 130 N O N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N O N 159 N H N 160 N H N 161 N N N 162 S C N 163 N C N 164 N O N 165 S C N 166 N C N 167 N C N 168 N C N 169 N O N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N N N 184 S C N 185 N C N 186 N O N 187 N C N 188 N C N 189 N C N 190 N C N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N N N 206 S C N 207 N C N 208 N O N 209 N C N 210 N C N 211 N C N 212 N C N 213 N N N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 N C N 235 N C N 236 N S N 237 N C N 238 N O N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N N N 251 S C N 252 N C N 253 N O N 254 N C Y 255 N C Y 256 N C Y 257 N C Y 258 N C Y 259 N C Y 260 N C N 261 N O N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N P N 274 N O N 275 N O N 276 N O N 277 N O N 278 N N N 279 S C N 280 N C N 281 N O N 282 N C N 283 N C N 284 N C N 285 N O N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N C N 296 N O Y 297 N N Y 298 N C Y 299 N C Y 300 N C Y 301 N C Y 302 N C Y 303 N C Y 304 N C Y 305 N C Y 306 N C N 307 N N N 308 S C N 309 N C N 310 N O N 311 N C N 312 N C N 313 N O N 314 N N N 315 R C N 316 N O N 317 S C N 318 N N N 319 N C Y 320 N C Y 321 N C Y 322 N C Y 323 N C Y 324 N C Y 325 N C N 326 N N N 327 N C N 328 S C N 329 N C N 330 N O N 331 N C N 332 S C N 333 N C N 334 N C N 335 N C N 336 N C N 337 S C N 338 N C N 339 N N N 340 N C N 341 N C N 342 N C N 343 N C N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N N N 395 S C N 396 N C N 397 N O N 398 R C N 399 N O N 400 N C N 401 N O N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N N N 412 S C N 413 N C N 414 N O N 415 N C Y 416 N C Y 417 N C Y 418 N C Y 419 N N Y 420 N C Y 421 N C Y 422 N C Y 423 N C Y 424 N C N 425 N O N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N N N 439 S C N 440 N C N 441 N O N 442 N C Y 443 N C Y 444 N C Y 445 N C Y 446 N C Y 447 N C Y 448 N C N 449 N O N 450 N O N 451 N H N 452 N H N 453 N H N 454 N H N 455 N H N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N N N 463 S C N 464 N C N 465 N O N 466 N C N 467 N C N 468 N C N 469 N O N 470 N H N 471 N H N 472 N H N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N doub N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N doub N 244 N sing N 245 N sing N 246 N sing N 247 N sing Y 248 N doub Y 249 N sing Y 250 N sing N 251 N sing Y 252 N doub N 253 N sing Y 254 N doub N 255 N sing Y 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N doub N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N doub N 282 N sing Y 283 N doub Y 284 N sing Y 285 N sing Y 286 N doub N 287 N sing Y 288 N sing N 289 N sing Y 290 N doub Y 291 N sing Y 292 N sing N 293 N sing Y 294 N doub N 295 N sing Y 296 N sing N 297 N sing Y 298 N doub N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N doub N 306 N sing N 307 N sing N 308 N sing N 309 N doub N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing Y 324 N doub Y 325 N sing Y 326 N sing N 327 N sing Y 328 N doub N 329 N sing Y 330 N doub N 331 N sing Y 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N doub N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N doub N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N doub N 407 N sing N 408 N sing N 409 N sing N 410 N sing Y 411 N doub Y 412 N sing Y 413 N sing N 414 N sing Y 415 N doub Y 416 N sing Y 417 N sing N 418 N sing Y 419 N sing Y 420 N doub N 421 N sing Y 422 N doub N 423 N sing Y 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N doub N 435 N sing N 436 N sing N 437 N sing N 438 N sing Y 439 N doub Y 440 N sing Y 441 N sing N 442 N sing Y 443 N doub N 444 N sing Y 445 N doub N 446 N sing Y 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N doub N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing US Acs Chem.Biol. 1554-8929 7 1536 1546 10.1021/cb300191k 22712830 Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease. 2012 10.2210/pdb3ekq/pdb pdb_00003ekq 300 1 Yale Mirrors IMAGE PLATE 2008-01-28 RIGAKU RAXIS IV Yale mirrors SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 10845.814 Protease 3.4.23.16 UNP residues 491-589 Q7K, L10I, G48V, I54V, V64I, V82T 2 man polymer 670.841 (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide 1 syn non-polymer 94.971 PHOSPHATE ION 2 syn non-polymer 18.015 water 74 nat water Retropepsin, PR no no PQITLWKRPIVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIVGIGGFVKVRQYDQIPIEICGHKAIGTVLVGPT PTNIIGRNLLTQIGCTLNF PQITLWKRPIVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIVGIGGFVKVRQYDQIPIEICGHKAIGTVLVGPT PTNIIGRNLLTQIGCTLNF A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n HIV-1 HXB2 sample gag-pol 11685 HIV-1 M:B_ARV2/SF2 562 Escherichia coli TAP106 Plasmid PXC35 1 2.15 42.69 VAPOR DIFFUSION, HANGING DROP 6.2 pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K 300 pdbx_unobs_or_zero_occ_atoms software chem_comp database_2 entity pdbx_entity_nonpoly pdbx_unobs_or_zero_occ_atoms struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Advisory Atomic model Database references Derived calculations Non-polymer description Refinement description Structure summary Version format compliance Database references Database references Other Advisory Refinement description Advisory Database references Derived calculations Structure summary Data collection Refinement description 1 0 2009-09-01 1 1 2011-07-13 1 2 2012-07-25 1 3 2012-10-17 1 4 2013-02-27 1 5 2017-10-25 1 6 2021-10-20 1 7 2023-08-30 _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_entity_nonpoly.name _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2008-09-19 REL REL ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide PO4 PHOSPHATE ION HOH water THE INHIBITOR ROC IS A HYDROXYETHYLAMINE CONTAINING TRANSITION STATE MIMETIC. 1F7A PDB ENTRY 1F7A PDB experimental model Inhibitor Saquinavir Peptide-like QNC 1 2 ROC ROC 100 A PO4 502 3 PO4 PO4 502 A PO4 501 3 PO4 PO4 501 B WAT 2 4 HOH HOH 503 A WAT 3 4 HOH HOH 504 A WAT 4 4 HOH HOH 505 A WAT 6 4 HOH HOH 506 A WAT 7 4 HOH HOH 507 A WAT 8 4 HOH HOH 508 A WAT 9 4 HOH HOH 509 A WAT 11 4 HOH HOH 510 A WAT 15 4 HOH HOH 511 A WAT 20 4 HOH HOH 512 A WAT 22 4 HOH HOH 513 A WAT 23 4 HOH HOH 514 A WAT 24 4 HOH HOH 515 A WAT 25 4 HOH HOH 516 A WAT 26 4 HOH HOH 517 A WAT 27 4 HOH HOH 518 A WAT 28 4 HOH HOH 519 A WAT 29 4 HOH HOH 520 A WAT 30 4 HOH HOH 521 A WAT 31 4 HOH HOH 522 A WAT 32 4 HOH HOH 523 A WAT 33 4 HOH HOH 524 A WAT 34 4 HOH HOH 525 A WAT 35 4 HOH HOH 526 A WAT 36 4 HOH HOH 527 A WAT 37 4 HOH HOH 528 A WAT 39 4 HOH HOH 529 A WAT 41 4 HOH HOH 530 A WAT 42 4 HOH HOH 531 A WAT 51 4 HOH HOH 532 A WAT 52 4 HOH HOH 533 A WAT 53 4 HOH HOH 534 A WAT 54 4 HOH HOH 535 A WAT 55 4 HOH HOH 536 A WAT 56 4 HOH HOH 537 A WAT 71 4 HOH HOH 538 A WAT 72 4 HOH HOH 539 A WAT 73 4 HOH HOH 540 A WAT 74 4 HOH HOH 541 A WAT 75 4 HOH HOH 542 A WAT 76 4 HOH HOH 543 A WAT 77 4 HOH HOH 544 A WAT 78 4 HOH HOH 545 A WAT 81 4 HOH HOH 546 A WAT 83 4 HOH HOH 547 A WAT 84 4 HOH HOH 548 A WAT 10 4 HOH HOH 549 A WAT 5 4 HOH HOH 506 B WAT 46 4 HOH HOH 507 B WAT 79 4 HOH HOH 508 B WAT 80 4 HOH HOH 509 B WAT 82 4 HOH HOH 510 B WAT 85 4 HOH HOH 511 B WAT 1 4 HOH HOH 512 B WAT 12 4 HOH HOH 513 B WAT 13 4 HOH HOH 514 B WAT 14 4 HOH HOH 515 B WAT 16 4 HOH HOH 516 B WAT 17 4 HOH HOH 517 B WAT 18 4 HOH HOH 518 B WAT 19 4 HOH HOH 519 B WAT 38 4 HOH HOH 520 B WAT 58 4 HOH HOH 521 B WAT 60 4 HOH HOH 522 B WAT 61 4 HOH HOH 523 B WAT 62 4 HOH HOH 524 B WAT 63 4 HOH HOH 525 B WAT 64 4 HOH HOH 526 B WAT 65 4 HOH HOH 527 B WAT 66 4 HOH HOH 528 B WAT 67 4 HOH HOH 529 B WAT 68 4 HOH HOH 530 B WAT 69 4 HOH HOH 531 B WAT 70 4 HOH HOH 532 B PRO 1 n 1 PRO 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A THR 4 n 4 THR 4 A LEU 5 n 5 LEU 5 A TRP 6 n 6 TRP 6 A ALA 7 n 7 LYS 7 A ARG 8 n 8 ARG 8 A PRO 9 n 9 PRO 9 A ILE 10 n 10 ILE 10 A VAL 11 n 11 VAL 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A ARG 14 n 14 ARG 14 A ILE 15 n 15 ILE 15 A GLY 16 n 16 GLY 16 A GLY 17 n 17 GLY 17 A GLN 18 n 18 GLN 18 A LEU 19 n 19 LEU 19 A LYS 20 n 20 LYS 20 A GLU 21 n 21 GLU 21 A ALA 22 n 22 ALA 22 A LEU 23 n 23 LEU 23 A LEU 24 n 24 LEU 24 A ASP 25 n 25 ASP 25 A THR 26 n 26 THR 26 A GLY 27 n 27 GLY 27 A ALA 28 n 28 ALA 28 A ASP 29 n 29 ASP 29 A ASP 30 n 30 ASP 30 A THR 31 n 31 THR 31 A VAL 32 n 32 VAL 32 A LEU 33 n 33 LEU 33 A GLU 34 n 34 GLU 34 A GLU 35 n 35 GLU 35 A MET 36 n 36 MET 36 A ASN 37 n 37 ASN 37 A LEU 38 n 38 LEU 38 A PRO 39 n 39 PRO 39 A GLY 40 n 40 GLY 40 A ALA 41 n 41 LYS 41 A TRP 42 n 42 TRP 42 A ALA 43 n 43 LYS 43 A PRO 44 n 44 PRO 44 A LYS 45 n 45 LYS 45 A MET 46 n 46 MET 46 A ILE 47 n 47 ILE 47 A VAL 48 n 48 VAL 48 A GLY 49 n 49 GLY 49 A ILE 50 n 50 ILE 50 A GLY 51 n 51 GLY 51 A GLY 52 n 52 GLY 52 A PHE 53 n 53 PHE 53 A VAL 54 n 54 VAL 54 A ALA 55 n 55 LYS 55 A VAL 56 n 56 VAL 56 A ARG 57 n 57 ARG 57 A GLN 58 n 58 GLN 58 A TYR 59 n 59 TYR 59 A ASP 60 n 60 ASP 60 A GLN 61 n 61 GLN 61 A ILE 62 n 62 ILE 62 A PRO 63 n 63 PRO 63 A ILE 64 n 64 ILE 64 A GLU 65 n 65 GLU 65 A ILE 66 n 66 ILE 66 A CYS 67 n 67 CYS 67 A GLY 68 n 68 GLY 68 A HIS 69 n 69 HIS 69 A LYS 70 n 70 LYS 70 A ALA 71 n 71 ALA 71 A ILE 72 n 72 ILE 72 A GLY 73 n 73 GLY 73 A THR 74 n 74 THR 74 A VAL 75 n 75 VAL 75 A LEU 76 n 76 LEU 76 A VAL 77 n 77 VAL 77 A GLY 78 n 78 GLY 78 A PRO 79 n 79 PRO 79 A THR 80 n 80 THR 80 A PRO 81 n 81 PRO 81 A ALA 82 n 82 THR 82 A ASN 83 n 83 ASN 83 A ILE 84 n 84 ILE 84 A ILE 85 n 85 ILE 85 A GLY 86 n 86 GLY 86 A ARG 87 n 87 ARG 87 A ASN 88 n 88 ASN 88 A LEU 89 n 89 LEU 89 A LEU 90 n 90 LEU 90 A THR 91 n 91 THR 91 A GLN 92 n 92 GLN 92 A ILE 93 n 93 ILE 93 A GLY 94 n 94 GLY 94 A CYS 95 n 95 CYS 95 A THR 96 n 96 THR 96 A LEU 97 n 97 LEU 97 A ASN 98 n 98 ASN 98 A PHE 99 n 99 PHE 99 A PRO 1 n 1 PRO 1 B GLN 2 n 2 GLN 2 B ILE 3 n 3 ILE 3 B THR 4 n 4 THR 4 B LEU 5 n 5 LEU 5 B TRP 6 n 6 TRP 6 B ALA 7 n 7 LYS 7 B ARG 8 n 8 ARG 8 B PRO 9 n 9 PRO 9 B ILE 10 n 10 ILE 10 B VAL 11 n 11 VAL 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B ALA 14 n 14 ARG 14 B ILE 15 n 15 ILE 15 B GLY 16 n 16 GLY 16 B GLY 17 n 17 GLY 17 B GLN 18 n 18 GLN 18 B LEU 19 n 19 LEU 19 B LYS 20 n 20 LYS 20 B GLU 21 n 21 GLU 21 B ALA 22 n 22 ALA 22 B LEU 23 n 23 LEU 23 B LEU 24 n 24 LEU 24 B ASP 25 n 25 ASP 25 B THR 26 n 26 THR 26 B GLY 27 n 27 GLY 27 B ALA 28 n 28 ALA 28 B ASP 29 n 29 ASP 29 B ASP 30 n 30 ASP 30 B THR 31 n 31 THR 31 B VAL 32 n 32 VAL 32 B LEU 33 n 33 LEU 33 B GLU 34 n 34 GLU 34 B GLU 35 n 35 GLU 35 B MET 36 n 36 MET 36 B ALA 37 n 37 ASN 37 B LEU 38 n 38 LEU 38 B PRO 39 n 39 PRO 39 B GLY 40 n 40 GLY 40 B ALA 41 n 41 LYS 41 B TRP 42 n 42 TRP 42 B ALA 43 n 43 LYS 43 B PRO 44 n 44 PRO 44 B LYS 45 n 45 LYS 45 B MET 46 n 46 MET 46 B ILE 47 n 47 ILE 47 B VAL 48 n 48 VAL 48 B GLY 49 n 49 GLY 49 B ILE 50 n 50 ILE 50 B GLY 51 n 51 GLY 51 B GLY 52 n 52 GLY 52 B PHE 53 n 53 PHE 53 B VAL 54 n 54 VAL 54 B LYS 55 n 55 LYS 55 B VAL 56 n 56 VAL 56 B ARG 57 n 57 ARG 57 B GLN 58 n 58 GLN 58 B TYR 59 n 59 TYR 59 B ASP 60 n 60 ASP 60 B GLN 61 n 61 GLN 61 B ILE 62 n 62 ILE 62 B PRO 63 n 63 PRO 63 B ILE 64 n 64 ILE 64 B GLU 65 n 65 GLU 65 B ILE 66 n 66 ILE 66 B CYS 67 n 67 CYS 67 B GLY 68 n 68 GLY 68 B HIS 69 n 69 HIS 69 B ALA 70 n 70 LYS 70 B ALA 71 n 71 ALA 71 B ILE 72 n 72 ILE 72 B GLY 73 n 73 GLY 73 B THR 74 n 74 THR 74 B VAL 75 n 75 VAL 75 B LEU 76 n 76 LEU 76 B VAL 77 n 77 VAL 77 B GLY 78 n 78 GLY 78 B PRO 79 n 79 PRO 79 B THR 80 n 80 THR 80 B PRO 81 n 81 PRO 81 B ALA 82 n 82 THR 82 B ASN 83 n 83 ASN 83 B ILE 84 n 84 ILE 84 B ILE 85 n 85 ILE 85 B GLY 86 n 86 GLY 86 B ARG 87 n 87 ARG 87 B ASN 88 n 88 ASN 88 B LEU 89 n 89 LEU 89 B LEU 90 n 90 LEU 90 B THR 91 n 91 THR 91 B GLN 92 n 92 GLN 92 B ILE 93 n 93 ILE 93 B GLY 94 n 94 GLY 94 B CYS 95 n 95 CYS 95 B THR 96 n 96 THR 96 B LEU 97 n 97 LEU 97 B ASN 98 n 98 ASN 98 B PHE 99 n 99 PHE 99 B 4.2750 2.7027 0.0999 7.5149 0.0582 0.4083 -0.1426 0.4732 0.4162 -0.6332 0.1385 0.2435 -0.0172 -0.2500 0.0041 0.0031 -0.0802 -0.0645 0.0052 0.0314 -0.0972 refined 20.2272 8.9636 2.5108 X-RAY DIFFRACTION 12.2035 -3.3844 -1.7160 1.9351 0.0026 0.4661 -0.3962 -0.5679 0.2745 0.0146 0.4136 -0.2390 0.1819 0.0818 -0.0174 -0.0144 -0.0178 0.0087 -0.0315 -0.0242 -0.0329 refined 28.6078 9.4922 12.1298 X-RAY DIFFRACTION 5.6208 3.9950 0.4607 4.9133 -0.6287 0.4786 -0.4040 0.7706 -0.2739 -0.1703 0.0743 0.5712 0.6178 -0.3841 0.3297 -0.0746 -0.0544 -0.0396 0.0677 -0.0622 -0.0914 refined 11.9680 -0.3245 4.8674 X-RAY DIFFRACTION 29.3749 10.6233 6.4842 11.8391 1.7662 1.4732 0.4616 -1.2747 0.0634 0.7436 -0.5552 0.3759 0.2606 -0.4565 0.0936 -0.0306 -0.0220 0.0220 -0.0166 -0.0111 -0.1221 refined 25.8005 -1.0047 26.3472 X-RAY DIFFRACTION 5.9051 2.5366 1.1991 5.9736 1.4423 1.5150 0.1515 -0.1992 -0.0003 0.5143 0.0201 0.5660 0.1758 0.1678 -0.1716 -0.1038 -0.0132 -0.0092 -0.0995 0.0165 0.0997 refined 15.2521 -10.5785 19.4980 X-RAY DIFFRACTION 3.0926 -1.5678 0.4809 3.5720 -0.0234 0.0923 0.0157 -0.1459 -0.0576 -0.1341 -0.1082 0.0422 0.4332 -0.0342 0.0925 -0.0365 -0.0016 -0.0070 -0.0468 0.0110 0.0199 refined 29.8621 -3.7834 16.4627 X-RAY DIFFRACTION 6.8730 -2.5731 1.0216 13.0735 3.1754 1.1971 0.2038 -0.7587 -0.3951 1.7455 0.0516 0.8200 -0.7089 0.1804 -0.2554 0.0227 -0.0725 0.0208 -0.0329 0.0838 0.0325 refined 10.5478 0.0829 18.9099 X-RAY DIFFRACTION 7.1636 -0.2318 -0.6286 5.1256 -1.0033 0.2599 0.0024 -0.1041 -0.1785 0.0514 -0.0220 0.2198 -0.0443 0.1894 0.0196 -0.0681 -0.0066 -0.0096 -0.0146 -0.0215 0.0200 refined 25.1494 4.2495 13.2486 X-RAY DIFFRACTION 10.0186 -2.4333 1.1927 5.1849 -0.4274 0.1461 -0.2772 -0.0540 -0.1564 -0.2057 -0.0564 -0.0484 0.0836 -0.0302 0.3336 -0.0442 0.0104 -0.0115 -0.0238 -0.0614 -0.0551 refined 15.3081 0.4111 10.2496 X-RAY DIFFRACTION 20.5527 -3.1504 -0.2268 13.4555 -2.1177 0.3596 -0.2209 -0.9087 -0.7591 0.4887 0.4670 0.8363 -0.5022 0.3530 -0.2461 0.0603 -0.0297 -0.0120 0.0664 0.0922 0.1203 refined 19.8884 -0.5903 18.0082 X-RAY DIFFRACTION A 1 A 5 X-RAY DIFFRACTION 1 B 1 B 5 X-RAY DIFFRACTION 1 A 94 A 99 X-RAY DIFFRACTION 1 B 94 B 99 X-RAY DIFFRACTION 1 A 86 A 92 X-RAY DIFFRACTION 2 B 86 B 92 X-RAY DIFFRACTION 3 A 44 A 55 X-RAY DIFFRACTION 4 B 44 B 55 X-RAY DIFFRACTION 5 A 77 A 85 X-RAY DIFFRACTION 6 B 77 B 85 X-RAY DIFFRACTION 7 A 24 A 31 X-RAY DIFFRACTION 8 B 24 B 31 X-RAY DIFFRACTION 9 A 100 A 100 X-RAY DIFFRACTION 10 author_and_software_defined_assembly PISA 2 dimeric 5010 -26 8950 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N ILE 3 A N ILE 3 B O LEU 97 B O LEU 97 B O THR 96 B O THR 96 A N ASN 98 A N ASN 98 A N LEU 97 A N LEU 97 B O ILE 3 B O ILE 3 A N LYS 43 A N LYS 43 A O GLN 58 A O GLN 58 A N ILE 66 A N ILE 66 A O HIS 69 A O HIS 69 A O LEU 76 A O LEU 76 A N LEU 33 A N LEU 33 A N VAL 32 A N VAL 32 A O ILE 84 A O ILE 84 A O ILE 85 A O ILE 85 A N LEU 23 A N LEU 23 A O LYS 20 A O LYS 20 A N ILE 13 A N ILE 13 A N ARG 14 A N ARG 14 A O GLU 65 A O GLU 65 B N LYS 43 B N LYS 43 B O GLN 58 B O GLN 58 B N ILE 64 B N ILE 64 B O ALA 71 B O ALA 71 B O LEU 76 B O LEU 76 B N LEU 33 B N LEU 33 B N VAL 32 B N VAL 32 B O ILE 84 B O ILE 84 B O ILE 85 B O ILE 85 B N LEU 23 B N LEU 23 B O LYS 20 B O LYS 20 B N ILE 13 B N ILE 13 B N ARG 14 B N ARG 14 B O GLU 65 B O GLU 65 1 A CG LYS 7 A CG LYS 7 1 Y 1 A CD LYS 7 A CD LYS 7 1 Y 1 A CE LYS 7 A CE LYS 7 1 Y 1 A NZ LYS 7 A NZ LYS 7 1 Y 1 A NE ARG 14 A NE ARG 14 0 Y 1 A CZ ARG 14 A CZ ARG 14 0 Y 1 A NH1 ARG 14 A NH1 ARG 14 0 Y 1 A NH2 ARG 14 A NH2 ARG 14 0 Y 1 A CG LYS 41 A CG LYS 41 1 Y 1 A CD LYS 41 A CD LYS 41 1 Y 1 A CE LYS 41 A CE LYS 41 1 Y 1 A NZ LYS 41 A NZ LYS 41 1 Y 1 A CG LYS 43 A CG LYS 43 1 Y 1 A CD LYS 43 A CD LYS 43 1 Y 1 A CE LYS 43 A CE LYS 43 1 Y 1 A NZ LYS 43 A NZ LYS 43 1 Y 1 A CG LYS 55 A CG LYS 55 1 Y 1 A CD LYS 55 A CD LYS 55 1 Y 1 A CE LYS 55 A CE LYS 55 1 Y 1 A NZ LYS 55 A NZ LYS 55 1 Y 1 A OG1 THR 82 A OG1 THR 82 1 Y 1 A CG2 THR 82 A CG2 THR 82 1 Y 1 B CG LYS 7 B CG LYS 7 1 Y 1 B CD LYS 7 B CD LYS 7 1 Y 1 B CE LYS 7 B CE LYS 7 1 Y 1 B NZ LYS 7 B NZ LYS 7 1 Y 1 B CG ARG 14 B CG ARG 14 1 Y 1 B CD ARG 14 B CD ARG 14 1 Y 1 B NE ARG 14 B NE ARG 14 1 Y 1 B CZ ARG 14 B CZ ARG 14 1 Y 1 B NH1 ARG 14 B NH1 ARG 14 1 Y 1 B NH2 ARG 14 B NH2 ARG 14 1 Y 1 B CD GLU 35 B CD GLU 35 0 Y 1 B OE1 GLU 35 B OE1 GLU 35 0 Y 1 B OE2 GLU 35 B OE2 GLU 35 0 Y 1 B CG ASN 37 B CG ASN 37 1 Y 1 B OD1 ASN 37 B OD1 ASN 37 1 Y 1 B ND2 ASN 37 B ND2 ASN 37 1 Y 1 B CG LYS 41 B CG LYS 41 1 Y 1 B CD LYS 41 B CD LYS 41 1 Y 1 B CE LYS 41 B CE LYS 41 1 Y 1 B NZ LYS 41 B NZ LYS 41 1 Y 1 B CG LYS 43 B CG LYS 43 1 Y 1 B CD LYS 43 B CD LYS 43 1 Y 1 B CE LYS 43 B CE LYS 43 1 Y 1 B NZ LYS 43 B NZ LYS 43 1 Y 1 B CD GLN 61 B CD GLN 61 0 Y 1 B OE1 GLN 61 B OE1 GLN 61 0 Y 1 B NE2 GLN 61 B NE2 GLN 61 0 Y 1 B CG LYS 70 B CG LYS 70 1 Y 1 B CD LYS 70 B CD LYS 70 1 Y 1 B CE LYS 70 B CE LYS 70 1 Y 1 B NZ LYS 70 B NZ LYS 70 1 Y 1 B OG1 THR 82 B OG1 THR 82 1 Y 1 B CG2 THR 82 B CG2 THR 82 1 Y 1 A PRO 79 -79.30 49.36 1 B GLU 34 -55.82 174.24 56.39 34.606 17.31 -1.140 0.000 0.000 -1.190 0.000 2.330 0.954 0.917 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.246 0.195 0.197 2.200 20.000 467 9751 4.800 98.380 1.00 0.00 9.298 0.182 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 0.334 0.232 0.800 0.800 1.200 PDB ENTRY 1F7A MAXIMUM LIKELIHOOD MASK 2.200 20.000 74 1610 59 0 1477 0.008 0.022 1583 0.005 0.020 1523 1.273 2.015 2170 0.714 3.000 3527 6.953 5.000 200 40.441 25.098 51 13.593 15.000 246 14.060 15.000 6 0.077 0.200 259 0.004 0.020 1723 0.001 0.020 285 0.179 0.200 208 0.205 0.200 1478 0.169 0.200 719 0.087 0.200 888 0.158 0.200 64 0.032 0.200 1 0.167 0.200 6 0.147 0.200 46 0.072 0.200 2 1.063 1.500 1276 0.124 1.500 414 1.022 2.000 1610 1.660 3.000 704 2.212 4.500 560 0.362 0.226 2.257 30 594 624 20 88.010 2.0 42 3EKQ 12975 12975 0 0 0.07 0.07 1 6.0 6.6 97.2 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.2.0005 data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.006 data reduction DENZO data scaling SCALEPACK phasing AMoRE Crystal structure of inhibitor saquinavir (SQV) in complex with multi-drug resistant HIV-1 protease (L63P/V82T/I84V) (referred to as ACT in paper) 1 N N 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N One dimer (A & B identifiers) in one asymmetric unit A GLY 86 A GLY 86 HELX_P A THR 91 A THR 91 1 1 6 B GLY 86 B GLY 86 HELX_P B THR 91 B THR 91 1 2 6 B GLN 92 B GLN 92 HELX_P B GLY 94 B GLY 94 5 3 3 HYDROLASE/HYDROLASE INHIBITOR protease inhibitor, drug resistance, entropy enthalpy compensation, AIDS, Hydrolase-hydrolase inhibitor complex, Protease POL_HV1A2 UNP 1 491 P03369 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 491 589 3EKQ 1 99 P03369 A 1 1 99 491 589 3EKQ 1 99 P03369 B 1 1 99 1 GLN engineered mutation LYS 7 3EKQ A P03369 UNP 497 7 1 LEU engineered mutation ILE 10 3EKQ A P03369 UNP 500 10 1 GLY engineered mutation VAL 48 3EKQ A P03369 UNP 538 48 1 ILE engineered mutation VAL 54 3EKQ A P03369 UNP 544 54 1 VAL engineered mutation ILE 64 3EKQ A P03369 UNP 554 64 1 VAL engineered mutation THR 82 3EKQ A P03369 UNP 572 82 2 GLN engineered mutation LYS 7 3EKQ B P03369 UNP 497 7 2 LEU engineered mutation ILE 10 3EKQ B P03369 UNP 500 10 2 GLY engineered mutation VAL 48 3EKQ B P03369 UNP 538 48 2 ILE engineered mutation VAL 54 3EKQ B P03369 UNP 544 54 2 VAL engineered mutation ILE 64 3EKQ B P03369 UNP 554 64 2 VAL engineered mutation THR 82 3EKQ B P03369 UNP 572 82 4 8 8 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel A GLN 2 A GLN 2 A ILE 3 A ILE 3 B THR 96 B THR 96 B ASN 98 B ASN 98 A THR 96 A THR 96 A ASN 98 A ASN 98 B GLN 2 B GLN 2 B ILE 3 B ILE 3 A LYS 43 A LYS 43 A GLY 49 A GLY 49 A GLY 52 A GLY 52 A ILE 66 A ILE 66 A HIS 69 A HIS 69 A VAL 77 A VAL 77 A VAL 32 A VAL 32 A LEU 33 A LEU 33 A ILE 84 A ILE 84 A ILE 85 A ILE 85 A GLN 18 A GLN 18 A LEU 24 A LEU 24 A ILE 10 A ILE 10 A ILE 15 A ILE 15 A GLY 52 A GLY 52 A ILE 66 A ILE 66 B LYS 43 B LYS 43 B GLY 49 B GLY 49 B GLY 52 B GLY 52 B ILE 66 B ILE 66 B HIS 69 B HIS 69 B VAL 77 B VAL 77 B VAL 32 B VAL 32 B LEU 33 B LEU 33 B ILE 84 B ILE 84 B ILE 85 B ILE 85 B GLN 18 B GLN 18 B LEU 24 B LEU 24 B ILE 10 B ILE 10 B ILE 15 B ILE 15 B GLY 52 B GLY 52 B ILE 66 B ILE 66 BINDING SITE FOR RESIDUE ROC A 100 A ROC 100 Software 19 BINDING SITE FOR RESIDUE PO4 A 502 A PO4 502 Software 2 BINDING SITE FOR RESIDUE PO4 B 501 B PO4 501 Software 4 A ASP 25 A ASP 25 19 1_555 A GLY 27 A GLY 27 19 1_555 A ALA 28 A ALA 28 19 1_555 A ASP 29 A ASP 29 19 1_555 A ASP 30 A ASP 30 19 1_555 A VAL 48 A VAL 48 19 1_555 A GLY 49 A GLY 49 19 1_555 A ILE 50 A ILE 50 19 1_555 A THR 80 A THR 80 19 1_555 A HOH 507 F HOH 19 1_555 A HOH 509 F HOH 19 1_555 A HOH 549 F HOH 19 1_555 B ARG 8 B ARG 8 19 1_555 B LEU 23 B LEU 23 19 1_555 B ASP 25 B ASP 25 19 1_555 B GLY 27 B GLY 27 19 1_555 B VAL 48 B VAL 48 19 1_555 B ILE 50 B ILE 50 19 1_555 B PRO 81 B PRO 81 19 1_555 A LYS 7 A LYS 7 2 1_555 A ARG 8 A ARG 8 2 1_555 B LYS 20 B LYS 20 4 1_555 B GLU 21 B GLU 21 4 1_555 B ASN 83 B ASN 83 4 1_555 B HOH 511 G HOH 4 1_555 19 P 21 21 21