0.034819 0.000000 0.000000 0.000000 0.015251 0.000000 0.000000 0.000000 0.010827 0.000000 0.000000 0.000000 Stout, C.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 28.720 65.570 92.360 C9 H7 N O2 161.157 1H-indole-6-carboxylic acid non-polymer C50 H64 N6 O10 909.077 benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate TL-3, C2 symmetric inhibitor peptide-like 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 C2 H6 O S 78.133 BETA-MERCAPTOETHANOL non-polymer 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 C5 H9 N O2 115.130 y PROLINE L-peptide linking 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 O N 2 N C N 3 N O Y 4 N C Y 5 N C Y 6 N C Y 7 N C Y 8 N C Y 9 N C Y 10 N N Y 11 N C Y 12 N C N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N C N 21 N O N 22 N O N 23 N C Y 24 N C Y 25 N C Y 26 N C Y 27 N C Y 28 N C Y 29 N C N 30 N N N 31 S C N 32 N C N 33 N O N 34 N C N 35 N N N 36 S C N 37 N C N 38 N O N 39 N C N 40 N C N 41 N C N 42 R C N 43 N O N 44 S C N 45 N N N 46 N C Y 47 N C Y 48 N C Y 49 N C Y 50 N C Y 51 N C Y 52 N C N 53 N N N 54 S C N 55 R C N 56 N O N 57 N C Y 58 N C Y 59 N C Y 60 N C Y 61 N C Y 62 N C Y 63 N C N 64 N N N 65 S C N 66 N C N 67 N O N 68 N C N 69 N C N 70 N C N 71 N N N 72 S C N 73 N C N 74 N O N 75 N C N 76 N C N 77 N O N 78 N O N 79 N C Y 80 N C Y 81 N C Y 82 N C Y 83 N C Y 84 N C Y 85 N C N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H 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 H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H 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 H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N N N 151 S C N 152 N C N 153 N O N 154 N C N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N N N 164 S C N 165 N C N 166 N O N 167 N C N 168 N C N 169 N C N 170 N N N 171 N C N 172 N N N 173 N N N 174 N O 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 H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N N N 191 S C N 192 N C N 193 N O N 194 N C N 195 N C N 196 N O N 197 N N N 198 N O 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 H N 206 N H N 207 N N N 208 S C N 209 N C N 210 N O N 211 N C N 212 N C N 213 N O N 214 N O N 215 N O 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 C N 224 N C N 225 N O N 226 N S N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N N N 234 R C N 235 N C N 236 N O N 237 N C N 238 N S N 239 N O 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 N N 248 S C N 249 N C N 250 N O N 251 N C N 252 N C N 253 N C N 254 N O N 255 N N N 256 N O N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N N N 268 S C N 269 N C N 270 N O N 271 N C N 272 N C N 273 N C N 274 N O N 275 N O N 276 N O N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N N N 287 N C N 288 N C N 289 N O N 290 N O N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N N N 297 S C N 298 N C N 299 N O N 300 N C Y 301 N C Y 302 N N Y 303 N C Y 304 N C Y 305 N N N 306 N O N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N O N 318 N H N 319 N H N 320 N N N 321 S C N 322 N C N 323 N O N 324 S C N 325 N C N 326 N C N 327 N C N 328 N O N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N N N 343 S C N 344 N C N 345 N O N 346 N C N 347 N C N 348 N C N 349 N C N 350 N O 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 N N 365 S C N 366 N C N 367 N O N 368 N C N 369 N C N 370 N C N 371 N C N 372 N N N 373 N O 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 N N 390 S C N 391 N C N 392 N O N 393 N C N 394 N C N 395 N S N 396 N C N 397 N O N 398 N H N 399 N H N 400 N H N 401 N H 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 N N 410 S C N 411 N C N 412 N O N 413 N C Y 414 N C Y 415 N C Y 416 N C Y 417 N C Y 418 N C Y 419 N C N 420 N O N 421 N H N 422 N H N 423 N H N 424 N H N 425 N H 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 N N 433 S C N 434 N C N 435 N O N 436 N C N 437 N C N 438 N C N 439 N O N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N N N 450 S C N 451 N C N 452 N O N 453 R C N 454 N O N 455 N C N 456 N O N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N H N 464 N H N 465 N H N 466 N N N 467 S C N 468 N C N 469 N O N 470 N C Y 471 N C Y 472 N C Y 473 N C Y 474 N N Y 475 N C Y 476 N C Y 477 N C Y 478 N C Y 479 N C N 480 N O N 481 N H N 482 N H N 483 N H N 484 N H N 485 N H N 486 N H N 487 N H N 488 N H N 489 N H N 490 N H N 491 N H N 492 N H N 493 N N N 494 S C N 495 N C N 496 N O N 497 N C Y 498 N C Y 499 N C Y 500 N C Y 501 N C Y 502 N C Y 503 N C N 504 N O N 505 N O N 506 N H N 507 N H N 508 N H N 509 N H N 510 N H N 511 N H N 512 N H N 513 N H N 514 N H N 515 N H N 516 N H N 517 N N N 518 S C N 519 N C N 520 N O N 521 N C N 522 N C N 523 N C N 524 N O N 525 N H N 526 N H N 527 N H N 528 N H N 529 N H N 530 N H N 531 N H N 532 N H N 533 N H N 534 N H N 535 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing Y 5 N doub Y 6 N sing Y 7 N sing N 8 N sing Y 9 N doub N 10 N sing Y 11 N sing Y 12 N sing Y 13 N doub N 14 N sing Y 15 N sing N 16 N sing Y 17 N sing Y 18 N doub N 19 N sing N 20 N sing N 21 N doub N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing Y 28 N doub Y 29 N sing Y 30 N sing N 31 N sing Y 32 N doub N 33 N sing Y 34 N sing N 35 N sing Y 36 N doub 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 doub N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N doub 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 sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing 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 sing Y 77 N doub Y 78 N sing Y 79 N sing N 80 N sing Y 81 N doub N 82 N sing Y 83 N doub N 84 N sing Y 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing 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 sing N 98 N sing N 99 N sing Y 100 N doub Y 101 N sing Y 102 N sing N 103 N sing Y 104 N doub N 105 N sing Y 106 N doub N 107 N sing Y 108 N sing 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 sing N 117 N doub 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 sing 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 doub N 134 N sing N 135 N sing N 136 N sing N 137 N doub N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing Y 143 N doub Y 144 N sing Y 145 N sing N 146 N sing Y 147 N doub N 148 N sing Y 149 N sing N 150 N sing Y 151 N doub 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 sing N 159 N sing N 160 N doub 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 doub 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 sing 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 doub 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 doub N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N doub 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 doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing 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 doub N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N doub N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N doub N 260 N sing 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 doub N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N doub N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N doub N 298 N sing N 299 N sing N 300 N sing N 301 N sing Y 302 N sing Y 303 N doub Y 304 N doub N 305 N sing Y 306 N sing N 307 N sing Y 308 N sing N 309 N sing 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 doub N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 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 doub N 342 N sing N 343 N sing 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 doub 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 doub N 387 N sing N 388 N sing N 389 N sing N 390 N sing 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 doub N 406 N sing N 407 N sing N 408 N sing N 409 N sing Y 410 N doub Y 411 N sing Y 412 N sing N 413 N sing Y 414 N doub N 415 N sing Y 416 N doub N 417 N sing Y 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N doub N 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N doub N 446 N sing N 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 sing N 459 N sing N 460 N sing N 461 N doub N 462 N sing N 463 N sing N 464 N sing N 465 N sing Y 466 N doub Y 467 N sing Y 468 N sing N 469 N sing Y 470 N doub Y 471 N sing Y 472 N sing N 473 N sing Y 474 N sing Y 475 N doub N 476 N sing Y 477 N doub N 478 N sing Y 479 N sing N 480 N sing N 481 N sing N 482 N sing N 483 N sing N 484 N sing N 485 N sing N 486 N sing N 487 N sing N 488 N sing N 489 N doub N 490 N sing N 491 N sing N 492 N sing N 493 N sing Y 494 N doub Y 495 N sing Y 496 N sing N 497 N sing Y 498 N doub N 499 N sing Y 500 N doub N 501 N sing Y 502 N sing N 503 N sing N 504 N sing N 505 N sing N 506 N sing N 507 N sing N 508 N sing N 509 N sing N 510 N sing N 511 N sing N 512 N sing N 513 N doub N 514 N sing N 515 N sing N 516 N sing N 517 N sing N 518 N sing N 519 N sing N 520 N sing N 521 N sing N 522 N sing N 523 N sing N 524 N sing US Chem.Biol.Drug Des. 1747-0277 75 257 268 10.1111/j.1747-0285.2009.00943.x 20659109 Fragment-based screen against HIV protease. 2010 10.2210/pdb3kfr/pdb pdb_00003kfr 100 1 Rh coated flat mirror CCD 2008-12-08 ADSC QUANTUM 315r Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. SINGLE WAVELENGTH M x-ray 1 0.97946 1.0 BL7-1 SSRL 0.97946 SYNCHROTRON SSRL BEAMLINE BL7-1 10831.833 Protease 3.4.23.16 2 man polymer 909.077 benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate 1 syn non-polymer 78.133 BETA-MERCAPTOETHANOL 2 syn non-polymer 161.157 1H-indole-6-carboxylic acid 1 syn non-polymer 18.015 water 169 nat water no no PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 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 R8 sample POL 11676 Human immunodeficiency virus 1 562 Escherichia coli BL21.DE3 PLASMID PET 21A+ 1 2.01 38.72 VAPOR DIFFUSION 5.8 0.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277K 277 database_2 struct_conn struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance Other Database references Derived calculations Data collection Refinement description 1 0 2010-02-23 1 1 2011-07-13 1 2 2013-02-27 1 3 2021-10-13 1 4 2023-09-06 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE HIV Protease with fragment 4D9 bound HIV Protease (PR) dimer without inhibitor; acetate in exo site HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap RCSB Y RCSB 2009-10-27 REL REL 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate BME BETA-MERCAPTOETHANOL 1F1 1H-indole-6-carboxylic acid HOH water THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE 2AZ8 HIV PR dimer generated from monomer with TL-3 bound in 2AZ8 PDB experimental model Inhibitor N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide Peptide-like 3TL 200 2 3TL 3TL 200 A BME 202 3 BME BME 202 A 1F1 201 4 1F1 1F1 201 B BME 203 3 BME BME 203 B HOH 204 5 HOH HOH 204 A HOH 206 5 HOH HOH 206 A HOH 211 5 HOH HOH 211 A HOH 213 5 HOH HOH 213 A HOH 214 5 HOH HOH 214 A HOH 217 5 HOH HOH 217 A HOH 219 5 HOH HOH 219 A HOH 220 5 HOH HOH 220 A HOH 224 5 HOH HOH 224 A HOH 225 5 HOH HOH 225 A HOH 226 5 HOH HOH 226 A HOH 229 5 HOH HOH 229 A HOH 231 5 HOH HOH 231 A HOH 232 5 HOH HOH 232 A HOH 233 5 HOH HOH 233 A HOH 235 5 HOH HOH 235 A HOH 236 5 HOH HOH 236 A HOH 237 5 HOH HOH 237 A HOH 240 5 HOH HOH 240 A HOH 241 5 HOH HOH 241 A HOH 244 5 HOH HOH 244 A HOH 246 5 HOH HOH 246 A HOH 247 5 HOH HOH 247 A HOH 250 5 HOH HOH 250 A HOH 253 5 HOH HOH 253 A HOH 255 5 HOH HOH 255 A HOH 258 5 HOH HOH 258 A HOH 259 5 HOH HOH 259 A HOH 260 5 HOH HOH 260 A HOH 263 5 HOH HOH 263 A HOH 266 5 HOH HOH 266 A HOH 272 5 HOH HOH 272 A HOH 276 5 HOH HOH 276 A HOH 277 5 HOH HOH 277 A HOH 281 5 HOH HOH 281 A HOH 283 5 HOH HOH 283 A HOH 286 5 HOH HOH 286 A HOH 287 5 HOH HOH 287 A HOH 288 5 HOH HOH 288 A HOH 289 5 HOH HOH 289 A HOH 290 5 HOH HOH 290 A HOH 292 5 HOH HOH 292 A HOH 295 5 HOH HOH 295 A HOH 298 5 HOH HOH 298 A HOH 299 5 HOH HOH 299 A HOH 300 5 HOH HOH 300 A HOH 302 5 HOH HOH 302 A HOH 314 5 HOH HOH 314 A HOH 316 5 HOH HOH 316 A HOH 317 5 HOH HOH 317 A HOH 320 5 HOH HOH 320 A HOH 329 5 HOH HOH 329 A HOH 330 5 HOH HOH 330 A HOH 331 5 HOH HOH 331 A HOH 332 5 HOH HOH 332 A HOH 334 5 HOH HOH 334 A HOH 337 5 HOH HOH 337 A HOH 339 5 HOH HOH 339 A HOH 340 5 HOH HOH 340 A HOH 342 5 HOH HOH 342 A HOH 345 5 HOH HOH 345 A HOH 349 5 HOH HOH 349 A HOH 350 5 HOH HOH 350 A HOH 354 5 HOH HOH 354 A HOH 355 5 HOH HOH 355 A HOH 356 5 HOH HOH 356 A HOH 358 5 HOH HOH 358 A HOH 361 5 HOH HOH 361 A HOH 362 5 HOH HOH 362 A HOH 364 5 HOH HOH 364 A HOH 365 5 HOH HOH 365 A HOH 366 5 HOH HOH 366 A HOH 367 5 HOH HOH 367 A HOH 368 5 HOH HOH 368 A HOH 369 5 HOH HOH 369 A HOH 371 5 HOH HOH 371 A HOH 373 5 HOH HOH 373 A HOH 375 5 HOH HOH 375 A HOH 380 5 HOH HOH 380 A HOH 381 5 HOH HOH 381 A HOH 382 5 HOH HOH 382 A HOH 383 5 HOH HOH 383 A HOH 384 5 HOH HOH 384 A HOH 385 5 HOH HOH 385 A HOH 205 5 HOH HOH 205 B HOH 207 5 HOH HOH 207 B HOH 208 5 HOH HOH 208 B HOH 209 5 HOH HOH 209 B HOH 210 5 HOH HOH 210 B HOH 212 5 HOH HOH 212 B HOH 215 5 HOH HOH 215 B HOH 216 5 HOH HOH 216 B HOH 218 5 HOH HOH 218 B HOH 221 5 HOH HOH 221 B HOH 222 5 HOH HOH 222 B HOH 223 5 HOH HOH 223 B HOH 227 5 HOH HOH 227 B HOH 234 5 HOH HOH 234 B HOH 238 5 HOH HOH 238 B HOH 239 5 HOH HOH 239 B HOH 243 5 HOH HOH 243 B HOH 245 5 HOH HOH 245 B HOH 248 5 HOH HOH 248 B HOH 249 5 HOH HOH 249 B HOH 252 5 HOH HOH 252 B HOH 254 5 HOH HOH 254 B HOH 256 5 HOH HOH 256 B HOH 257 5 HOH HOH 257 B HOH 261 5 HOH HOH 261 B HOH 262 5 HOH HOH 262 B HOH 264 5 HOH HOH 264 B HOH 265 5 HOH HOH 265 B HOH 269 5 HOH HOH 269 B HOH 270 5 HOH HOH 270 B HOH 273 5 HOH HOH 273 B HOH 274 5 HOH HOH 274 B HOH 275 5 HOH HOH 275 B HOH 278 5 HOH HOH 278 B HOH 280 5 HOH HOH 280 B HOH 282 5 HOH HOH 282 B HOH 284 5 HOH HOH 284 B HOH 285 5 HOH HOH 285 B HOH 291 5 HOH HOH 291 B HOH 293 5 HOH HOH 293 B HOH 294 5 HOH HOH 294 B HOH 296 5 HOH HOH 296 B HOH 297 5 HOH HOH 297 B HOH 301 5 HOH HOH 301 B HOH 303 5 HOH HOH 303 B HOH 306 5 HOH HOH 306 B HOH 307 5 HOH HOH 307 B HOH 308 5 HOH HOH 308 B HOH 309 5 HOH HOH 309 B HOH 310 5 HOH HOH 310 B HOH 311 5 HOH HOH 311 B HOH 312 5 HOH HOH 312 B HOH 313 5 HOH HOH 313 B HOH 319 5 HOH HOH 319 B HOH 322 5 HOH HOH 322 B HOH 323 5 HOH HOH 323 B HOH 324 5 HOH HOH 324 B HOH 325 5 HOH HOH 325 B HOH 326 5 HOH HOH 326 B HOH 327 5 HOH HOH 327 B HOH 328 5 HOH HOH 328 B HOH 333 5 HOH HOH 333 B HOH 335 5 HOH HOH 335 B HOH 336 5 HOH HOH 336 B HOH 338 5 HOH HOH 338 B HOH 341 5 HOH HOH 341 B HOH 343 5 HOH HOH 343 B HOH 344 5 HOH HOH 344 B HOH 346 5 HOH HOH 346 B HOH 347 5 HOH HOH 347 B HOH 348 5 HOH HOH 348 B HOH 351 5 HOH HOH 351 B HOH 352 5 HOH HOH 352 B HOH 353 5 HOH HOH 353 B HOH 357 5 HOH HOH 357 B HOH 359 5 HOH HOH 359 B HOH 360 5 HOH HOH 360 B HOH 363 5 HOH HOH 363 B HOH 370 5 HOH HOH 370 B HOH 372 5 HOH HOH 372 B HOH 374 5 HOH HOH 374 B HOH 376 5 HOH HOH 376 B HOH 377 5 HOH HOH 377 B HOH 378 5 HOH HOH 378 B HOH 379 5 HOH HOH 379 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 LYS 7 n 7 LYS 7 A ARG 8 n 8 ARG 8 A PRO 9 n 9 PRO 9 A LEU 10 n 10 LEU 10 A VAL 11 n 11 VAL 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A LYS 14 n 14 LYS 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 ARG 41 n 41 ARG 41 A TRP 42 n 42 TRP 42 A LYS 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 GLY 48 n 48 GLY 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 ILE 54 n 54 ILE 54 A LYS 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 LEU 63 n 63 LEU 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 VAL 82 n 82 VAL 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 LYS 7 n 7 LYS 7 B ARG 8 n 8 ARG 8 B PRO 9 n 9 PRO 9 B LEU 10 n 10 LEU 10 B VAL 11 n 11 VAL 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B LYS 14 n 14 LYS 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 ASN 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 ARG 41 n 41 ARG 41 B TRP 42 n 42 TRP 42 B LYS 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 GLY 48 n 48 GLY 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 ILE 54 n 54 ILE 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 LEU 63 n 63 LEU 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 LYS 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 VAL 82 n 82 VAL 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 author_and_software_defined_assembly PISA 2 dimeric 3550 -22 10150 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 64 A N ILE 64 A O ALA 71 A O ALA 71 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 LYS 14 A N LYS 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 TYR 59 B N TYR 59 B O VAL 75 B O VAL 75 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 LYS 14 B N LYS 14 B O GLU 65 B O GLU 65 1 A C18 3TL 200 PLANAR 1 A C2 3TL 200 PLANAR 1 A C68 3TL 200 PLANAR 1 A PRO 39 -40.80 79.36 1 B PRO 79 -82.94 48.64 46.65 16.693 7.37 0.090 0.000 0.000 -0.020 0.000 -0.070 0.957 0.949 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY 0.207 0.183 0.184 1.300 25.300 2151 42972 5.000 98.000 1.00 1.00 1.626 0.032 RANDOM 1 Anisotropic THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.065 0.057 0.800 0.800 1.200 HIV PR dimer generated from monomer with TL-3 bound in 2AZ8 MAXIMUM LIKELIHOOD MASK 1.300 25.300 169 1775 86 0 1520 0.010 0.022 1634 1.437 2.043 2208 6.481 5.000 196 36.783 24.815 54 10.527 15.000 288 13.812 15.000 8 0.086 0.200 255 0.007 0.021 1182 1.182 1.500 976 1.928 2.000 1586 2.434 3.000 658 3.801 4.500 622 1.290 3.000 1634 4.003 3.000 169 3.197 3.000 1606 0.263 0.212 1.334 154 2915 3069 2915 20 97.650 12.0 1.15 25.3 3KFR 63048 61661 0.0 0.0 0.051 0.051 1 6.7 3.8 97.8 0.800 1.15 1.18 0.9 4432 0.800 1 3.9 96.6 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0090 data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.005 data collection Blu-Ice data reduction MOSFLM data scaling SCALA phasing MOLREP HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap 1 N N 1 N N 2 N N 3 N N 4 N N 3 N N 5 N N 5 N N A GLY 86 A GLY 86 HELX_P A THR 91 A THR 91 1 1 6 A GLN 92 A GLN 92 HELX_P A GLY 94 A GLY 94 5 2 3 B GLY 86 B GLY 86 HELX_P B THR 91 B THR 91 1 3 6 B GLN 92 B GLN 92 HELX_P B GLY 94 B GLY 94 5 4 3 covale 2.341 none A CYS 67 A SG CYS 67 1_555 A BME 202 D S2 BME 1_555 covale 2.137 none B CYS 67 B SG CYS 67 1_555 B BME 203 F S2 BME 1_555 HYDROLASE/HYDROLASE INHIBITOR HIV-1, PROTEASE, Aspartyl protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX Q903N5_9HIV1 UNP 1 1 Q903N5 PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 1 99 3KFR 1 99 Q903N5 A 1 1 99 1 99 3KFR 1 99 Q903N5 B 1 1 99 1 ARG engineered mutation LYS 7 3KFR A Q903N5 UNP 7 7 2 ARG engineered mutation LYS 7 3KFR B Q903N5 UNP 7 7 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 LEU 10 A LEU 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 LEU 10 B LEU 10 B ILE 15 B ILE 15 B GLY 52 B GLY 52 B ILE 66 B ILE 66 BINDING SITE FOR RESIDUE 3TL A 200 A 3TL 200 Software 28 BINDING SITE FOR RESIDUE BME A 202 A BME 202 Software 6 BINDING SITE FOR RESIDUE 1F1 B 201 B 1F1 201 Software 11 BINDING SITE FOR RESIDUE BME B 203 B BME 203 Software 6 A ARG 8 A ARG 8 28 1_555 A ASP 25 A ASP 25 28 1_555 A GLY 27 A GLY 27 28 1_555 A ALA 28 A ALA 28 28 1_555 A ASP 29 A ASP 29 28 1_555 A PRO 44 A PRO 44 28 4_455 A MET 46 A MET 46 28 1_555 A ILE 47 A ILE 47 28 1_555 A GLY 48 A GLY 48 28 1_555 A GLY 49 A GLY 49 28 1_555 A ILE 50 A ILE 50 28 1_555 A PRO 79 A PRO 79 28 4_555 A PRO 81 A PRO 81 28 1_555 A VAL 82 A VAL 82 28 1_555 A ILE 84 A ILE 84 28 1_555 A HOH 263 G HOH 28 1_555 A HOH 283 G HOH 28 1_555 B ASP 25 B ASP 25 28 1_555 B GLY 27 B GLY 27 28 1_555 B ALA 28 B ALA 28 28 1_555 B ASP 29 B ASP 29 28 1_555 B ASP 30 B ASP 30 28 1_555 B GLY 48 B GLY 48 28 1_555 B GLY 49 B GLY 49 28 1_555 B ILE 50 B ILE 50 28 1_555 B PHE 53 B PHE 53 28 1_555 B VAL 82 B VAL 82 28 1_555 B ILE 84 B ILE 84 28 1_555 A VAL 11 A VAL 11 6 1_555 A THR 12 A THR 12 6 1_555 A CYS 67 A CYS 67 6 1_555 A HOH 287 G HOH 6 1_555 A HOH 356 G HOH 6 1_555 B LYS 7 B LYS 7 6 1_455 B PRO 44 B PRO 44 11 1_555 B LYS 45 B LYS 45 11 1_555 B LYS 55 B LYS 55 11 1_555 B VAL 56 B VAL 56 11 1_555 B ARG 57 B ARG 57 11 1_555 B THR 91 B THR 91 11 3_454 B GLN 92 B GLN 92 11 3_454 B GLY 94 B GLY 94 11 3_454 B HOH 210 H HOH 11 3_454 B HOH 310 H HOH 11 1_555 B HOH 333 H HOH 11 1_555 A LYS 7 A LYS 7 6 1_655 B VAL 11 B VAL 11 6 1_555 B THR 12 B THR 12 6 1_555 B CYS 67 B CYS 67 6 1_555 B HOH 222 H HOH 6 1_555 B HOH 311 H HOH 6 1_555 19 P 21 21 21