0.034542 0.000000 0.000000 0.000000 0.015072 0.000000 0.000000 0.000000 0.010756 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 28.950 66.350 92.970 C10 H8 O2 S 192.234 1-benzothiophen-2-ylacetic 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 C2 H6 O S 78.133 DIMETHYL SULFOXIDE non-polymer 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 C Y 11 N C Y 12 N S N 13 N C 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 H N 21 N H N 22 N C N 23 N O N 24 N O N 25 N C Y 26 N C Y 27 N C Y 28 N C Y 29 N C Y 30 N C Y 31 N C N 32 N N N 33 S C N 34 N C N 35 N O N 36 N C N 37 N N N 38 S C N 39 N C N 40 N O N 41 N C N 42 N C N 43 N C N 44 R C N 45 N O N 46 S C N 47 N N N 48 N C Y 49 N C Y 50 N C Y 51 N C Y 52 N C Y 53 N C Y 54 N C N 55 N N N 56 S C N 57 R C N 58 N O N 59 N C Y 60 N C Y 61 N C Y 62 N C Y 63 N C Y 64 N C Y 65 N C N 66 N N N 67 S C N 68 N C N 69 N O N 70 N C N 71 N C N 72 N C N 73 N N N 74 S C N 75 N C N 76 N O N 77 N C N 78 N C N 79 N O N 80 N O N 81 N C Y 82 N C Y 83 N C Y 84 N C Y 85 N C Y 86 N C Y 87 N C 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 H N 151 N H N 152 N N N 153 S C N 154 N C N 155 N O N 156 N C N 157 N O N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N N N 166 S C N 167 N C N 168 N O N 169 N C N 170 N C N 171 N C N 172 N N N 173 N C N 174 N N N 175 N N N 176 N O 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 H N 191 N H N 192 N N N 193 S C N 194 N C N 195 N O N 196 N C N 197 N C N 198 N O N 199 N N N 200 N O 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 H N 208 N H N 209 N N N 210 S C N 211 N C N 212 N O N 213 N C N 214 N C N 215 N O N 216 N O N 217 N O 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 C N 226 N C N 227 N O N 228 N S N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N N N 236 R C N 237 N C N 238 N O N 239 N C N 240 N S N 241 N O 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 S N 250 N O N 251 N C N 252 N C N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N N N 260 S C N 261 N C N 262 N O N 263 N C N 264 N C N 265 N C N 266 N O N 267 N N N 268 N O N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N N N 280 S C N 281 N C N 282 N O N 283 N C N 284 N C N 285 N C N 286 N O N 287 N O N 288 N O 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 H N 296 N H N 297 N H N 298 N N N 299 N C N 300 N C N 301 N O N 302 N O N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N N N 309 S C N 310 N C N 311 N O N 312 N C Y 313 N C Y 314 N N Y 315 N C Y 316 N C Y 317 N N N 318 N O N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N O N 330 N H N 331 N H N 332 N N N 333 S C N 334 N C N 335 N O N 336 S C N 337 N C N 338 N C N 339 N C N 340 N O N 341 N H N 342 N H N 343 N H 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 N N 355 S C N 356 N C N 357 N O N 358 N C N 359 N C N 360 N C N 361 N C N 362 N O 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 N N 377 S C N 378 N C N 379 N O N 380 N C N 381 N C N 382 N C N 383 N C N 384 N N N 385 N O 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 H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N N N 402 S C N 403 N C N 404 N O N 405 N C N 406 N C N 407 N S N 408 N C N 409 N O N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N N N 422 S C N 423 N C N 424 N O N 425 N C Y 426 N C Y 427 N C Y 428 N C Y 429 N C Y 430 N C Y 431 N C N 432 N O N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N N N 445 S C N 446 N C N 447 N O N 448 N C N 449 N C N 450 N C N 451 N O 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 N N 462 S C N 463 N C N 464 N O N 465 R C N 466 N O N 467 N C N 468 N O N 469 N H 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 N N 479 S C N 480 N C N 481 N O N 482 N C Y 483 N C Y 484 N C Y 485 N C Y 486 N N Y 487 N C Y 488 N C Y 489 N C Y 490 N C Y 491 N C N 492 N O N 493 N H N 494 N H N 495 N H N 496 N H N 497 N H N 498 N H N 499 N H N 500 N H N 501 N H N 502 N H N 503 N H N 504 N H N 505 N N N 506 S C N 507 N C N 508 N O N 509 N C Y 510 N C Y 511 N C Y 512 N C Y 513 N C Y 514 N C Y 515 N C N 516 N O N 517 N O N 518 N H N 519 N H N 520 N H N 521 N H N 522 N H N 523 N H N 524 N H N 525 N H N 526 N H N 527 N H N 528 N H N 529 N N N 530 S C N 531 N C N 532 N O N 533 N C N 534 N C N 535 N C N 536 N O N 537 N H N 538 N H N 539 N H N 540 N H N 541 N H N 542 N H N 543 N H N 544 N H N 545 N H N 546 N H N 547 N H N 1 N sing N 2 N sing N 3 N sing N 4 N doub Y 5 N sing Y 6 N doub N 7 N sing Y 8 N sing N 9 N sing Y 10 N doub Y 11 N sing Y 12 N sing N 13 N sing Y 14 N doub N 15 N sing Y 16 N sing N 17 N sing Y 18 N doub N 19 N sing Y 20 N sing N 21 N sing N 22 N sing N 23 N doub N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing Y 30 N doub Y 31 N sing Y 32 N sing N 33 N sing Y 34 N doub N 35 N sing Y 36 N sing N 37 N sing Y 38 N doub 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 sing N 46 N doub 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 sing N 55 N sing N 56 N doub 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 N 77 N sing N 78 N sing Y 79 N doub Y 80 N sing Y 81 N sing N 82 N sing Y 83 N doub N 84 N sing Y 85 N doub N 86 N sing Y 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 N 100 N sing N 101 N sing Y 102 N doub Y 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N sing Y 108 N doub N 109 N sing Y 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 sing N 118 N sing N 119 N doub 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 sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N doub N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing Y 145 N doub Y 146 N sing Y 147 N sing N 148 N sing Y 149 N doub N 150 N sing Y 151 N sing N 152 N sing Y 153 N doub 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 sing N 161 N sing N 162 N doub 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 doub 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 sing N 187 N sing N 188 N doub 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 doub 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 doub N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N doub 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 sing N 239 N sing N 240 N doub 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 doub N 248 N sing N 249 N sing N 250 N sing N 251 N sing 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 sing N 260 N sing N 261 N sing N 262 N doub 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 N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N doub 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 sing N 298 N sing N 299 N doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N doub N 309 N sing N 310 N sing N 311 N sing N 312 N sing Y 313 N sing Y 314 N doub Y 315 N doub N 316 N sing Y 317 N sing N 318 N sing Y 319 N sing N 320 N sing 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 doub 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 sing 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 doub 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 doub 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 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 doub 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 sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N doub N 417 N sing N 418 N sing N 419 N sing N 420 N sing Y 421 N doub Y 422 N sing Y 423 N sing N 424 N sing Y 425 N doub N 426 N sing Y 427 N doub N 428 N sing Y 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 doub N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing 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 doub N 457 N sing N 458 N sing 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 N 470 N sing N 471 N sing N 472 N doub N 473 N sing N 474 N sing N 475 N sing N 476 N sing Y 477 N doub Y 478 N sing Y 479 N sing N 480 N sing Y 481 N doub Y 482 N sing Y 483 N sing N 484 N sing Y 485 N sing Y 486 N doub N 487 N sing Y 488 N doub N 489 N sing Y 490 N sing N 491 N sing N 492 N sing N 493 N sing N 494 N sing N 495 N sing N 496 N sing N 497 N sing N 498 N sing N 499 N sing N 500 N doub N 501 N sing N 502 N sing N 503 N sing N 504 N sing Y 505 N doub Y 506 N sing Y 507 N sing N 508 N sing Y 509 N doub N 510 N sing Y 511 N doub N 512 N sing Y 513 N sing 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 doub N 525 N sing N 526 N sing N 527 N sing N 528 N sing N 529 N sing N 530 N sing N 531 N sing N 532 N sing N 533 N sing N 534 N sing N 535 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/pdb3kfs/pdb pdb_00003kfs 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 100 1 Rh coated flat mirror CCD 2009-04-17 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 DIMETHYL SULFOXIDE 3 syn non-polymer 78.133 BETA-MERCAPTOETHANOL 2 syn non-polymer 192.234 1-benzothiophen-2-ylacetic acid 1 syn non-polymer 18.015 water 68 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 2.06 40.31 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 1F1 in the outside/top of flap RCSB Y RCSB 2009-10-28 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 DMS DIMETHYL SULFOXIDE BME BETA-MERCAPTOETHANOL 2FX 1-benzothiophen-2-ylacetic acid HOH water THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE 2AZ8 HIV Protease dimer generated from PDB entry 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 DMS 302 3 DMS DMS 302 A DMS 304 3 DMS DMS 304 A BME 401 4 BME BME 401 A 2FX 201 5 2FX 2FX 201 B DMS 305 3 DMS DMS 305 B BME 402 4 BME BME 402 B HOH 202 6 HOH HOH 202 A HOH 205 6 HOH HOH 205 A HOH 206 6 HOH HOH 206 A HOH 209 6 HOH HOH 209 A HOH 211 6 HOH HOH 211 A HOH 219 6 HOH HOH 219 A HOH 222 6 HOH HOH 222 A HOH 225 6 HOH HOH 225 A HOH 226 6 HOH HOH 226 A HOH 231 6 HOH HOH 231 A HOH 232 6 HOH HOH 232 A HOH 233 6 HOH HOH 233 A HOH 235 6 HOH HOH 235 A HOH 237 6 HOH HOH 237 A HOH 238 6 HOH HOH 238 A HOH 242 6 HOH HOH 242 A HOH 243 6 HOH HOH 243 A HOH 245 6 HOH HOH 245 A HOH 247 6 HOH HOH 247 A HOH 251 6 HOH HOH 251 A HOH 252 6 HOH HOH 252 A HOH 255 6 HOH HOH 255 A HOH 256 6 HOH HOH 256 A HOH 258 6 HOH HOH 258 A HOH 260 6 HOH HOH 260 A HOH 261 6 HOH HOH 261 A HOH 263 6 HOH HOH 263 A HOH 265 6 HOH HOH 265 A HOH 269 6 HOH HOH 269 A HOH 272 6 HOH HOH 272 A HOH 273 6 HOH HOH 273 A HOH 279 6 HOH HOH 279 A HOH 280 6 HOH HOH 280 A HOH 203 6 HOH HOH 203 B HOH 204 6 HOH HOH 204 B HOH 208 6 HOH HOH 208 B HOH 210 6 HOH HOH 210 B HOH 212 6 HOH HOH 212 B HOH 213 6 HOH HOH 213 B HOH 215 6 HOH HOH 215 B HOH 216 6 HOH HOH 216 B HOH 218 6 HOH HOH 218 B HOH 220 6 HOH HOH 220 B HOH 223 6 HOH HOH 223 B HOH 227 6 HOH HOH 227 B HOH 228 6 HOH HOH 228 B HOH 229 6 HOH HOH 229 B HOH 234 6 HOH HOH 234 B HOH 236 6 HOH HOH 236 B HOH 239 6 HOH HOH 239 B HOH 240 6 HOH HOH 240 B HOH 241 6 HOH HOH 241 B HOH 246 6 HOH HOH 246 B HOH 248 6 HOH HOH 248 B HOH 249 6 HOH HOH 249 B HOH 250 6 HOH HOH 250 B HOH 253 6 HOH HOH 253 B HOH 254 6 HOH HOH 254 B HOH 257 6 HOH HOH 257 B HOH 259 6 HOH HOH 259 B HOH 262 6 HOH HOH 262 B HOH 264 6 HOH HOH 264 B HOH 267 6 HOH HOH 267 B HOH 268 6 HOH HOH 268 B HOH 274 6 HOH HOH 274 B HOH 275 6 HOH HOH 275 B HOH 277 6 HOH HOH 277 B HOH 278 6 HOH HOH 278 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 -24 10090 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 45 A N LYS 45 A O VAL 56 A O VAL 56 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 ALA 22 A O ALA 22 A N VAL 11 A N VAL 11 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 ALA 22 B O ALA 22 B N VAL 11 B N VAL 11 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 C1 3TL 200 WRONG HAND 1 A C68 3TL 200 PLANAR 1 A A OD2 O1 ASP 3TL 25 200 2.12 1 A A CB CG GLU GLU 21 21 -0.121 0.019 1.517 1.396 N 1 A A CB SG CYS CYS 67 67 -0.104 0.016 1.812 1.708 N 1 A MET 36 161.97 172.34 1 A ASN 37 -105.07 53.89 1 A PRO 39 -43.10 78.91 1 B GLU 34 -49.61 152.26 62.42 19.249 4.05 -0.360 0.000 0.000 1.450 0.000 -1.090 0.940 0.918 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY 0.250 0.203 0.205 1.800 38.07 872 17333 17199 5.100 99.390 1.00 1.00 3.300 0.100 RANDOM 1 Isotropic THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.150 0.140 0.800 0.800 1.400 HIV Protease dimer generated from PDB entry 2AZ8 MAXIMUM LIKELIHOOD MASK 1.800 38.07 68 1685 99 0 1518 0.024 2.110 0.337 0.312 1.847 63 1159 1222 1159 20 98.470 16.6 1.80 46.5 3KFS 17333 17246 0.0 0.0 0.138 0.138 1 3.9 3.8 99.5 0.715 1.80 1.85 1.1 1225 0.715 1 3.9 98.8 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0072 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 2F4 in the outside/top of flap 1 N N 1 N N 2 N N 3 N N 3 N N 4 N N 5 N N 3 N N 4 N N 6 N N 6 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 2.007 none A CYS 67 A SG CYS 67 1_555 A BME 401 F S2 BME 1_555 covale 2.012 none B CYS 67 B SG CYS 67 1_555 B BME 402 I 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 3KFS 1 99 Q903N5 A 1 1 99 1 99 3KFS 1 99 Q903N5 B 1 1 99 1 ARG engineered mutation LYS 7 3KFS A Q903N5 UNP 7 7 2 ARG engineered mutation LYS 7 3KFS 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 THR 31 A THR 31 A LEU 33 A LEU 33 A ILE 84 A ILE 84 A ILE 85 A ILE 85 A LEU 19 A LEU 19 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 22 BINDING SITE FOR RESIDUE DMS A 302 A DMS 302 Software 7 BINDING SITE FOR RESIDUE DMS A 304 A DMS 304 Software 5 BINDING SITE FOR RESIDUE BME A 401 A BME 401 Software 5 BINDING SITE FOR RESIDUE 2FX B 201 B 2FX 201 Software 9 BINDING SITE FOR RESIDUE DMS B 305 B DMS 305 Software 4 BINDING SITE FOR RESIDUE BME B 402 B BME 402 Software 3 A ARG 8 A ARG 8 22 1_555 A ASP 25 A ASP 25 22 1_555 A GLY 27 A GLY 27 22 1_555 A ALA 28 A ALA 28 22 1_555 A ASP 29 A ASP 29 22 1_555 A MET 46 A MET 46 22 1_555 A ILE 47 A ILE 47 22 1_555 A GLY 48 A GLY 48 22 1_555 A GLY 49 A GLY 49 22 1_555 A ILE 50 A ILE 50 22 1_555 A PRO 81 A PRO 81 22 1_555 A HOH 265 J HOH 22 1_555 B ASP 25 B ASP 25 22 1_555 B GLY 27 B GLY 27 22 1_555 B ALA 28 B ALA 28 22 1_555 B ASP 29 B ASP 29 22 1_555 B ASP 30 B ASP 30 22 1_555 B GLY 48 B GLY 48 22 1_555 B GLY 49 B GLY 49 22 1_555 B ILE 50 B ILE 50 22 1_555 B VAL 82 B VAL 82 22 1_555 B ILE 84 B ILE 84 22 1_555 A LYS 14 A LYS 14 7 1_555 A ILE 15 A ILE 15 7 1_555 A GLY 16 A GLY 16 7 1_555 A GLY 17 A GLY 17 7 1_555 A LEU 63 A LEU 63 7 1_555 A ILE 64 A ILE 64 7 1_555 A GLU 65 A GLU 65 7 1_555 A TRP 6 A TRP 6 5 1_555 B LEU 19 B LEU 19 5 1_455 B ARG 87 B ARG 87 5 1_555 B ASN 88 B ASN 88 5 1_555 B HOH 278 K HOH 5 1_555 A VAL 11 A VAL 11 5 1_555 A THR 12 A THR 12 5 1_555 A CYS 67 A CYS 67 5 1_555 B LYS 7 B LYS 7 5 1_455 B HOH 254 K HOH 5 1_455 A TRP 6 A TRP 6 9 3_445 B PRO 44 B PRO 44 9 1_555 B LYS 45 B LYS 45 9 1_555 B LYS 55 B LYS 55 9 1_555 B VAL 56 B VAL 56 9 1_555 B GLN 92 B GLN 92 9 3_445 B ILE 93 B ILE 93 9 3_445 B GLY 94 B GLY 94 9 3_445 B HOH 208 K HOH 9 3_445 B GLY 73 B GLY 73 4 1_555 B THR 74 B THR 74 4 1_555 B ASN 88 B ASN 88 4 1_555 B GLN 92 B GLN 92 4 1_555 B VAL 11 B VAL 11 3 1_555 B THR 12 B THR 12 3 1_555 B CYS 67 B CYS 67 3 1_555 19 P 21 21 21