0.016028 0.009254 0.000000 0.000000 0.018508 0.000000 0.000000 0.000000 0.012186 0.00000 0.00000 0.00000 Stout, C.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 62.390 62.390 82.060 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 C N 2 N O N 3 N O N 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 N 11 N N N 12 S C N 13 N C N 14 N O N 15 N C N 16 N N N 17 S C N 18 N C N 19 N O N 20 N C N 21 N C N 22 N C N 23 R C N 24 N O N 25 S C N 26 N N N 27 N C Y 28 N C Y 29 N C Y 30 N C Y 31 N C Y 32 N C Y 33 N C N 34 N N N 35 S C N 36 R C N 37 N O N 38 N C Y 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C Y 44 N C N 45 N N N 46 S C N 47 N C N 48 N O N 49 N C N 50 N C N 51 N C N 52 N N N 53 S C N 54 N C N 55 N O N 56 N C N 57 N C N 58 N O N 59 N O N 60 N C Y 61 N C Y 62 N C Y 63 N C Y 64 N C Y 65 N C Y 66 N C 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 H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H 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 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 N N 132 S C N 133 N C N 134 N O N 135 N C N 136 N O 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 N N 145 S C N 146 N C N 147 N O N 148 N C N 149 N C N 150 N C N 151 N N N 152 N C N 153 N N N 154 N N 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 H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N N N 172 S C N 173 N C N 174 N O N 175 N C N 176 N C N 177 N O N 178 N N N 179 N O 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 N N 189 S C N 190 N C N 191 N O N 192 N C N 193 N C N 194 N O N 195 N O N 196 N O 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 C N 205 N C N 206 N O N 207 N S N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N N N 215 R C N 216 N C N 217 N O N 218 N C N 219 N S N 220 N O 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 S N 229 N O N 230 N C N 231 N C N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N N N 239 S C N 240 N C N 241 N O N 242 N C N 243 N C N 244 N C N 245 N O N 246 N N N 247 N O N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N N N 259 S C N 260 N C N 261 N O N 262 N C N 263 N C N 264 N C N 265 N O N 266 N O N 267 N O N 268 N H 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 N N 278 N C N 279 N C N 280 N O N 281 N O N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N N N 288 S C N 289 N C N 290 N O N 291 N C Y 292 N C Y 293 N N Y 294 N C Y 295 N C Y 296 N N N 297 N O N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N O N 309 N H N 310 N H N 311 N N N 312 S C N 313 N C N 314 N O N 315 S C N 316 N C N 317 N C N 318 N C N 319 N O 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 H N 330 N H N 331 N H N 332 N H N 333 N N N 334 S C N 335 N C N 336 N O N 337 N C N 338 N C N 339 N C N 340 N C N 341 N O 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 H N 355 N N N 356 S C N 357 N C N 358 N O N 359 N C N 360 N C N 361 N C N 362 N C N 363 N N N 364 N O 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 N N 381 S C N 382 N C N 383 N O N 384 N C N 385 N C N 386 N S N 387 N C N 388 N O 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 N N 401 S C N 402 N C N 403 N O N 404 N C Y 405 N C Y 406 N C Y 407 N C Y 408 N C Y 409 N C Y 410 N C N 411 N O 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 H N 422 N H N 423 N N N 424 S C N 425 N C N 426 N O N 427 N C N 428 N C N 429 N C N 430 N O 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 H N 439 N H N 440 N N N 441 S C N 442 N C N 443 N O N 444 R C N 445 N O N 446 N C N 447 N O N 448 N H N 449 N H N 450 N H 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 N N 458 S C N 459 N C N 460 N O N 461 N C Y 462 N C Y 463 N C Y 464 N C Y 465 N N Y 466 N C Y 467 N C Y 468 N C Y 469 N C Y 470 N C N 471 N O 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 481 N H N 482 N H N 483 N H N 484 N N N 485 S C N 486 N C N 487 N O N 488 N C Y 489 N C Y 490 N C Y 491 N C Y 492 N C Y 493 N C Y 494 N C N 495 N O N 496 N O 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 H N 506 N H N 507 N H N 508 N N N 509 S C N 510 N C N 511 N O N 512 N C N 513 N C N 514 N C N 515 N O N 516 N H N 517 N H 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 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing Y 8 N doub Y 9 N sing Y 10 N sing N 11 N sing Y 12 N doub N 13 N sing Y 14 N sing N 15 N sing Y 16 N doub N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub 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 sing N 34 N doub 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 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 sing N 55 N sing N 56 N sing Y 57 N doub Y 58 N sing Y 59 N sing N 60 N sing Y 61 N doub N 62 N sing Y 63 N doub N 64 N sing Y 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 N 79 N sing Y 80 N doub Y 81 N sing Y 82 N sing N 83 N sing Y 84 N doub N 85 N sing Y 86 N doub N 87 N sing Y 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 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 sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub 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 Y 123 N doub Y 124 N sing Y 125 N sing N 126 N sing Y 127 N doub N 128 N sing Y 129 N sing N 130 N sing Y 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N doub N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 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 doub 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 sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub 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 doub N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N doub 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 doub N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N doub N 200 N sing 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 doub N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N doub 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 sing N 248 N doub 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 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 doub N 268 N sing N 269 N sing N 270 N sing 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 doub N 278 N sing 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 doub N 287 N sing N 288 N sing N 289 N sing N 290 N sing Y 291 N sing Y 292 N doub Y 293 N doub N 294 N sing Y 295 N sing N 296 N sing Y 297 N sing N 298 N sing 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 sing 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 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 doub 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 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 doub 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 doub 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 doub N 395 N sing N 396 N sing N 397 N sing N 398 N sing Y 399 N doub Y 400 N sing Y 401 N sing N 402 N sing Y 403 N doub N 404 N sing Y 405 N doub N 406 N sing Y 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 sing N 417 N doub N 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 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 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 sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N doub N 451 N sing N 452 N sing N 453 N sing N 454 N sing Y 455 N doub Y 456 N sing Y 457 N sing N 458 N sing Y 459 N doub Y 460 N sing Y 461 N sing N 462 N sing Y 463 N sing Y 464 N doub N 465 N sing Y 466 N doub N 467 N sing Y 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N doub N 479 N sing N 480 N sing N 481 N sing N 482 N sing Y 483 N doub Y 484 N sing Y 485 N sing N 486 N sing Y 487 N doub N 488 N sing Y 489 N doub N 490 N sing Y 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 sing N 501 N sing N 502 N doub 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 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/pdb3kfp/pdb pdb_00003kfp 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 2009-04-07 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 1 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 1 syn non-polymer 18.015 water 100 nat water no no PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF A 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 2.13 42.20 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 pdbx_unobs_or_zero_occ_atoms 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 Advisory 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) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap 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 DMS DIMETHYL SULFOXIDE BME BETA-MERCAPTOETHANOL HOH water IN THIS STRUCTURE THE INHIBITOR TL-3 (PDB LIGAND 3TL) IS BOUND TO HIV-1 PROTEASE DIMER. BECAUSE TL-3 HAS INTERNAL 2-FOLD SYMMETRY, ONLY ONE-HALF OF THE INHIBITOR (PDB LIGAND INT) IS PRESENT IN THE ASYMMETRIC UNIT. 2-FOLD ROTATION GENERATES A FULL TL-3 INHIBITOR WITH A BOND BETWEEN C2-C2. THE LONG C2-C2 BOND IN THIS STRUCTURE (2.41 A RATHER THAN 1.54 A) IS DUE TO ERROR IN REFINEMENT 2AZ8 HIV Protease monomer 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 DMS 300 3 DMS DMS 300 A DMS 301 3 DMS DMS 301 A DMS 302 3 DMS DMS 302 A BME 303 4 BME BME 303 A HOH 305 5 HOH HOH 305 A HOH 306 5 HOH HOH 306 A HOH 307 5 HOH HOH 307 A HOH 309 5 HOH HOH 309 A HOH 310 5 HOH HOH 310 A HOH 312 5 HOH HOH 312 A HOH 313 5 HOH HOH 313 A HOH 314 5 HOH HOH 314 A HOH 315 5 HOH HOH 315 A HOH 316 5 HOH HOH 316 A HOH 317 5 HOH HOH 317 A HOH 318 5 HOH HOH 318 A HOH 319 5 HOH HOH 319 A HOH 320 5 HOH HOH 320 A HOH 321 5 HOH HOH 321 A HOH 322 5 HOH HOH 322 A HOH 324 5 HOH HOH 324 A HOH 325 5 HOH HOH 325 A HOH 326 5 HOH HOH 326 A HOH 327 5 HOH HOH 327 A HOH 328 5 HOH HOH 328 A HOH 329 5 HOH HOH 329 A HOH 330 5 HOH HOH 330 A HOH 332 5 HOH HOH 332 A HOH 333 5 HOH HOH 333 A HOH 334 5 HOH HOH 334 A HOH 335 5 HOH HOH 335 A HOH 336 5 HOH HOH 336 A HOH 337 5 HOH HOH 337 A HOH 338 5 HOH HOH 338 A HOH 339 5 HOH HOH 339 A HOH 340 5 HOH HOH 340 A HOH 342 5 HOH HOH 342 A HOH 343 5 HOH HOH 343 A HOH 344 5 HOH HOH 344 A HOH 345 5 HOH HOH 345 A HOH 346 5 HOH HOH 346 A HOH 347 5 HOH HOH 347 A HOH 348 5 HOH HOH 348 A HOH 349 5 HOH HOH 349 A HOH 351 5 HOH HOH 351 A HOH 352 5 HOH HOH 352 A HOH 353 5 HOH HOH 353 A HOH 354 5 HOH HOH 354 A HOH 355 5 HOH HOH 355 A HOH 356 5 HOH HOH 356 A HOH 357 5 HOH HOH 357 A HOH 358 5 HOH HOH 358 A HOH 359 5 HOH HOH 359 A HOH 360 5 HOH HOH 360 A HOH 361 5 HOH HOH 361 A HOH 362 5 HOH HOH 362 A HOH 363 5 HOH HOH 363 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 370 5 HOH HOH 370 A HOH 371 5 HOH HOH 371 A HOH 372 5 HOH HOH 372 A HOH 373 5 HOH HOH 373 A HOH 374 5 HOH HOH 374 A HOH 375 5 HOH HOH 375 A HOH 376 5 HOH HOH 376 A HOH 377 5 HOH HOH 377 A HOH 378 5 HOH HOH 378 A HOH 379 5 HOH HOH 379 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 386 5 HOH HOH 386 A HOH 387 5 HOH HOH 387 A HOH 388 5 HOH HOH 388 A HOH 389 5 HOH HOH 389 A HOH 390 5 HOH HOH 390 A HOH 391 5 HOH HOH 391 A HOH 392 5 HOH HOH 392 A HOH 393 5 HOH HOH 393 A HOH 394 5 HOH HOH 394 A HOH 395 5 HOH HOH 395 A HOH 396 5 HOH HOH 396 A HOH 397 5 HOH HOH 397 A HOH 398 5 HOH HOH 398 A HOH 399 5 HOH HOH 399 A HOH 400 5 HOH HOH 400 A HOH 401 5 HOH HOH 401 A HOH 402 5 HOH HOH 402 A HOH 403 5 HOH HOH 403 A HOH 404 5 HOH HOH 404 A HOH 405 5 HOH HOH 405 A HOH 406 5 HOH HOH 406 A HOH 407 5 HOH HOH 407 A HOH 408 5 HOH HOH 408 A HOH 409 5 HOH HOH 409 A HOH 410 5 HOH HOH 410 A 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 software_defined_assembly PISA 2 dimeric 3830 -25.3 9640 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 -0.5000000000 0.8660254038 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 y,x,-z+1/3 crystal symmetry operation 0.0000000000 0.0000000000 27.3533333333 A N LYS 45 A N LYS 45 A O VAL 56 A O VAL 56 A N TYR 59 A N TYR 59 A O VAL 75 A O VAL 75 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 1 A HOH 306 G HOH 1 A HOH 342 G HOH 1 A A C2 O DMS HOH 302 305 2.01 1 A A NH2 O ARG HOH 8 383 2.13 1 A A GLY ARG 40 41 -148.52 1 7.41 1.20 111.50 118.91 A A A CB CA C CYS CYS CYS 67 67 67 N 1 A A CB CG TRP TRP 6 6 -0.127 0.018 1.498 1.371 N 1 A A CB SG CYS CYS 67 67 -0.111 0.016 1.812 1.701 N 1 A A O O HOH HOH 383 383 2.19 1_555 11_555 1 A A O O HOH HOH 346 346 2.19 1_555 12_545 1 A GLU 34 -48.75 156.08 1 A MET 36 -170.19 142.83 1 A PRO 39 -37.16 109.29 1 A PRO 79 -76.12 43.68 38.229 0.50 0.25 0.00 0.50 0.00 -0.74 0.954 0.915 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.31318 0.22571 0.22969 1.77 32.67 462 9716 9095 4.8 97.67 1.00 0.50 4.53 0.14 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.16 0.17 0.80 0.80 1.20 HIV Protease monomer in 2AZ8 MAXIMUM LIKELIHOOD MASK 1.77 32.67 100 908 49 0 759 0.023 0.02 916 1.987 1.99 1399 7.159 7.50 196 41.771 24.81 27 17.999 15.00 144 15.335 15.00 4 0.139 0.20 128 0.008 0.02 986 0.290 0.274 1.812 44 635 20 97.14 1.77 54.03 3KFP 9716 9561 0.0 0.0 0.099 0.099 1 4.1 6.5 98.4 0.734 1.77 1.81 0.8 0.734 1 6.7 98.1 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) with inhibitor TL-3 bound, and DMSOs in exo site 1 N N 2 N N 3 N N 3 N N 3 N N 4 N N 5 N N A GLY 86 A GLY 86 HELX_P A THR 91 A THR 91 1 1 6 covale 2.020 none A CYS 67 A SG CYS 67 1_555 A BME 303 F S2 BME 1_555 covale 2.407 none A 3TL 200 B C2 3TL 1_555 A 3TL 200 B C2 3TL 7_555 HYDROLASE/HYDROLASE INHIBITOR HIV-1, PROTEASE, EXO SITE, Aspartyl protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX Q903N5_9HIV1 UNP 1 1 Q903N5 PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 1 99 3KFP 1 99 Q903N5 A 1 1 99 1 ARG engineered mutation LYS 7 3KFP A Q903N5 UNP 7 7 8 anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel 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 BINDING SITE FOR RESIDUE 3TL A 200 A 3TL 200 Software 15 BINDING SITE FOR RESIDUE DMS A 300 A DMS 300 Software 7 BINDING SITE FOR RESIDUE DMS A 301 A DMS 301 Software 5 BINDING SITE FOR RESIDUE DMS A 302 A DMS 302 Software 7 BINDING SITE FOR RESIDUE BME A 303 A BME 303 Software 3 A ARG 8 A ARG 8 15 7_555 A ASP 25 A ASP 25 15 1_555 A ASP 25 A ASP 25 15 7_555 A GLY 27 A GLY 27 15 1_555 A ALA 28 A ALA 28 15 1_555 A ASP 29 A ASP 29 15 1_555 A ILE 47 A ILE 47 15 1_555 A GLY 48 A GLY 48 15 1_555 A GLY 49 A GLY 49 15 1_555 A ILE 50 A ILE 50 15 1_555 A PRO 81 A PRO 81 15 7_555 A VAL 82 A VAL 82 15 7_555 A ILE 84 A ILE 84 15 1_555 A HOH 306 G HOH 15 7_555 A HOH 306 G HOH 15 1_555 A THR 12 A THR 12 7 1_555 A THR 12 A THR 12 7 12_545 A LYS 14 A LYS 14 7 1_555 A GLU 65 A GLU 65 7 1_555 A ILE 66 A ILE 66 7 1_555 A CYS 67 A CYS 67 7 1_555 A GLY 68 A GLY 68 7 1_555 A PRO 39 A PRO 39 5 1_555 A ILE 62 A ILE 62 5 1_555 A LEU 63 A LEU 63 5 1_555 A DMS 302 E DMS 5 1_555 A HOH 305 G HOH 5 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 DMS 301 D DMS 7 1_555 A HOH 305 G HOH 7 1_555 A VAL 11 A VAL 11 3 1_555 A THR 12 A THR 12 3 1_555 A CYS 67 A CYS 67 3 1_555 178 P 61 2 2