0.019506 0.000000 0.000000 0.000000 0.016911 0.000000 0.000000 0.000000 0.016148 0.00000 0.00000 0.00000 Prabu-Jeyabalan, M. Nalivaika, E.A. King, N.M. Schiffer, C.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 51.265 59.133 61.926 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 C3 H7 N O3 105.093 y SERINE 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 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 N N 296 S C N 297 N C N 298 N O N 299 N C N 300 N O N 301 N O 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 H N 309 N N N 310 S C N 311 N C N 312 N O N 313 R C N 314 N O N 315 N C N 316 N O N 317 N H N 318 N H 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 N N 327 S C N 328 N C N 329 N O N 330 N C Y 331 N C Y 332 N C Y 333 N C Y 334 N N Y 335 N C Y 336 N C Y 337 N C Y 338 N C Y 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 N N 354 S C N 355 N C N 356 N O N 357 N C Y 358 N C Y 359 N C Y 360 N C Y 361 N C Y 362 N C Y 363 N C N 364 N O N 365 N O 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 N N 378 S C N 379 N C N 380 N O N 381 N C N 382 N C N 383 N C N 384 N O 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 H N 395 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 sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N doub N 288 N sing 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 sing N 298 N sing N 299 N sing N 300 N doub 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 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 doub N 317 N sing N 318 N sing N 319 N sing N 320 N sing Y 321 N doub Y 322 N sing Y 323 N sing N 324 N sing Y 325 N doub Y 326 N sing Y 327 N sing N 328 N sing Y 329 N sing Y 330 N doub N 331 N sing Y 332 N doub N 333 N sing Y 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 doub N 345 N sing N 346 N sing N 347 N sing N 348 N sing Y 349 N doub Y 350 N sing Y 351 N sing N 352 N sing Y 353 N doub N 354 N sing Y 355 N doub N 356 N sing Y 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 doub 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 US J.Virol. JOVIAM 0825 0022-538X 77 1305 1315 10.1128/JVI.77.2.1306-1315.2003 12502847 Viability of drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy 2003 UK J.Mol.Biol. JMOBAK 0070 0022-2836 301 1207 1220 10.1006/jmbi.2000.4018 How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease 2000 UK Structure STRUE6 2005 0969-2126 10 369 381 10.1016/S0969-2126(02)00720-7 Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes 2002 US Protein Sci. PRCIEI 0795 0961-8368 11 418 429 10.1110/ps.2520102 Lack of synergy for inhibitors targeting a multi-drug resistant HIV-1 protease 2002 10.2210/pdb1mt9/pdb pdb_00001mt9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298 1 Yale mirrors IMAGE PLATE 1999-11-30 RIGAKU RAXIS IV Yale Mirrors SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 10772.724 PROTEASE RETROPEPSIN 3.4.23.16 Q7K, D25N, L63P, V82A 2 man polymer 1173.325 p1-p6 Gag substrate decapeptide 1 syn polymer 94.971 PHOSPHATE ION 6 syn non-polymer 18.015 water 88 nat water HIV-1 PROTEASE E.C.3.4.23.16 no no PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT PANIIGRNLLTQIGCTLNF PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT PANIIGRNLLTQIGCTLNF A,B polypeptide(L) no no RPGNFLQSRP RPGNFLQSRP P 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 n n n n n n n n n n Lentivirus Escherichia sample 11676 Human immunodeficiency virus 1 562 Escherichia coli TAP106 PLASMID pXC35-pEN18 1 2.06 40.41 VAPOR DIFFUSION, HANGING DROP 6.2 sodium phosphate, sodium citrate, ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP at 298K 298 software database_2 struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Refinement description Database references Derived calculations Data collection Refinement description 1 0 2003-01-07 1 1 2008-04-28 1 2 2011-07-13 1 3 2017-10-11 1 4 2021-10-27 1 5 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Inactive wild-type HIV-1 protease (D25N) complexed with its Gag substrate peptide MA-CA. HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC INHIBITOR RCSB Y RCSB 2002-09-20 REL PO4 PHOSPHATE ION HOH water This peptide sequence occurs naturally in Gag of HIV-1 sample 1MTR PDB experimental model PO4 504 3 PO4 PO4 504 A PO4 506 3 PO4 PO4 506 A PO4 507 3 PO4 PO4 507 A PO4 501 3 PO4 PO4 501 B PO4 502 3 PO4 PO4 502 B PO4 503 3 PO4 PO4 503 B HOH 4 4 HOH HOH 508 A HOH 11 4 HOH HOH 509 A HOH 15 4 HOH HOH 510 A HOH 18 4 HOH HOH 511 A HOH 21 4 HOH HOH 512 A HOH 22 4 HOH HOH 513 A HOH 23 4 HOH HOH 514 A HOH 24 4 HOH HOH 515 A HOH 26 4 HOH HOH 516 A HOH 27 4 HOH HOH 517 A HOH 30 4 HOH HOH 518 A HOH 32 4 HOH HOH 519 A HOH 33 4 HOH HOH 520 A HOH 34 4 HOH HOH 521 A HOH 35 4 HOH HOH 522 A HOH 43 4 HOH HOH 523 A HOH 46 4 HOH HOH 524 A HOH 47 4 HOH HOH 525 A HOH 49 4 HOH HOH 526 A HOH 51 4 HOH HOH 527 A HOH 52 4 HOH HOH 528 A HOH 57 4 HOH HOH 529 A HOH 59 4 HOH HOH 530 A HOH 60 4 HOH HOH 531 A HOH 61 4 HOH HOH 532 A HOH 75 4 HOH HOH 533 A HOH 82 4 HOH HOH 534 A HOH 83 4 HOH HOH 535 A HOH 91 4 HOH HOH 536 A HOH 9105 4 HOH HOH 537 A HOH 102 4 HOH HOH 538 A HOH 103 4 HOH HOH 539 A HOH 104 4 HOH HOH 540 A HOH 107 4 HOH HOH 541 A HOH 108 4 HOH HOH 542 A HOH 109 4 HOH HOH 543 A HOH 110 4 HOH HOH 544 A HOH 114 4 HOH HOH 545 A HOH 115 4 HOH HOH 546 A HOH 116 4 HOH HOH 547 A HOH 117 4 HOH HOH 548 A HOH 118 4 HOH HOH 549 A HOH 1 4 HOH HOH 504 B HOH 2 4 HOH HOH 505 B HOH 5 4 HOH HOH 506 B HOH 7 4 HOH HOH 507 B HOH 8 4 HOH HOH 508 B HOH 12 4 HOH HOH 509 B HOH 13 4 HOH HOH 510 B HOH 14 4 HOH HOH 511 B HOH 16 4 HOH HOH 512 B HOH 17 4 HOH HOH 513 B HOH 19 4 HOH HOH 514 B HOH 25 4 HOH HOH 515 B HOH 28 4 HOH HOH 516 B HOH 36 4 HOH HOH 517 B HOH 37 4 HOH HOH 518 B HOH 39 4 HOH HOH 519 B HOH 40 4 HOH HOH 520 B HOH 41 4 HOH HOH 521 B HOH 42 4 HOH HOH 522 B HOH 44 4 HOH HOH 523 B HOH 45 4 HOH HOH 524 B HOH 48 4 HOH HOH 525 B HOH 50 4 HOH HOH 526 B HOH 53 4 HOH HOH 527 B HOH 54 4 HOH HOH 528 B HOH 56 4 HOH HOH 529 B HOH 58 4 HOH HOH 530 B HOH 62 4 HOH HOH 531 B HOH 64 4 HOH HOH 532 B HOH 68 4 HOH HOH 533 B HOH 70 4 HOH HOH 534 B HOH 77 4 HOH HOH 535 B HOH 81 4 HOH HOH 536 B HOH 88 4 HOH HOH 537 B HOH 89 4 HOH HOH 538 B HOH 101 4 HOH HOH 539 B HOH 105 4 HOH HOH 540 B HOH 106 4 HOH HOH 541 B HOH 111 4 HOH HOH 542 B HOH 112 4 HOH HOH 543 B HOH 113 4 HOH HOH 544 B HOH 119 4 HOH HOH 545 B HOH 120 4 HOH HOH 546 B HOH 3 4 HOH HOH 11 P HOH 31 4 HOH HOH 12 P HOH 142 4 HOH HOH 13 P 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 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 ASN 25 n 25 ASN 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 LYS 41 n 41 LYS 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 PRO 63 n 63 PRO 63 A VAL 64 n 64 VAL 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 ALA 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 ARG 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 ASN 25 n 25 ASN 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 LYS 41 n 41 LYS 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 PRO 63 n 63 PRO 63 B VAL 64 n 64 VAL 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 ALA 82 n 82 ALA 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 ARG 1 n 1 ARG 1 P PRO 2 n 2 PRO 2 P GLY 3 n 3 GLY 3 P ASN 4 n 4 ASN 4 P PHE 5 n 5 PHE 5 P LEU 6 n 6 LEU 6 P GLN 7 n 7 GLN 7 P SER 8 n 8 SER 8 P ARG 9 n 9 ARG 9 P PRO 10 n 10 PRO 10 P author_and_software_defined_assembly PISA 3 trimeric 6550 -60 9030 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 N ASN 98 B N ASN 98 A O THR 96 A O THR 96 A O LEU 97 A O LEU 97 B N ILE 3 B N ILE 3 A O VAL 11 A O VAL 11 A N ALA 22 A N ALA 22 A O LEU 23 A O LEU 23 A N ILE 85 A N ILE 85 A N THR 31 A N THR 31 A O THR 74 A O THR 74 A O VAL 77 A O VAL 77 A N ARG 57 A N ARG 57 A O GLU 65 A O GLU 65 A N ARG 14 A N ARG 14 A N ILE 15 A N ILE 15 A O GLN 18 A O GLN 18 A N THR 31 A N THR 31 A O THR 74 A O THR 74 A O VAL 77 A O VAL 77 A N ARG 57 A N ARG 57 A N GLN 58 A N GLN 58 A O LYS 43 A O LYS 43 B O VAL 11 B O VAL 11 B N ALA 22 B N ALA 22 B O LEU 23 B O LEU 23 B N ILE 85 B N ILE 85 B N THR 31 B N THR 31 B O THR 74 B O THR 74 B O VAL 77 B O VAL 77 B N ARG 57 B N ARG 57 B O GLU 65 B O GLU 65 B N ARG 14 B N ARG 14 B N ILE 15 B N ILE 15 B O GLN 18 B O GLN 18 B N THR 31 B N THR 31 B O THR 74 B O THR 74 B O VAL 77 B O VAL 77 B N ARG 57 B N ARG 57 B N GLN 58 B N GLN 58 B O LYS 43 B O LYS 43 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 CG ARG 14 A CG ARG 14 1 Y 1 A CD ARG 14 A CD ARG 14 1 Y 1 A NE ARG 14 A NE ARG 14 1 Y 1 A CZ ARG 14 A CZ ARG 14 1 Y 1 A NH1 ARG 14 A NH1 ARG 14 1 Y 1 A NH2 ARG 14 A NH2 ARG 14 1 Y 1 A CG ASN 37 A CG ASN 37 1 Y 1 A OD1 ASN 37 A OD1 ASN 37 1 Y 1 A ND2 ASN 37 A ND2 ASN 37 1 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 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 GLN 18 B CG GLN 18 1 Y 1 B CD GLN 18 B CD GLN 18 1 Y 1 B OE1 GLN 18 B OE1 GLN 18 1 Y 1 B NE2 GLN 18 B NE2 GLN 18 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 CG LYS 45 B CG LYS 45 1 Y 1 B CD LYS 45 B CD LYS 45 1 Y 1 B CE LYS 45 B CE LYS 45 1 Y 1 B NZ LYS 45 B NZ LYS 45 1 Y 1 B CG LYS 55 B CG LYS 55 1 Y 1 B CD LYS 55 B CD LYS 55 1 Y 1 B CE LYS 55 B CE LYS 55 1 Y 1 B NZ LYS 55 B NZ LYS 55 1 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 P CG ARG 1 C CG ARG 1 1 Y 1 P CD ARG 1 C CD ARG 1 1 Y 1 P NE ARG 1 C NE ARG 1 1 Y 1 P CZ ARG 1 C CZ ARG 1 1 Y 1 P NH1 ARG 1 C NH1 ARG 1 1 Y 1 P NH2 ARG 1 C NH2 ARG 1 1 Y 1 A GLU 35 -39.16 127.95 1 A GLU 35 -39.82 127.95 1 B GLU 35 A -39.61 132.16 1 B GLU 35 B -38.69 131.01 1 P PHE 5 -90.93 44.61 1 P PHE 5 -92.88 44.61 PROTEIN_REP.PARAM PROTEIN.TOP WATER_REP.PARAM WATER.TOP ION.PARAM ION.TOP 23.8 -0.66 0.00 0.00 -0.64 0.00 1.30 0.21 0.006 0.179 0.179 2.00 32.84 1272 12659 10.3 95.4 RANDOM 172172.14 0.000 1 RESTRAINED THROUGHOUT 0.0 0.0 FOURIER SYNTHESIS 1MTR Engh & Huber FLAT MODEL 67.3885 0.367432 0.26 0.18 2.00 32.84 88 1654 30 0 1536 0.005 1.8 26.0 0.87 0.29 0.028 0.22 2.07 103 1002 1182 10 9.3 92.0 12.4 2.00 32.84 1MT9 12659 12659 0 0 0.09 1 7.7 95.4 0.33 2.00 2.07 1182 92 data scaling SCALEPACK refinement CNS phasing CNS Viability of a drug-resistant HIV-1 protease mutant: structural insights for better antiviral therapy 1 N N 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 4 N N 4 N N 4 N N The entire dimer is provided in the coordinate set and the monomers are distinguished by the chain IDs `A' and `B'. The decamer sequence corresponding to the MA-CA cleavage site of HIV-1 Gag polyprotein. 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 HYDROLASE/HYDROLASE SUBSTRATE Matrix, Capsid, Gag cleavage, drug resistance, substrate recognition, HYDROLASE, HYDROLASE-HYDROLASE SUBSTRATE COMPLEX POL_HV1A2 UNP 1 57 P03369 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 1MT9 PDB 2 1MT9 RPGNFLQSRP 57 155 1MT9 1 99 P03369 A 1 1 99 57 155 1MT9 1 99 P03369 B 1 1 99 1 10 1MT9 1 10 1MT9 P 2 1 10 1 GLN engineered mutation LYS 7 1MT9 A P03369 UNP 63 7 1 ASP engineered mutation ASN 25 1MT9 A P03369 UNP 81 25 1 VAL engineered mutation ALA 82 1MT9 A P03369 UNP 138 82 2 GLN engineered mutation LYS 7 1MT9 B P03369 UNP 63 7 2 ASP engineered mutation ASN 25 1MT9 B P03369 UNP 81 25 2 VAL engineered mutation ALA 82 1MT9 B P03369 UNP 138 82 4 3 5 4 3 5 4 anti-parallel anti-parallel anti-parallel anti-parallel parallel parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel parallel parallel anti-parallel anti-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 LEU 10 A LEU 10 A VAL 11 A VAL 11 A ALA 22 A ALA 22 A LEU 24 A LEU 24 A ILE 84 A ILE 84 A ILE 85 A ILE 85 A THR 31 A THR 31 A LEU 33 A LEU 33 A HIS 69 A HIS 69 A VAL 77 A VAL 77 A GLY 52 A GLY 52 A ILE 66 A ILE 66 A ILE 13 A ILE 13 A ILE 15 A ILE 15 A GLN 18 A GLN 18 A LEU 19 A LEU 19 A THR 31 A THR 31 A LEU 33 A LEU 33 A HIS 69 A HIS 69 A VAL 77 A VAL 77 A GLY 52 A GLY 52 A ILE 66 A ILE 66 A LYS 43 A LYS 43 A GLY 49 A GLY 49 B LEU 10 B LEU 10 B VAL 11 B VAL 11 B ALA 22 B ALA 22 B LEU 24 B LEU 24 B ILE 84 B ILE 84 B ILE 85 B ILE 85 B THR 31 B THR 31 B LEU 33 B LEU 33 B HIS 69 B HIS 69 B VAL 77 B VAL 77 B GLY 52 B GLY 52 B ILE 66 B ILE 66 B ILE 13 B ILE 13 B ILE 15 B ILE 15 B GLN 18 B GLN 18 B LEU 19 B LEU 19 B THR 31 B THR 31 B LEU 33 B LEU 33 B HIS 69 B HIS 69 B VAL 77 B VAL 77 B GLY 52 B GLY 52 B ILE 66 B ILE 66 B LYS 43 B LYS 43 B GLY 49 B GLY 49 BINDING SITE FOR RESIDUE PO4 B 501 B PO4 501 Software 4 BINDING SITE FOR RESIDUE PO4 B 502 B PO4 502 Software 3 BINDING SITE FOR RESIDUE PO4 B 503 B PO4 503 Software 5 BINDING SITE FOR RESIDUE PO4 A 504 A PO4 504 Software 3 BINDING SITE FOR RESIDUE PO4 A 506 A PO4 506 Software 3 BINDING SITE FOR RESIDUE PO4 A 507 A PO4 507 Software 5 BINDING SITE FOR CHAIN P OF P1-P6 GAG SUBSTRATE DECAPEPTIDE Software 35 A PRO 1 A PRO 1 4 4_456 B HIS 69 B HIS 69 4 1_555 B LYS 70 B LYS 70 4 1_555 B PHE 99 B PHE 99 4 4_456 B PRO 1 B PRO 1 3 1_555 B ARG 57 B ARG 57 3 2_455 B HIS 69 B HIS 69 3 1_555 A GLY 16 A GLY 16 5 1_455 A GLY 17 A GLY 17 5 1_455 B ARG 14 B ARG 14 5 1_555 B GLY 17 B GLY 17 5 1_555 B HOH 533 K HOH 5 1_555 A LYS 7 A LYS 7 3 1_555 A ARG 8 A ARG 8 3 1_555 B ARG 87 B ARG 87 3 1_555 A GLY 73 A GLY 73 3 1_555 A THR 74 A THR 74 3 1_555 A ASN 88 A ASN 88 3 1_555 A PRO 39 A PRO 39 5 1_555 A GLY 40 A GLY 40 5 1_555 A HOH 547 J HOH 5 1_555 B MET 36 B MET 36 5 1_655 B ASN 37 B ASN 37 5 1_655 A TRP 6 A TRP 6 35 3_545 A ARG 8 A ARG 8 35 1_555 A GLY 27 A GLY 27 35 1_555 A ALA 28 A ALA 28 35 1_555 A ASP 29 A ASP 29 35 1_555 A ASP 30 A ASP 30 35 1_555 A VAL 32 A VAL 32 35 1_555 A ILE 47 A ILE 47 35 1_555 A GLY 48 A GLY 48 35 1_555 A GLY 49 A GLY 49 35 1_555 A ILE 50 A ILE 50 35 1_555 A GLN 61 A GLN 61 35 2_554 A PRO 81 A PRO 81 35 1_555 A ILE 84 A ILE 84 35 1_555 A HOH 509 J HOH 35 1_555 B ARG 8 B ARG 8 35 1_555 B ASN 25 B ASN 25 35 1_555 B GLY 27 B GLY 27 35 1_555 B ALA 28 B ALA 28 35 1_555 B ASP 29 B ASP 29 35 1_555 B ASP 30 B ASP 30 35 1_555 B MET 46 B MET 46 35 1_555 B ILE 47 B ILE 47 35 1_555 B GLY 48 B GLY 48 35 1_555 B GLY 49 B GLY 49 35 1_555 B ILE 50 B ILE 50 35 1_555 B GLN 58 B GLN 58 35 1_555 B THR 74 B THR 74 35 1_555 B LEU 76 B LEU 76 35 1_555 B PRO 81 B PRO 81 35 1_555 B HOH 504 K HOH 35 1_555 B HOH 546 K HOH 35 1_555 P HOH 11 L HOH 35 1_555 P HOH 12 L HOH 35 1_555 P HOH 13 L HOH 35 1_555 19 orthorhombic P 21 21 21