0.019499 0.000000 0.000000 0.000000 0.016929 0.000000 0.000000 0.000000 0.016178 0.00000 0.00000 0.00000 Schiffer, C.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 51.285 59.071 61.813 C2 H3 O2 -1 59.044 ACETATE ION non-polymer 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 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 C N 2 N O N 3 N O N 4 N C N 5 N H N 6 N H N 7 N H N 8 N N N 9 S C N 10 N C N 11 N O N 12 N C N 13 N O 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 N N 22 S C N 23 N C N 24 N O N 25 N C N 26 N C N 27 N C N 28 N N N 29 N C N 30 N N N 31 N N N 32 N O 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 H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N N N 49 S C N 50 N C N 51 N O N 52 N C N 53 N C N 54 N O N 55 N N N 56 N O N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N N N 66 S C N 67 N C N 68 N O N 69 N C N 70 N C N 71 N O N 72 N O N 73 N O 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 N N 82 R C N 83 N C N 84 N O N 85 N C N 86 N S N 87 N O 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 N N 96 S C N 97 N C N 98 N O N 99 N C N 100 N C N 101 N C N 102 N O N 103 N N N 104 N O 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 N N 116 S C N 117 N C N 118 N O N 119 N C N 120 N C N 121 N C N 122 N O N 123 N O N 124 N O 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 N N 135 N C N 136 N C N 137 N O N 138 N O 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 Y 149 N C Y 150 N N Y 151 N C Y 152 N C Y 153 N N N 154 N O N 155 N H 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 O N 166 N H N 167 N H N 168 N N N 169 S C N 170 N C N 171 N O N 172 S C N 173 N C N 174 N C N 175 N C 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 N N 191 S C N 192 N C N 193 N O N 194 N C N 195 N C N 196 N C N 197 N C 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 H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N N N 213 S C N 214 N C N 215 N O N 216 N C N 217 N C N 218 N C N 219 N C N 220 N N N 221 N O 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 H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N N N 238 S C N 239 N C N 240 N O N 241 N C N 242 N C N 243 N S N 244 N C N 245 N O N 246 N H N 247 N H 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 N N 258 S C N 259 N C N 260 N O N 261 N C Y 262 N C Y 263 N C Y 264 N C Y 265 N C Y 266 N C Y 267 N C 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 H N 280 N N N 281 S C N 282 N C N 283 N O N 284 N C N 285 N C N 286 N C N 287 N O 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 H N 296 N H N 297 N N N 298 S C N 299 N C N 300 N O N 301 N C N 302 N O N 303 N O N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H 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 R C N 316 N O N 317 N C 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 N N 329 S C N 330 N C N 331 N O N 332 N C Y 333 N C Y 334 N C Y 335 N C Y 336 N N Y 337 N C Y 338 N C Y 339 N C Y 340 N C Y 341 N C N 342 N O 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 Y 360 N C Y 361 N C Y 362 N C Y 363 N C Y 364 N C Y 365 N C N 366 N O N 367 N O 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 N N 380 S C N 381 N C N 382 N O N 383 N C N 384 N C N 385 N C N 386 N O 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 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 N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing 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 sing N 25 N doub 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 sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub 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 doub 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 doub N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub 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 N 80 N sing N 81 N sing N 82 N doub 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 sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub 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 sing N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub 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 doub 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 sing N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing Y 146 N sing Y 147 N doub Y 148 N doub N 149 N sing Y 150 N sing N 151 N sing Y 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 sing N 161 N sing N 162 N sing N 163 N sing N 164 N doub 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 sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N doub 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 sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N doub 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 sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub 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 sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N doub N 250 N sing N 251 N sing N 252 N sing N 253 N sing Y 254 N doub Y 255 N sing Y 256 N sing N 257 N sing Y 258 N doub N 259 N sing Y 260 N doub N 261 N sing Y 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 sing N 271 N sing N 272 N doub 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 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 sing N 300 N sing N 301 N sing N 302 N doub 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 sing N 317 N sing N 318 N doub N 319 N sing N 320 N sing N 321 N sing N 322 N sing Y 323 N doub Y 324 N sing Y 325 N sing N 326 N sing Y 327 N doub Y 328 N sing Y 329 N sing N 330 N sing Y 331 N sing Y 332 N doub N 333 N sing Y 334 N doub N 335 N sing Y 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 doub N 347 N sing N 348 N sing N 349 N sing N 350 N sing Y 351 N doub Y 352 N sing Y 353 N sing N 354 N sing Y 355 N doub N 356 N sing Y 357 N doub N 358 N sing Y 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 doub 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 UK Structure STRUE6 2005 0969-2126 10 369 381 10.1016/S0969-2126(02)00720-7 12005435 Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. 2002 10.2210/pdb1kjf/pdb pdb_00001kjf 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.0 1 MIRRORS IMAGE PLATE 1999-07-07 RIGAKU YALE MIRRORS SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 1.5418 ROTATING ANODE RIGAKU 10800.777 POL POLYPROTEIN 3.4.23.16 HIV-1 PROTEASE, RESIDUES 57-155 D25N,Q7K 2 man polymer 1173.325 GAG POLYPROTEIN p1-p6 SUBSTRATE PEPTIDE, RESIDUES 443-452 1 syn polymer 59.044 ACETATE ION 4 syn non-polymer 18.015 water 101 nat water no no PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 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 POL 11676 Human immunodeficiency virus 1 562 Escherichia coli 1 2.05 40.12 VAPOR DIFFUSION, HANGING DROP AMMONIUM SULPHATE, SODIUM PHOSPHATE, SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 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 Database references Derived calculations Data collection Refinement description 1 0 2002-03-06 1 1 2008-04-27 1 2 2011-07-13 1 3 2021-10-27 1 4 2023-08-16 _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 HOW DOES A SYMMETRIC DIMER RECOGNIZE AN ASYMMETRIC SUBSTRATE? A SUBSTRATE COMPLEX OF HIV-1 PROTEASE SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES RCSB Y RCSB 2001-12-04 REL ACT ACETATE ION HOH water 1F7A PDB ENTRY 1F7A PDB experimental model ACT 504 3 ACT ACT 504 A ACT 501 3 ACT ACT 501 B ACT 502 3 ACT ACT 502 B ACT 503 3 ACT ACT 503 B WAT 4 4 HOH HOH 505 A WAT 7 4 HOH HOH 506 A WAT 10 4 HOH HOH 507 A WAT 11 4 HOH HOH 508 A WAT 14 4 HOH HOH 509 A WAT 15 4 HOH HOH 510 A WAT 17 4 HOH HOH 511 A WAT 18 4 HOH HOH 512 A WAT 20 4 HOH HOH 513 A WAT 22 4 HOH HOH 514 A WAT 24 4 HOH HOH 515 A WAT 23 4 HOH HOH 516 A WAT 30 4 HOH HOH 517 A WAT 35 4 HOH HOH 518 A WAT 42 4 HOH HOH 519 A WAT 43 4 HOH HOH 520 A WAT 46 4 HOH HOH 521 A WAT 47 4 HOH HOH 522 A WAT 58 4 HOH HOH 523 A WAT 120 4 HOH HOH 524 A WAT 103 4 HOH HOH 525 A WAT 105 4 HOH HOH 526 A WAT 109 4 HOH HOH 527 A WAT 112 4 HOH HOH 528 A WAT 114 4 HOH HOH 529 A WAT 115 4 HOH HOH 530 A WAT 118 4 HOH HOH 531 A WAT 123 4 HOH HOH 532 A WAT 126 4 HOH HOH 533 A WAT 127 4 HOH HOH 534 A WAT 128 4 HOH HOH 535 A WAT 129 4 HOH HOH 536 A WAT 134 4 HOH HOH 537 A WAT 135 4 HOH HOH 538 A WAT 143 4 HOH HOH 539 A WAT 145 4 HOH HOH 540 A WAT 146 4 HOH HOH 541 A WAT 150 4 HOH HOH 542 A WAT 155 4 HOH HOH 543 A WAT 158 4 HOH HOH 544 A WAT 160 4 HOH HOH 545 A WAT 161 4 HOH HOH 546 A WAT 171 4 HOH HOH 547 A WAT 172 4 HOH HOH 548 A WAT 183 4 HOH HOH 549 A WAT 198 4 HOH HOH 550 A WAT 1 4 HOH HOH 504 B WAT 2 4 HOH HOH 505 B WAT 5 4 HOH HOH 506 B WAT 6 4 HOH HOH 507 B WAT 8 4 HOH HOH 508 B WAT 12 4 HOH HOH 509 B WAT 13 4 HOH HOH 510 B WAT 16 4 HOH HOH 511 B WAT 19 4 HOH HOH 512 B WAT 25 4 HOH HOH 513 B WAT 26 4 HOH HOH 514 B WAT 28 4 HOH HOH 515 B WAT 31 4 HOH HOH 516 B WAT 32 4 HOH HOH 517 B WAT 36 4 HOH HOH 518 B WAT 45 4 HOH HOH 519 B WAT 50 4 HOH HOH 520 B WAT 52 4 HOH HOH 521 B WAT 53 4 HOH HOH 522 B WAT 54 4 HOH HOH 523 B WAT 55 4 HOH HOH 524 B WAT 56 4 HOH HOH 525 B WAT 62 4 HOH HOH 526 B WAT 64 4 HOH HOH 527 B WAT 67 4 HOH HOH 528 B WAT 68 4 HOH HOH 529 B WAT 70 4 HOH HOH 530 B WAT 75 4 HOH HOH 531 B WAT 76 4 HOH HOH 532 B WAT 77 4 HOH HOH 533 B WAT 78 4 HOH HOH 534 B WAT 81 4 HOH HOH 535 B WAT 89 4 HOH HOH 536 B WAT 101 4 HOH HOH 537 B WAT 106 4 HOH HOH 538 B WAT 131 4 HOH HOH 539 B WAT 140 4 HOH HOH 540 B WAT 147 4 HOH HOH 541 B WAT 156 4 HOH HOH 542 B WAT 159 4 HOH HOH 543 B WAT 162 4 HOH HOH 544 B WAT 164 4 HOH HOH 545 B WAT 165 4 HOH HOH 546 B WAT 168 4 HOH HOH 547 B WAT 169 4 HOH HOH 548 B WAT 173 4 HOH HOH 549 B WAT 189 4 HOH HOH 550 B WAT 194 4 HOH HOH 551 B WAT 196 4 HOH HOH 552 B WAT 197 4 HOH HOH 553 B WAT 3 4 HOH HOH 11 P WAT 51 4 HOH HOH 12 P WAT 142 4 HOH HOH 13 P WAT 144 4 HOH HOH 14 P WAT 195 4 HOH HOH 15 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 ALA 41 n 41 LYS 41 A TRP 42 n 42 TRP 42 A ALA 43 n 43 LYS 43 A PRO 44 n 44 PRO 44 A LYS 45 n 45 LYS 45 A MET 46 n 46 MET 46 A ILE 47 n 47 ILE 47 A 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 ALA 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 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 ALA 41 n 41 LYS 41 B TRP 42 n 42 TRP 42 B ALA 43 n 43 LYS 43 B PRO 44 n 44 PRO 44 B LYS 45 n 45 LYS 45 B MET 46 n 46 MET 46 B ILE 47 n 47 ILE 47 B 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 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 ALA 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 6130 -34 9360 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 ASN 98 B O ASN 98 A N THR 96 A N THR 96 A O LEU 97 A O LEU 97 B N ILE 3 B N ILE 3 A N GLY 49 A N GLY 49 A O GLY 52 A O GLY 52 A N GLU 65 A N GLU 65 A O ARG 14 A O ARG 14 A N ILE 15 A N ILE 15 A O GLN 18 A O GLN 18 A O LEU 23 A O LEU 23 A N ILE 85 A N ILE 85 A N ILE 84 A N ILE 84 A O VAL 32 A O VAL 32 A N LEU 33 A N LEU 33 A O LEU 76 A O LEU 76 A O VAL 77 A O VAL 77 A N ARG 57 A N ARG 57 P O SER 8 C O SER 8 B N GLY 48 B N GLY 48 B N GLY 49 B N GLY 49 B O GLY 52 B O GLY 52 B O GLU 65 B O GLU 65 B N ARG 14 B N ARG 14 B O ILE 15 B O ILE 15 B N GLN 18 B N GLN 18 B O LEU 23 B O LEU 23 B N ILE 85 B N ILE 85 B N ILE 84 B N ILE 84 B O VAL 32 B O VAL 32 B N LEU 33 B N LEU 33 B O LEU 76 B O LEU 76 B O VAL 77 B O VAL 77 B N ARG 57 B N ARG 57 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 70 A CG LYS 70 1 Y 1 A CD LYS 70 A CD LYS 70 1 Y 1 A CE LYS 70 A CE LYS 70 1 Y 1 A NZ LYS 70 A NZ LYS 70 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 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 1 -31.35 123.39 1 A GLU 35 2 -30.01 121.79 1 P PHE 5 -97.87 47.11 PROTEIN_REP.PARAM PROTEIN.TOP WATER_REP.PARAM WATER.TOP ION.PARAM ION.TOP ACE.PARAM ACE.TOP 30.3 -2.23 0.00 0.00 -0.87 0.00 3.11 0.2510000 0.007 0.2030000 0.2030000 2.00 32.82 1208 12376 12376 10.3 93.4 RANDOM 189103.10 0.000000 1 RESTRAINED THROUGHOUT 0.0 FOURIER SYNTHESIS PDB ENTRY 1F7A ENGH & HUBER FLAT MODEL 66.3761 0.350292 0.33 0.24 5.00 0.34 0.26 2.00 32.82 101 1740 16 0 1623 0.006 1.3 26.1 0.87 22.7 2.000 32.82 1KJF 12376 12376 0 0 0.0670000 1 9.6000 5.00 93.4 refinement CNS data reduction DENZO data scaling SCALEPACK phasing CNS SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES 1 N N 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 4 N N 4 N N 4 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 HYDROLASE p1-p6, SUBSTRATE RECOGNITION, HYDROLASE POL_HV1A2 UNP 1 1 P03369 FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGGENNSLSEAGADRQGTVSFNFPQITLWQRPLVTIRIGGQLKEALL DTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPI ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQ DFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMT KILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIM LPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHEVYYDPSKDL VAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKVSTESIVIWGKIPKFKLPIQKETWEAWWMEY WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSIADTTNQKTELQAIHLA LQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLNGI DKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKIILVAVHVASGYIE AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVVESMNNELKKIIGQV RDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDNKDPLWKGPAKLLWKG EGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED POL_HV1JR UNP 2 443 P20875 RPGNFLQSRP 57 155 1KJF 1 99 P03369 A 1 1 99 57 155 1KJF 1 99 P03369 B 1 1 99 443 452 1KJF 1 10 P20875 P 2 1 10 1 GLN engineered mutation LYS 7 1KJF A P03369 UNP 63 7 1 ASP engineered mutation ASN 25 1KJF A P03369 UNP 81 25 2 GLN engineered mutation LYS 7 1KJF B P03369 UNP 63 7 2 ASP engineered mutation ASN 25 1KJF B P03369 UNP 81 25 4 8 9 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel A GLN 2 A GLN 2 A THR 4 A THR 4 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 THR 4 B THR 4 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 LEU 10 A LEU 10 A ILE 15 A ILE 15 A GLN 18 A GLN 18 A LEU 24 A LEU 24 A ILE 84 A ILE 84 A ILE 85 A ILE 85 A VAL 32 A VAL 32 A GLU 34 A GLU 34 A HIS 69 A HIS 69 A GLY 78 A GLY 78 A GLY 52 A GLY 52 A ILE 66 A ILE 66 P GLN 7 C GLN 7 P SER 8 C SER 8 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 LEU 10 B LEU 10 B ILE 15 B ILE 15 B GLN 18 B GLN 18 B LEU 24 B LEU 24 B ILE 84 B ILE 84 B ILE 85 B ILE 85 B VAL 32 B VAL 32 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 BINDING SITE FOR RESIDUE ACT B 501 B ACT 501 Software 5 BINDING SITE FOR RESIDUE ACT B 502 B ACT 502 Software 3 BINDING SITE FOR RESIDUE ACT B 503 B ACT 503 Software 6 BINDING SITE FOR RESIDUE ACT A 504 A ACT 504 Software 3 A PRO 1 A PRO 1 5 4_456 B HIS 69 B HIS 69 5 1_555 B LYS 70 B LYS 70 5 1_555 B HOH 552 I HOH 5 1_555 B HOH 553 I HOH 5 1_555 B PRO 1 B PRO 1 3 1_555 B HIS 69 B HIS 69 3 1_555 B HOH 521 I HOH 3 1_555 A ARG 14 A ARG 14 6 1_455 A GLY 17 A GLY 17 6 1_455 A HOH 526 H HOH 6 1_455 B ARG 14 B ARG 14 6 1_555 B GLY 17 B GLY 17 6 1_555 B HOH 529 I HOH 6 1_555 A LYS 7 A LYS 7 3 1_555 A ARG 8 A ARG 8 3 1_555 A HOH 517 H HOH 3 1_555 19 P 21 21 21