0.015646 0.000000 0.000000 0.000000 0.015646 0.000000 0.000000 0.000000 0.009389 0.00000 0.00000 0.00000 Lubkowski, J. Li, M. Gustchina, A. Zhou, D. Dauter, Z. Wlodawer, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 63.915 63.915 106.509 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 K 1 39.098 POTASSIUM ION non-polymer 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 K N 184 N N N 185 S C N 186 N C N 187 N O N 188 N C N 189 N C N 190 N C N 191 N C N 192 N O 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 H N 206 N N N 207 S C N 208 N C N 209 N O N 210 N C N 211 N C N 212 N C N 213 N C N 214 N N N 215 N O N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N 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 N N 232 S C N 233 N C N 234 N O N 235 N C N 236 N C N 237 N S N 238 N C N 239 N O N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N N N 252 S C N 253 N C N 254 N O N 255 N C Y 256 N C Y 257 N C Y 258 N C Y 259 N C Y 260 N C Y 261 N C N 262 N O 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 H N 274 N P N 275 N O N 276 N O N 277 N O N 278 N O 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 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 H N 296 N N N 297 S C N 298 N C N 299 N O 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 H N 309 N H N 310 N N N 311 S C N 312 N C N 313 N O N 314 R C N 315 N O N 316 N C N 317 N O 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 H N 327 N N N 328 S C N 329 N C N 330 N O N 331 N C Y 332 N C Y 333 N C Y 334 N C Y 335 N N Y 336 N C Y 337 N C Y 338 N C Y 339 N C Y 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 N N 355 S C N 356 N C N 357 N O N 358 N C Y 359 N C Y 360 N C Y 361 N C Y 362 N C Y 363 N C Y 364 N C N 365 N O N 366 N O 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 N N 379 S C N 380 N C N 381 N O N 382 N C N 383 N C N 384 N C 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 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 Nat.Struct.Mol.Biol. 1545-9993 18 227 229 10.1038/nsmb.1964 21258323 Crystal structure of XMRV protease differs from the structures of other retropepsins. 2011 10.2210/pdb3nr6/pdb pdb_00003nr6 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 MIRRORS CCD 2010-04-10 MARMOSAIC 300 mm CCD DOUBLE CRYSTAL SI-220 SINGLE WAVELENGTH M x-ray 1 1.0 1.0 22-ID APS 1.0 SYNCHROTRON APS BEAMLINE 22-ID 14345.290 Protease p14 3.4.23.- 2 man polymer 39.098 POTASSIUM ION 1 syn non-polymer 94.971 PHOSPHATE ION 1 syn non-polymer 18.015 water 66 nat water no no MHHHHHHTLGDQGGQGQEPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHL ATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQVL MHHHHHHTLGDQGGQGQEPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHL ATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQVL 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n RETROVIRAL PROTEASE FROM XMRV pCDNA3.1-XMRV-VP63 sample gag-pol 373193 Xenotropic MuLV-related virus VP62 469008 Escherichia coli BL21(DE3)tonA pRARE PLASMID pDEST-521 1 1.90 35.11 VAPOR DIFFUSION, HANGING DROP 8.0 PROTEIN CONCENTRATION: 10 MG/ML PRECIPITANT: 0.06 M KH2PO4, 1.34 M NA2HPO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K 293.0 software chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Refinement description Data collection Database references Derived calculations Refinement description 1 0 2011-02-02 1 1 2011-07-13 1 2 2017-11-08 1 3 2023-12-27 1 4 2024-04-03 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_seq_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id HUMAN IMMUNODEFICIENCY VIRUS 1 (HIV-1) PROTEASE. RELATED RETROVIRAL, ASPARTIC PROTEASE FELINE IMMUNODEFICIENCY VIRUS (FIV) PROTEASE. RELATED RETROVIRAL, ASPARTIC PROTEASE EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) PROTEASE. RELATED RETROVIRAL, ASPARTIC PROTEASE DAMAGE-INDUCIBLE PROTEIN, DDI1. RETROVIRAL PROTEASE-LIKE DOMAIN, RESIDUES 180-325 STRUCTURE OF THE ASPARTIC PROTEASE FROM ROUS SARCOMA RETROVIRUS REFINED AT 2 ANGSTROMS RESOLUTION RCSB Y RCSB 2010-06-30 REL REL K POTASSIUM ION PO4 PHOSPHATE ION HOH water ASSEMBLY OF RETROVIRAL PROTEASES Other in silico model K 1 2 K K 126 A PO4 1 3 PO4 PO4 127 A HOH 4 4 HOH HOH 128 A HOH 6 4 HOH HOH 129 A HOH 7 4 HOH HOH 130 A HOH 8 4 HOH HOH 131 A HOH 9 4 HOH HOH 132 A HOH 12 4 HOH HOH 133 A HOH 15 4 HOH HOH 134 A HOH 16 4 HOH HOH 135 A HOH 18 4 HOH HOH 136 A HOH 19 4 HOH HOH 137 A HOH 21 4 HOH HOH 138 A HOH 22 4 HOH HOH 139 A HOH 23 4 HOH HOH 140 A HOH 24 4 HOH HOH 141 A HOH 25 4 HOH HOH 142 A HOH 26 4 HOH HOH 143 A HOH 27 4 HOH HOH 144 A HOH 28 4 HOH HOH 145 A HOH 30 4 HOH HOH 146 A HOH 31 4 HOH HOH 147 A HOH 32 4 HOH HOH 148 A HOH 33 4 HOH HOH 149 A HOH 35 4 HOH HOH 150 A HOH 36 4 HOH HOH 151 A HOH 37 4 HOH HOH 152 A HOH 46 4 HOH HOH 153 A HOH 48 4 HOH HOH 154 A HOH 49 4 HOH HOH 155 A HOH 50 4 HOH HOH 156 A HOH 59 4 HOH HOH 157 A HOH 62 4 HOH HOH 158 A HOH 63 4 HOH HOH 159 A HOH 64 4 HOH HOH 160 A HOH 65 4 HOH HOH 161 A HOH 66 4 HOH HOH 162 A HOH 1 4 HOH HOH 126 B HOH 2 4 HOH HOH 127 B HOH 3 4 HOH HOH 128 B HOH 5 4 HOH HOH 129 B HOH 10 4 HOH HOH 130 B HOH 11 4 HOH HOH 131 B HOH 13 4 HOH HOH 132 B HOH 14 4 HOH HOH 133 B HOH 17 4 HOH HOH 134 B HOH 20 4 HOH HOH 135 B HOH 29 4 HOH HOH 136 B HOH 34 4 HOH HOH 137 B HOH 38 4 HOH HOH 138 B HOH 39 4 HOH HOH 139 B HOH 40 4 HOH HOH 140 B HOH 41 4 HOH HOH 141 B HOH 42 4 HOH HOH 142 B HOH 43 4 HOH HOH 143 B HOH 44 4 HOH HOH 144 B HOH 45 4 HOH HOH 145 B HOH 47 4 HOH HOH 146 B HOH 51 4 HOH HOH 147 B HOH 52 4 HOH HOH 148 B HOH 53 4 HOH HOH 149 B HOH 54 4 HOH HOH 150 B HOH 55 4 HOH HOH 151 B HOH 56 4 HOH HOH 152 B HOH 57 4 HOH HOH 153 B HOH 58 4 HOH HOH 154 B HOH 60 4 HOH HOH 155 B HOH 61 4 HOH HOH 156 B n 1 -6 A n 2 -5 A n 3 -4 A n 4 -3 A n 5 -2 A n 6 -1 A n 7 0 A THR 1 n 8 THR 1 A LEU 2 n 9 LEU 2 A GLY 3 n 10 GLY 3 A ASP 4 n 11 ASP 4 A GLN 5 n 12 GLN 5 A GLY 6 n 13 GLY 6 A GLY 7 n 14 GLY 7 A GLN 8 n 15 GLN 8 A GLY 9 n 16 GLY 9 A GLN 10 n 17 GLN 10 A GLU 11 n 18 GLU 11 A PRO 12 n 19 PRO 12 A PRO 13 n 20 PRO 13 A PRO 14 n 21 PRO 14 A GLU 15 n 22 GLU 15 A PRO 16 n 23 PRO 16 A ARG 17 n 24 ARG 17 A ILE 18 n 25 ILE 18 A THR 19 n 26 THR 19 A LEU 20 n 27 LEU 20 A LYS 21 n 28 LYS 21 A VAL 22 n 29 VAL 22 A GLY 23 n 30 GLY 23 A GLY 24 n 31 GLY 24 A GLN 25 n 32 GLN 25 A PRO 26 n 33 PRO 26 A VAL 27 n 34 VAL 27 A THR 28 n 35 THR 28 A PHE 29 n 36 PHE 29 A LEU 30 n 37 LEU 30 A VAL 31 n 38 VAL 31 A ASP 32 n 39 ASP 32 A THR 33 n 40 THR 33 A GLY 34 n 41 GLY 34 A ALA 35 n 42 ALA 35 A GLN 36 n 43 GLN 36 A HIS 37 n 44 HIS 37 A SER 38 n 45 SER 38 A VAL 39 n 46 VAL 39 A LEU 40 n 47 LEU 40 A THR 41 n 48 THR 41 A GLN 42 n 49 GLN 42 A ASN 43 n 50 ASN 43 A PRO 44 n 51 PRO 44 A GLY 45 n 52 GLY 45 A PRO 46 n 53 PRO 46 A LEU 47 n 54 LEU 47 A SER 48 n 55 SER 48 A ASP 49 n 56 ASP 49 A LYS 50 n 57 LYS 50 A SER 51 n 58 SER 51 A ALA 52 n 59 ALA 52 A TRP 53 n 60 TRP 53 A VAL 54 n 61 VAL 54 A GLN 55 n 62 GLN 55 A n 63 56 A n 64 57 A n 65 58 A n 66 59 A GLY 60 n 67 GLY 60 A LYS 61 n 68 LYS 61 A ARG 62 n 69 ARG 62 A TYR 63 n 70 TYR 63 A ARG 64 n 71 ARG 64 A TRP 65 n 72 TRP 65 A THR 66 n 73 THR 66 A THR 67 n 74 THR 67 A ASP 68 n 75 ASP 68 A ARG 69 n 76 ARG 69 A LYS 70 n 77 LYS 70 A VAL 71 n 78 VAL 71 A HIS 72 n 79 HIS 72 A LEU 73 n 80 LEU 73 A ALA 74 n 81 ALA 74 A THR 75 n 82 THR 75 A GLY 76 n 83 GLY 76 A LYS 77 n 84 LYS 77 A VAL 78 n 85 VAL 78 A THR 79 n 86 THR 79 A HIS 80 n 87 HIS 80 A SER 81 n 88 SER 81 A PHE 82 n 89 PHE 82 A LEU 83 n 90 LEU 83 A HIS 84 n 91 HIS 84 A VAL 85 n 92 VAL 85 A PRO 86 n 93 PRO 86 A ASP 87 n 94 ASP 87 A CYS 88 n 95 CYS 88 A PRO 89 n 96 PRO 89 A TYR 90 n 97 TYR 90 A PRO 91 n 98 PRO 91 A LEU 92 n 99 LEU 92 A LEU 93 n 100 LEU 93 A GLY 94 n 101 GLY 94 A ARG 95 n 102 ARG 95 A ASP 96 n 103 ASP 96 A LEU 97 n 104 LEU 97 A LEU 98 n 105 LEU 98 A THR 99 n 106 THR 99 A LYS 100 n 107 LYS 100 A LEU 101 n 108 LEU 101 A LYS 102 n 109 LYS 102 A ALA 103 n 110 ALA 103 A GLN 104 n 111 GLN 104 A ILE 105 n 112 ILE 105 A HIS 106 n 113 HIS 106 A PHE 107 n 114 PHE 107 A GLU 108 n 115 GLU 108 A GLY 109 n 116 GLY 109 A SER 110 n 117 SER 110 A GLY 111 n 118 GLY 111 A ALA 112 n 119 ALA 112 A GLN 113 n 120 GLN 113 A VAL 114 n 121 VAL 114 A VAL 115 n 122 VAL 115 A GLY 116 n 123 GLY 116 A PRO 117 n 124 PRO 117 A MET 118 n 125 MET 118 A GLY 119 n 126 GLY 119 A GLN 120 n 127 GLN 120 A PRO 121 n 128 PRO 121 A LEU 122 n 129 LEU 122 A GLN 123 n 130 GLN 123 A VAL 124 n 131 VAL 124 A n 132 125 A n 1 -6 B n 2 -5 B n 3 -4 B n 4 -3 B n 5 -2 B n 6 -1 B n 7 0 B THR 1 n 8 THR 1 B LEU 2 n 9 LEU 2 B GLY 3 n 10 GLY 3 B ASP 4 n 11 ASP 4 B GLN 5 n 12 GLN 5 B n 13 6 B n 14 7 B n 15 8 B n 16 9 B n 17 10 B n 18 11 B PRO 12 n 19 PRO 12 B PRO 13 n 20 PRO 13 B PRO 14 n 21 PRO 14 B GLU 15 n 22 GLU 15 B PRO 16 n 23 PRO 16 B ARG 17 n 24 ARG 17 B ILE 18 n 25 ILE 18 B THR 19 n 26 THR 19 B LEU 20 n 27 LEU 20 B LYS 21 n 28 LYS 21 B VAL 22 n 29 VAL 22 B GLY 23 n 30 GLY 23 B GLY 24 n 31 GLY 24 B GLN 25 n 32 GLN 25 B PRO 26 n 33 PRO 26 B VAL 27 n 34 VAL 27 B THR 28 n 35 THR 28 B PHE 29 n 36 PHE 29 B LEU 30 n 37 LEU 30 B VAL 31 n 38 VAL 31 B ASP 32 n 39 ASP 32 B THR 33 n 40 THR 33 B GLY 34 n 41 GLY 34 B ALA 35 n 42 ALA 35 B GLN 36 n 43 GLN 36 B HIS 37 n 44 HIS 37 B SER 38 n 45 SER 38 B VAL 39 n 46 VAL 39 B LEU 40 n 47 LEU 40 B THR 41 n 48 THR 41 B GLN 42 n 49 GLN 42 B ASN 43 n 50 ASN 43 B PRO 44 n 51 PRO 44 B GLY 45 n 52 GLY 45 B PRO 46 n 53 PRO 46 B LEU 47 n 54 LEU 47 B SER 48 n 55 SER 48 B ASP 49 n 56 ASP 49 B LYS 50 n 57 LYS 50 B SER 51 n 58 SER 51 B ALA 52 n 59 ALA 52 B TRP 53 n 60 TRP 53 B VAL 54 n 61 VAL 54 B n 62 55 B n 63 56 B n 64 57 B n 65 58 B n 66 59 B GLY 60 n 67 GLY 60 B LYS 61 n 68 LYS 61 B ARG 62 n 69 ARG 62 B TYR 63 n 70 TYR 63 B ARG 64 n 71 ARG 64 B TRP 65 n 72 TRP 65 B THR 66 n 73 THR 66 B THR 67 n 74 THR 67 B ASP 68 n 75 ASP 68 B ARG 69 n 76 ARG 69 B LYS 70 n 77 LYS 70 B VAL 71 n 78 VAL 71 B HIS 72 n 79 HIS 72 B LEU 73 n 80 LEU 73 B ALA 74 n 81 ALA 74 B THR 75 n 82 THR 75 B GLY 76 n 83 GLY 76 B LYS 77 n 84 LYS 77 B VAL 78 n 85 VAL 78 B THR 79 n 86 THR 79 B HIS 80 n 87 HIS 80 B SER 81 n 88 SER 81 B PHE 82 n 89 PHE 82 B LEU 83 n 90 LEU 83 B HIS 84 n 91 HIS 84 B VAL 85 n 92 VAL 85 B PRO 86 n 93 PRO 86 B ASP 87 n 94 ASP 87 B CYS 88 n 95 CYS 88 B PRO 89 n 96 PRO 89 B TYR 90 n 97 TYR 90 B PRO 91 n 98 PRO 91 B LEU 92 n 99 LEU 92 B LEU 93 n 100 LEU 93 B GLY 94 n 101 GLY 94 B ARG 95 n 102 ARG 95 B ASP 96 n 103 ASP 96 B LEU 97 n 104 LEU 97 B LEU 98 n 105 LEU 98 B THR 99 n 106 THR 99 B LYS 100 n 107 LYS 100 B LEU 101 n 108 LEU 101 B LYS 102 n 109 LYS 102 B ALA 103 n 110 ALA 103 B GLN 104 n 111 GLN 104 B ILE 105 n 112 ILE 105 B HIS 106 n 113 HIS 106 B PHE 107 n 114 PHE 107 B GLU 108 n 115 GLU 108 B GLY 109 n 116 GLY 109 B SER 110 n 117 SER 110 B GLY 111 n 118 GLY 111 B ALA 112 n 119 ALA 112 B GLN 113 n 120 GLN 113 B VAL 114 n 121 VAL 114 B VAL 115 n 122 VAL 115 B GLY 116 n 123 GLY 116 B PRO 117 n 124 PRO 117 B MET 118 n 125 MET 118 B GLY 119 n 126 GLY 119 B GLN 120 n 127 GLN 120 B PRO 121 n 128 PRO 121 B LEU 122 n 129 LEU 122 B GLN 123 n 130 GLN 123 B VAL 124 n 131 VAL 124 B LEU 125 n 132 LEU 125 B 3.2387 0.4637 -1.4235 4.0084 -0.9411 4.5200 -0.0732 0.0230 -0.1454 -0.0354 0.0143 0.1128 0.1332 -0.1435 0.0589 0.0545 0.0191 -0.0131 0.0701 -0.0094 0.0406 refined 11.1122 21.3554 14.6024 X-RAY DIFFRACTION 6.7048 -1.3269 2.1263 2.9177 0.4850 5.5570 -0.1293 -0.3786 -0.1642 0.2565 0.0793 0.1573 0.0569 -0.2462 0.0499 0.1154 0.0489 0.0362 0.0901 0.0470 0.0480 refined 9.3748 22.8382 38.6955 X-RAY DIFFRACTION A 1 A 124 X-RAY DIFFRACTION 1 B 1 B 125 X-RAY DIFFRACTION 2 author_and_software_defined_assembly PISA 2 dimeric software_defined_assembly PISA 8 octameric 1960 -13 11290 15020 -57 37980 A GLN 5 A O GLN 12 1_555 A K 126 C K K 1_555 A GLN 8 A OE1 GLN 15 1_555 89.3 A GLN 5 A O GLN 12 1_555 A K 126 C K K 1_555 A PRO 26 A O PRO 33 1_555 105.4 A GLN 8 A OE1 GLN 15 1_555 A K 126 C K K 1_555 A PRO 26 A O PRO 33 1_555 105.1 A GLN 5 A O GLN 12 1_555 A K 126 C K K 1_555 A HOH 139 E O HOH 1_555 72.0 A GLN 8 A OE1 GLN 15 1_555 A K 126 C K K 1_555 A HOH 139 E O HOH 1_555 95.5 A PRO 26 A O PRO 33 1_555 A K 126 C K K 1_555 A HOH 139 E O HOH 1_555 159.2 A GLN 5 A O GLN 12 1_555 A K 126 C K K 1_555 A HOH 153 E O HOH 1_555 159.9 A GLN 8 A OE1 GLN 15 1_555 A K 126 C K K 1_555 A HOH 153 E O HOH 1_555 80.5 A PRO 26 A O PRO 33 1_555 A K 126 C K K 1_555 A HOH 153 E O HOH 1_555 94.0 A HOH 139 E O HOH 1_555 A K 126 C K K 1_555 A HOH 153 E O HOH 1_555 91.7 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_665 -x+1,-y+1,z crystal symmetry operation 63.9150000000 63.9150000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_655 -y+1,x,z crystal symmetry operation 63.9150000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_565 y,-x+1,z crystal symmetry operation 0.0000000000 63.9150000000 0.0000000000 A O VAL 78 A O VAL 85 A N VAL 71 A N VAL 78 A O HIS 72 A O HIS 79 A N LYS 21 A N LYS 28 A N LEU 20 A N LEU 27 A O VAL 27 A O VAL 34 A N LEU 30 A N LEU 37 A O LEU 93 A O LEU 100 A N LEU 40 A N LEU 47 A O LEU 83 A O LEU 90 A N VAL 54 A N VAL 61 A O LYS 61 A O LYS 68 A O GLN 113 A O GLN 120 A N HIS 106 A N HIS 113 A N ILE 105 A N ILE 112 B O ILE 105 B O ILE 112 B N HIS 106 B N HIS 113 B O GLN 113 B O GLN 120 B O VAL 78 B O VAL 85 B N VAL 71 B N VAL 78 B O HIS 72 B O HIS 79 B N LYS 21 B N LYS 28 B N LEU 20 B N LEU 27 B O VAL 27 B O VAL 34 B N LEU 30 B N LEU 37 B O LEU 93 B O LEU 100 B N LEU 40 B N LEU 47 B O LEU 83 B O LEU 90 B N SER 48 B N SER 55 B O TRP 65 B O TRP 72 1 A MET -6 A MET 1 1 Y 1 A HIS -5 A HIS 2 1 Y 1 A HIS -4 A HIS 3 1 Y 1 A HIS -3 A HIS 4 1 Y 1 A HIS -2 A HIS 5 1 Y 1 A HIS -1 A HIS 6 1 Y 1 A HIS 0 A HIS 7 1 Y 1 A GLY 56 A GLY 63 1 Y 1 A ALA 57 A ALA 64 1 Y 1 A THR 58 A THR 65 1 Y 1 A GLY 59 A GLY 66 1 Y 1 A LEU 125 A LEU 132 1 Y 1 B MET -6 B MET 1 1 Y 1 B HIS -5 B HIS 2 1 Y 1 B HIS -4 B HIS 3 1 Y 1 B HIS -3 B HIS 4 1 Y 1 B HIS -2 B HIS 5 1 Y 1 B HIS -1 B HIS 6 1 Y 1 B HIS 0 B HIS 7 1 Y 1 B GLY 6 B GLY 13 1 Y 1 B GLY 7 B GLY 14 1 Y 1 B GLN 8 B GLN 15 1 Y 1 B GLY 9 B GLY 16 1 Y 1 B GLN 10 B GLN 17 1 Y 1 B GLU 11 B GLU 18 1 Y 1 B GLN 55 B GLN 62 1 Y 1 B GLY 56 B GLY 63 1 Y 1 B ALA 57 B ALA 64 1 Y 1 B THR 58 B THR 65 1 Y 1 B GLY 59 B GLY 66 1 Y 1 B B O O HOH HOH 136 143 2.11 1 A A O O HOH HOH 159 162 2.16 1 B B O O LEU HOH 125 139 2.19 1 A A O O HOH HOH 137 137 2.19 1_555 2_565 1 A ASP 87 -76.89 32.07 1 B ASN 43 29.93 70.26 1 B ASP 87 -83.29 33.40 1 B GLU 108 -101.59 -169.98 47.871 0.48 0.00 0.00 0.48 0.00 -0.97 0.958 0.950 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.23322 0.19568 0.19737 0.19737 1.97 20.00 815 15336 5.0 98.46 8.324 0.108 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.164 0.80 0.80 1.20 ASSEMBLY OF RETROVIRAL PROTEASES MAXIMUM LIKELIHOOD MASK 1.97 20.00 66 1863 6 0 1791 0.020 0.022 1863 1.837 1.975 2538 7.603 5.000 231 35.578 24.211 76 17.844 15.000 302 15.200 15.000 10 0.145 0.200 283 0.010 0.022 1408 2.739 2.000 1168 4.062 3.000 1898 3.676 2.000 695 5.066 3.000 639 0.285 0.224 2.016 60 920 980 20 83.76 37.8 1.97 50.0 3NR6 16141 16141 -1.74 -3 0.044 0.044 1 32.1 4.3 98.5 0.257 1.97 2.00 3.23 667 0.257 2.9 82.1 data collection MAR345 phasing PHASER model building Rosetta refinement REFMAC 5.5.0104 data reduction HKL-3000 data scaling HKL-3000 phasing Rosetta Crystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N A GLY 7 A GLY 14 HELX_P A GLU 11 A GLU 18 5 1 5 A GLY 94 A GLY 101 HELX_P A LYS 102 A LYS 109 1 2 9 B GLY 94 B GLY 101 HELX_P B LYS 102 B LYS 109 1 3 9 metalc 2.804 A GLN 5 A O GLN 12 1_555 A K 126 C K K 1_555 metalc 2.804 A GLN 8 A OE1 GLN 15 1_555 A K 126 C K K 1_555 metalc 2.952 A PRO 26 A O PRO 33 1_555 A K 126 C K K 1_555 metalc 2.929 A K 126 C K K 1_555 A HOH 139 E O HOH 1_555 metalc 2.575 A K 126 C K K 1_555 A HOH 153 E O HOH 1_555 HYDROLASE/INHIBITOR DIMER, PROTEASE, HYDROLASE-INHIBITOR complex A GLU 15 A GLU 22 1 A PRO 16 A PRO 23 -0.30 B GLU 15 B GLU 22 1 B PRO 16 B PRO 23 -3.22 B GLU 15 B GLU 22 1 B PRO 16 B PRO 23 -2.07 POL_XMRV6 UNP 1 533 A1Z651 TLGDQGGQGQEPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTH SFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQVL 533 657 3NR6 1 125 A1Z651 A 1 8 132 533 657 3NR6 1 125 A1Z651 B 1 8 132 1 expression tag MET -6 3NR6 A A1Z651 UNP 1 1 expression tag HIS -5 3NR6 A A1Z651 UNP 2 1 expression tag HIS -4 3NR6 A A1Z651 UNP 3 1 expression tag HIS -3 3NR6 A A1Z651 UNP 4 1 expression tag HIS -2 3NR6 A A1Z651 UNP 5 1 expression tag HIS -1 3NR6 A A1Z651 UNP 6 1 expression tag HIS 0 3NR6 A A1Z651 UNP 7 2 expression tag MET -6 3NR6 B A1Z651 UNP 1 2 expression tag HIS -5 3NR6 B A1Z651 UNP 2 2 expression tag HIS -4 3NR6 B A1Z651 UNP 3 2 expression tag HIS -3 3NR6 B A1Z651 UNP 4 2 expression tag HIS -2 3NR6 B A1Z651 UNP 5 2 expression tag HIS -1 3NR6 B A1Z651 UNP 6 2 expression tag HIS 0 3NR6 B A1Z651 UNP 7 5 2 2 4 5 2 2 anti-parallel anti-parallel anti-parallel parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel parallel anti-parallel A GLY 76 A GLY 83 A HIS 80 A HIS 87 A ARG 69 A ARG 76 A LEU 73 A LEU 80 A ARG 17 A ARG 24 A VAL 22 A VAL 29 A GLN 25 A GLN 32 A VAL 31 A VAL 38 A LEU 92 A LEU 99 A LEU 93 A LEU 100 A VAL 39 A VAL 46 A LEU 40 A LEU 47 A LEU 83 A LEU 90 A HIS 84 A HIS 91 A LEU 47 A LEU 54 A VAL 54 A VAL 61 A LYS 61 A LYS 68 A THR 66 A THR 73 A ALA 112 A ALA 119 A VAL 115 A VAL 122 A GLN 104 A GLN 111 A PHE 107 A PHE 114 B GLN 104 B GLN 111 B GLU 108 B GLU 115 B GLY 111 B GLY 118 B VAL 115 B VAL 122 B GLY 76 B GLY 83 B HIS 80 B HIS 87 B ARG 69 B ARG 76 B LEU 73 B LEU 80 B ARG 17 B ARG 24 B VAL 22 B VAL 29 B GLN 25 B GLN 32 B VAL 31 B VAL 38 B LEU 92 B LEU 99 B LEU 93 B LEU 100 B VAL 39 B VAL 46 B LEU 40 B LEU 47 B LEU 83 B LEU 90 B HIS 84 B HIS 91 B LEU 47 B LEU 54 B TRP 53 B TRP 60 B ARG 62 B ARG 69 B THR 66 B THR 73 BINDING SITE FOR RESIDUE K A 126 A K 126 Software 5 BINDING SITE FOR RESIDUE PO4 A 127 A PO4 127 Software 3 A GLN 5 A GLN 12 5 1_555 A GLN 8 A GLN 15 5 1_555 A PRO 26 A PRO 33 5 1_555 A HOH 139 E HOH 5 1_555 A HOH 153 E HOH 5 1_555 A GLY 6 A GLY 13 3 1_555 A GLY 7 A GLY 14 3 1_555 A LYS 50 A LYS 57 3 3_655 89 P 4 2 2