0.023317 0.000000 0.000000 0.000000 0.010337 0.000000 0.000000 0.000000 0.020047 0.00000 0.00000 0.00000 Janowski, R. Kozak, M. Jankowska, E. Grzonka, Z. Jaskolski, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 42.89 96.74 49.88 C H2 N2 42.040 diazomethane DIAZOMETHYL GROUP 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 C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C8 H7 Cl O2 170.593 benzyl chlorocarbonate 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 C N 2 N N N 3 N N N 4 N H N 5 N H N 6 N N N 7 S C N 8 N C N 9 N O N 10 N C N 11 N O N 12 N H N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N N N 20 S C N 21 N C N 22 N O N 23 N C N 24 N C N 25 N C N 26 N N N 27 N C N 28 N N N 29 N N N 30 N O 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 H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N N N 47 S C N 48 N C N 49 N O N 50 N C N 51 N C N 52 N O N 53 N N N 54 N O N 55 N H N 56 N H 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 N N 64 S C N 65 N C N 66 N O N 67 N C N 68 N C N 69 N O N 70 N O N 71 N O 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 N N 80 R C N 81 N C N 82 N O N 83 N C N 84 N S N 85 N O 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 N N 94 S C N 95 N C N 96 N O N 97 N C N 98 N C N 99 N C N 100 N O N 101 N N N 102 N O 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 N N 114 S C N 115 N C N 116 N O N 117 N C N 118 N C N 119 N C N 120 N O N 121 N O N 122 N O N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N N N 133 N C N 134 N C N 135 N O 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 N N 143 S C N 144 N C N 145 N O N 146 N C Y 147 N C Y 148 N N Y 149 N C Y 150 N C Y 151 N N N 152 N O N 153 N H N 154 N H 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 O N 164 N H N 165 N H N 166 N N N 167 S C N 168 N C N 169 N O N 170 S C N 171 N C N 172 N C N 173 N C N 174 N O 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 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 C N 195 N C 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 H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N N N 211 S C N 212 N C N 213 N O N 214 N C N 215 N C N 216 N C N 217 N C N 218 N N N 219 N O 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 H N 232 N H N 233 N H N 234 N H N 235 N N N 236 S C N 237 N C N 238 N O N 239 N C Y 240 N C Y 241 N C Y 242 N C Y 243 N C Y 244 N C Y 245 N C N 246 N O 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 H N 258 N C N 259 N O 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 CL 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 N N 277 S C N 278 N C N 279 N O N 280 N C N 281 N C N 282 N C N 283 N O N 284 N H N 285 N H 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 N N 294 S C N 295 N C N 296 N O N 297 N C N 298 N O N 299 N O 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 N N 308 S C N 309 N C N 310 N O N 311 R C N 312 N O N 313 N C N 314 N O N 315 N H N 316 N H 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 N N 325 S C N 326 N C N 327 N O N 328 N C Y 329 N C Y 330 N C Y 331 N C Y 332 N N Y 333 N C Y 334 N C Y 335 N C Y 336 N C Y 337 N C N 338 N O N 339 N H N 340 N H 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 N N 352 S C N 353 N C N 354 N O N 355 N C Y 356 N C Y 357 N C Y 358 N C Y 359 N C Y 360 N C Y 361 N C N 362 N O N 363 N O N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N N N 376 S C N 377 N C N 378 N O N 379 N C N 380 N C N 381 N C N 382 N O N 383 N H N 384 N H 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 1 N doub N 2 N doub 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 doub 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 sing N 20 N sing N 21 N sing N 22 N sing N 23 N doub N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing 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 doub 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 doub N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N doub 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 sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N doub 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 N 80 N doub 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 sing N 90 N sing N 91 N sing N 92 N sing N 93 N doub N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub 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 doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N doub N 131 N sing 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 doub N 140 N sing N 141 N sing N 142 N sing N 143 N sing Y 144 N sing Y 145 N doub Y 146 N doub N 147 N sing Y 148 N sing N 149 N sing Y 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 sing N 159 N sing N 160 N sing N 161 N sing N 162 N doub N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N 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 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 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 doub 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 sing N 225 N sing N 226 N sing N 227 N sing N 228 N doub N 229 N sing N 230 N sing N 231 N sing N 232 N sing Y 233 N doub Y 234 N sing Y 235 N sing N 236 N sing Y 237 N doub N 238 N sing Y 239 N doub N 240 N sing Y 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing Y 252 N doub Y 253 N sing Y 254 N sing N 255 N sing Y 256 N doub N 257 N sing Y 258 N sing N 259 N sing Y 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 doub 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 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 doub N 287 N sing 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 doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N 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 doub N 316 N sing N 317 N sing N 318 N sing N 319 N sing Y 320 N doub Y 321 N sing Y 322 N sing N 323 N sing Y 324 N doub Y 325 N sing Y 326 N sing N 327 N sing Y 328 N sing Y 329 N doub N 330 N sing Y 331 N doub N 332 N sing Y 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 doub N 344 N sing N 345 N sing N 346 N sing N 347 N sing Y 348 N doub Y 349 N sing Y 350 N sing N 351 N sing Y 352 N doub N 353 N sing Y 354 N doub N 355 N sing Y 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 doub 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 sing N 376 N sing N 377 N sing N 378 N sing DK J.Pept.Res. JPERFA 2150 1397-002X 64 141 150 10.1111/j.1399-3011.2004.00181.x 15357669 Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor 2004 PL ACTA BIOCHIM.POL. ABPLAF 1139 0001-527X 44 601 605 Crystallization and preliminary crystallographic studies of a new crystal form of papain from Carica papaya. 1997 PL ACTA BIOCHIM.POL. ABPLAF 1139 0001-527X 48 1 20 Structural studies of cysteine proteases and their inhibitors 2001 US Biochemistry BICHAW 0033 0006-2960 15 3731 3738 Binding of chloromethyl ketone substrate analogues to crystalline papain. 1976 DK ACTA CRYSTALLOGR.,SECT.B ASBSDK 0622 0108-7681 48 59 66 10.1107/S0108768191006572 Structure of monoclinic papain at 1.60 Angstroms resolution 1992 NE BIOCHIM.BIOPHYS.ACTA BBACAQ 0113 0006-3002 1431 290 305 10.1016/S0167-4838(99)00053-9 Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity? 1999 10.2210/pdb1khq/pdb pdb_00001khq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 289 1 IMAGE PLATE 1999-04-22 MARRESEARCH GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE MACSCIENCE 23452.301 Papain 3.4.22.2 Papain, Residues 134-345 1 nat polymer 512.001 peptidic inhibitor 1 syn polymer 18.015 water 105 nat water Papaya proteinase I, PPI no no IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN A polypeptide(L) no yes (PHQ)LFG(0HQ) XLFGX I 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n papaya Carica sample 3649 Carica papaya 1 2.12 42 VAPOR DIFFUSION, HANGING DROP 9.2 72% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K 292 chem_comp_atom chem_comp_bond database_2 pdbx_database_remark pdbx_initial_refinement_model struct_conn repository Initial release Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance Other Advisory Data collection Database references Derived calculations Refinement description 1 0 2003-09-09 1 1 2008-04-27 1 2 2011-07-13 1 3 2013-02-27 1 4 2023-08-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_remark.text _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id PAPAIN-ACETYL-ALANYL-ALANYL-PHENYLALANYL-METHYLENYLALANYL DERIVATIVE (/ACAAPACK) PAPAIN-BENZYLOXYCARBONYL-GLYCYL-PHENYLALANYL-METHYLENYLGLYCYL DERIVATIVE (/ZGPGCK) PAPAIN-BENZYLOXYCARBONYL-PHENYLALANYL-METHYLENYLALANYL DERIVATIVE (/ZPACK) PAPAIN CYS 25 OXIDIZED PAPAIN CYS 25 WITH BOUND ATOM PAPAIN-CYSTEINYL DERIVATIVE OF CYS 25 (/PAPSSCYS) PAPAIN COMPLEX WITH E-64-C PAPAIN COMPLEX WITH SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE PAPAIN COMPLEX WITH E64-C (FORM II) 2-HYDROXYETHYLTHIOPAPAIN - CRYSTAL FORM D PAPAIN COMPLEX WITH LEUPEPTIN (N-ACETYL-L-LEUCYL-L-LEUCYL-L-ARGININAL) PAPAIN (CYS 25 CARBOXYMETHYLATED) COMPLEXED WITH THE INHIBITOR STEFIN B (CYSTATIN B) MUTANT WITH CYS I 8 REPLACED BY SER (C(I 8)S) PAPAIN WITH CLIK148 (CATHEPSIN L SPECIFIC INHIBITOR) MONOCLINIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX HETEROGEN THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP OF THE HETGROUP GLM (-N-CH2-CO-CH2-). THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL- (Z- OR CBZ-) GROUP (NOT VISIBLE IN ELECTRON DENSITY). RCSB Y RCSB 2001-11-30 REL REL HOH water THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP. THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL-GROUP PHQ WHICH IS NOT VISIBLE IN ELECTRON DENSITY 1PPN PDB ENTRY 1PPN PDB experimental model Inhibitor L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide Peptide-like HOH 301 3 HOH HOH 301 A HOH 302 3 HOH HOH 302 A HOH 303 3 HOH HOH 303 A HOH 304 3 HOH HOH 304 A HOH 305 3 HOH HOH 305 A HOH 306 3 HOH HOH 306 A HOH 307 3 HOH HOH 307 A HOH 308 3 HOH HOH 308 A HOH 309 3 HOH HOH 309 A HOH 310 3 HOH HOH 310 A HOH 311 3 HOH HOH 311 A HOH 312 3 HOH HOH 312 A HOH 313 3 HOH HOH 313 A HOH 314 3 HOH HOH 314 A HOH 315 3 HOH HOH 315 A HOH 316 3 HOH HOH 316 A HOH 317 3 HOH HOH 317 A HOH 318 3 HOH HOH 318 A HOH 319 3 HOH HOH 319 A HOH 320 3 HOH HOH 320 A HOH 321 3 HOH HOH 321 A HOH 322 3 HOH HOH 322 A HOH 323 3 HOH HOH 323 A HOH 324 3 HOH HOH 324 A HOH 325 3 HOH HOH 325 A HOH 326 3 HOH HOH 326 A HOH 327 3 HOH HOH 327 A HOH 328 3 HOH HOH 328 A HOH 329 3 HOH HOH 329 A HOH 330 3 HOH HOH 330 A HOH 331 3 HOH HOH 331 A HOH 332 3 HOH HOH 332 A HOH 333 3 HOH HOH 333 A HOH 334 3 HOH HOH 334 A HOH 335 3 HOH HOH 335 A HOH 336 3 HOH HOH 336 A HOH 337 3 HOH HOH 337 A HOH 338 3 HOH HOH 338 A HOH 339 3 HOH HOH 339 A HOH 340 3 HOH HOH 340 A HOH 341 3 HOH HOH 341 A HOH 342 3 HOH HOH 342 A HOH 343 3 HOH HOH 343 A HOH 344 3 HOH HOH 344 A HOH 345 3 HOH HOH 345 A HOH 346 3 HOH HOH 346 A HOH 347 3 HOH HOH 347 A HOH 348 3 HOH HOH 348 A HOH 349 3 HOH HOH 349 A HOH 350 3 HOH HOH 350 A HOH 351 3 HOH HOH 351 A HOH 352 3 HOH HOH 352 A HOH 353 3 HOH HOH 353 A HOH 354 3 HOH HOH 354 A HOH 355 3 HOH HOH 355 A HOH 356 3 HOH HOH 356 A HOH 357 3 HOH HOH 357 A HOH 358 3 HOH HOH 358 A HOH 359 3 HOH HOH 359 A HOH 360 3 HOH HOH 360 A HOH 361 3 HOH HOH 361 A HOH 362 3 HOH HOH 362 A HOH 363 3 HOH HOH 363 A HOH 364 3 HOH HOH 364 A HOH 365 3 HOH HOH 365 A HOH 366 3 HOH HOH 366 A HOH 367 3 HOH HOH 367 A HOH 368 3 HOH HOH 368 A HOH 369 3 HOH HOH 369 A HOH 370 3 HOH HOH 370 A HOH 371 3 HOH HOH 371 A HOH 372 3 HOH HOH 372 A HOH 373 3 HOH HOH 373 A HOH 374 3 HOH HOH 374 A HOH 375 3 HOH HOH 375 A HOH 376 3 HOH HOH 376 A HOH 377 3 HOH HOH 377 A HOH 378 3 HOH HOH 378 A HOH 379 3 HOH HOH 379 A HOH 380 3 HOH HOH 380 A HOH 381 3 HOH HOH 381 A HOH 382 3 HOH HOH 382 A HOH 383 3 HOH HOH 383 A HOH 384 3 HOH HOH 384 A HOH 385 3 HOH HOH 385 A HOH 386 3 HOH HOH 386 A HOH 387 3 HOH HOH 387 A HOH 388 3 HOH HOH 388 A HOH 389 3 HOH HOH 389 A HOH 390 3 HOH HOH 390 A HOH 391 3 HOH HOH 391 A HOH 392 3 HOH HOH 392 A HOH 393 3 HOH HOH 393 A HOH 394 3 HOH HOH 394 A HOH 395 3 HOH HOH 395 A HOH 396 3 HOH HOH 396 A HOH 397 3 HOH HOH 397 A HOH 398 3 HOH HOH 398 A HOH 399 3 HOH HOH 399 A HOH 400 3 HOH HOH 400 A HOH 401 3 HOH HOH 401 A HOH 402 3 HOH HOH 402 A HOH 403 3 HOH HOH 403 A HOH 404 3 HOH HOH 404 A HOH 405 3 HOH HOH 405 A ILE 1 n 1 ILE 1 A PRO 2 n 2 PRO 2 A GLU 3 n 3 GLU 3 A TYR 4 n 4 TYR 4 A VAL 5 n 5 VAL 5 A ASP 6 n 6 ASP 6 A TRP 7 n 7 TRP 7 A ARG 8 n 8 ARG 8 A GLN 9 n 9 GLN 9 A LYS 10 n 10 LYS 10 A GLY 11 n 11 GLY 11 A ALA 12 n 12 ALA 12 A VAL 13 n 13 VAL 13 A THR 14 n 14 THR 14 A PRO 15 n 15 PRO 15 A VAL 16 n 16 VAL 16 A LYS 17 n 17 LYS 17 A ASN 18 n 18 ASN 18 A GLN 19 n 19 GLN 19 A GLY 20 n 20 GLY 20 A SER 21 n 21 SER 21 A CYS 22 n 22 CYS 22 A GLY 23 n 23 GLY 23 A SER 24 n 24 SER 24 A CYS 25 n 25 CYS 25 A TRP 26 n 26 TRP 26 A ALA 27 n 27 ALA 27 A PHE 28 n 28 PHE 28 A SER 29 n 29 SER 29 A ALA 30 n 30 ALA 30 A VAL 31 n 31 VAL 31 A VAL 32 n 32 VAL 32 A THR 33 n 33 THR 33 A ILE 34 n 34 ILE 34 A GLU 35 n 35 GLU 35 A GLY 36 n 36 GLY 36 A ILE 37 n 37 ILE 37 A ILE 38 n 38 ILE 38 A LYS 39 n 39 LYS 39 A ILE 40 n 40 ILE 40 A ARG 41 n 41 ARG 41 A THR 42 n 42 THR 42 A GLY 43 n 43 GLY 43 A ASN 44 n 44 ASN 44 A LEU 45 n 45 LEU 45 A ASN 46 n 46 ASN 46 A GLU 47 n 47 GLU 47 A TYR 48 n 48 TYR 48 A SER 49 n 49 SER 49 A GLU 50 n 50 GLU 50 A GLN 51 n 51 GLN 51 A GLU 52 n 52 GLU 52 A LEU 53 n 53 LEU 53 A LEU 54 n 54 LEU 54 A ASP 55 n 55 ASP 55 A CYS 56 n 56 CYS 56 A ASP 57 n 57 ASP 57 A ARG 58 n 58 ARG 58 A ARG 59 n 59 ARG 59 A SER 60 n 60 SER 60 A TYR 61 n 61 TYR 61 A GLY 62 n 62 GLY 62 A CYS 63 n 63 CYS 63 A ASN 64 n 64 ASN 64 A GLY 65 n 65 GLY 65 A GLY 66 n 66 GLY 66 A TYR 67 n 67 TYR 67 A PRO 68 n 68 PRO 68 A TRP 69 n 69 TRP 69 A SER 70 n 70 SER 70 A ALA 71 n 71 ALA 71 A LEU 72 n 72 LEU 72 A GLN 73 n 73 GLN 73 A LEU 74 n 74 LEU 74 A VAL 75 n 75 VAL 75 A ALA 76 n 76 ALA 76 A GLN 77 n 77 GLN 77 A TYR 78 n 78 TYR 78 A GLY 79 n 79 GLY 79 A ILE 80 n 80 ILE 80 A HIS 81 n 81 HIS 81 A TYR 82 n 82 TYR 82 A ARG 83 n 83 ARG 83 A ASN 84 n 84 ASN 84 A THR 85 n 85 THR 85 A TYR 86 n 86 TYR 86 A PRO 87 n 87 PRO 87 A TYR 88 n 88 TYR 88 A GLU 89 n 89 GLU 89 A GLY 90 n 90 GLY 90 A VAL 91 n 91 VAL 91 A GLN 92 n 92 GLN 92 A ARG 93 n 93 ARG 93 A TYR 94 n 94 TYR 94 A CYS 95 n 95 CYS 95 A ARG 96 n 96 ARG 96 A SER 97 n 97 SER 97 A ARG 98 n 98 ARG 98 A GLU 99 n 99 GLU 99 A LYS 100 n 100 LYS 100 A GLY 101 n 101 GLY 101 A PRO 102 n 102 PRO 102 A TYR 103 n 103 TYR 103 A ALA 104 n 104 ALA 104 A ALA 105 n 105 ALA 105 A LYS 106 n 106 LYS 106 A THR 107 n 107 THR 107 A ASP 108 n 108 ASP 108 A GLY 109 n 109 GLY 109 A VAL 110 n 110 VAL 110 A ARG 111 n 111 ARG 111 A GLN 112 n 112 GLN 112 A VAL 113 n 113 VAL 113 A GLN 114 n 114 GLN 114 A PRO 115 n 115 PRO 115 A TYR 116 n 116 TYR 116 A ASN 117 n 117 ASN 117 A GLU 118 n 118 GLU 118 A GLY 119 n 119 GLY 119 A ALA 120 n 120 ALA 120 A LEU 121 n 121 LEU 121 A LEU 122 n 122 LEU 122 A TYR 123 n 123 TYR 123 A SER 124 n 124 SER 124 A ILE 125 n 125 ILE 125 A ALA 126 n 126 ALA 126 A ASN 127 n 127 ASN 127 A GLN 128 n 128 GLN 128 A PRO 129 n 129 PRO 129 A VAL 130 n 130 VAL 130 A SER 131 n 131 SER 131 A VAL 132 n 132 VAL 132 A VAL 133 n 133 VAL 133 A LEU 134 n 134 LEU 134 A GLU 135 n 135 GLU 135 A ALA 136 n 136 ALA 136 A ALA 137 n 137 ALA 137 A GLY 138 n 138 GLY 138 A LYS 139 n 139 LYS 139 A ASP 140 n 140 ASP 140 A PHE 141 n 141 PHE 141 A GLN 142 n 142 GLN 142 A LEU 143 n 143 LEU 143 A TYR 144 n 144 TYR 144 A ARG 145 n 145 ARG 145 A GLY 146 n 146 GLY 146 A GLY 147 n 147 GLY 147 A ILE 148 n 148 ILE 148 A PHE 149 n 149 PHE 149 A VAL 150 n 150 VAL 150 A GLY 151 n 151 GLY 151 A PRO 152 n 152 PRO 152 A CYS 153 n 153 CYS 153 A GLY 154 n 154 GLY 154 A ASN 155 n 155 ASN 155 A LYS 156 n 156 LYS 156 A VAL 157 n 157 VAL 157 A ASP 158 n 158 ASP 158 A HIS 159 n 159 HIS 159 A ALA 160 n 160 ALA 160 A VAL 161 n 161 VAL 161 A ALA 162 n 162 ALA 162 A ALA 163 n 163 ALA 163 A VAL 164 n 164 VAL 164 A GLY 165 n 165 GLY 165 A TYR 166 n 166 TYR 166 A GLY 167 n 167 GLY 167 A PRO 168 n 168 PRO 168 A ASN 169 n 169 ASN 169 A TYR 170 n 170 TYR 170 A ILE 171 n 171 ILE 171 A LEU 172 n 172 LEU 172 A ILE 173 n 173 ILE 173 A LYS 174 n 174 LYS 174 A ASN 175 n 175 ASN 175 A SER 176 n 176 SER 176 A TRP 177 n 177 TRP 177 A GLY 178 n 178 GLY 178 A THR 179 n 179 THR 179 A GLY 180 n 180 GLY 180 A TRP 181 n 181 TRP 181 A GLY 182 n 182 GLY 182 A GLU 183 n 183 GLU 183 A ASN 184 n 184 ASN 184 A GLY 185 n 185 GLY 185 A TYR 186 n 186 TYR 186 A ILE 187 n 187 ILE 187 A ARG 188 n 188 ARG 188 A ILE 189 n 189 ILE 189 A LYS 190 n 190 LYS 190 A ARG 191 n 191 ARG 191 A GLY 192 n 192 GLY 192 A THR 193 n 193 THR 193 A GLY 194 n 194 GLY 194 A ASN 195 n 195 ASN 195 A SER 196 n 196 SER 196 A TYR 197 n 197 TYR 197 A GLY 198 n 198 GLY 198 A VAL 199 n 199 VAL 199 A CYS 200 n 200 CYS 200 A GLY 201 n 201 GLY 201 A LEU 202 n 202 LEU 202 A TYR 203 n 203 TYR 203 A THR 204 n 204 THR 204 A SER 205 n 205 SER 205 A SER 206 n 206 SER 206 A PHE 207 n 207 PHE 207 A TYR 208 n 208 TYR 208 A PRO 209 n 209 PRO 209 A VAL 210 n 210 VAL 210 A LYS 211 n 211 LYS 211 A ASN 212 n 212 ASN 212 A n 1 250 I LEU 251 n 2 LEU 251 I PHE 252 n 3 PHE 252 I GLM 253 n 4 GLY 253 I GLM 254 n 5 0HQ 254 I author_and_software_defined_assembly PISA 2 dimeric 780 -6 9480 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 VAL 130 A N VAL 130 A O ALA 163 A O ALA 163 A O TYR 166 A O TYR 166 A N VAL 5 A N VAL 5 A N VAL 130 A N VAL 130 A O ALA 163 A O ALA 163 A N ALA 162 A N ALA 162 A O LYS 174 A O LYS 174 A N ILE 173 A N ILE 173 A O ILE 187 A O ILE 187 A O ARG 188 A O ARG 188 A N PHE 149 A N PHE 149 A N ARG 111 A N ARG 111 A O TYR 208 A O TYR 208 1 I PHQ 250 B PHQ 1 1 Y 1 A ASP 158 -151.10 7.30 14.80 -0.96 0.00 0.00 0.52 0.00 0.44 MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. PARAMETERS WERE USED. THE CBZ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE IN ELECTRON DENSITY DUE TO DISORDER AND WAS NOT INCLUDED IN THE MODEL. 0.169 0.147 0.149 0.149 1.6 10.0 1304 24603 24603 5.0 95.1 1.91608 0.06724 RANDOM 1 THROUGHOUT 0.0 0.0 MOLECULAR REPLACEMENT 0.07936 0.07645 PDB ENTRY 1PPN Engh & Huber 1.6 10.0 105 1784 0 0 1679 0.014 0.021 0.024 0.030 1.564 0.918 1.5 1.626 2.000 2.707 3.00 4.432 4.5 0.007 0.020 0.104 0.200 23.10 1.6 20.0 1KHQ 26000 26000 -3 -3 0.059 1 14.7 8.1 94.5 0.29 1.61 1.67 3.8 1 3.0 89.6 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement REFMAC ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX 1 N N 2 N N 3 N N A SER 24 A SER 24 HELX_P A GLY 43 A GLY 43 1 1 20 A SER 49 A SER 49 HELX_P A ASP 57 A ASP 57 1 2 9 A TYR 61 A TYR 61 HELX_P A GLY 65 A GLY 65 5 3 5 A TYR 67 A TYR 67 HELX_P A TYR 78 A TYR 78 1 4 12 A ASN 117 A ASN 117 HELX_P A GLN 128 A GLN 128 1 5 12 A GLY 138 A GLY 138 HELX_P A LEU 143 A LEU 143 1 6 6 A GLY 198 A GLY 198 HELX_P A LEU 202 A LEU 202 5 7 5 disulf 2.039 A CYS 22 A SG CYS 22 1_555 A CYS 63 A SG CYS 63 1_555 disulf 2.010 A CYS 56 A SG CYS 56 1_555 A CYS 95 A SG CYS 95 1_555 disulf 2.062 A CYS 153 A SG CYS 153 1_555 A CYS 200 A SG CYS 200 1_555 covale 1.804 one A CYS 25 A SG CYS 25 1_555 I 0HQ 254 B C1 0HQ 5 1_555 covale 1.531 both I GLY 253 B C GLY 4 1_555 I 0HQ 254 B C1 0HQ 5 1_555 HYDROLASE/HYDROLASE INHIBITOR PROTEASE INHIBITOR, DIAZOMETHYLKETONE INHIBITOR, IRREVERSIBLE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX A GLY 151 A GLY 151 1 A PRO 152 A PRO 152 0.91 PAPA_CARPA UNP 1 1 P00784 MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYID ETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWA FSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKT DGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYI RIKRGTGNSYGVCGLYTSSFYPVKN 1KHQ PDB 2 1 1KHQ (PHQ)LFG(OHQ) 134 345 1KHQ 1 212 P00784 A 1 1 212 250 254 1KHQ 250 254 1KHQ I 2 1 5 3 5 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel A VAL 130 A VAL 130 A LEU 134 A LEU 134 A HIS 159 A HIS 159 A GLY 167 A GLY 167 A VAL 5 A VAL 5 A ASP 6 A ASP 6 A VAL 130 A VAL 130 A LEU 134 A LEU 134 A HIS 159 A HIS 159 A GLY 167 A GLY 167 A TYR 170 A TYR 170 A LYS 174 A LYS 174 A TYR 186 A TYR 186 A LYS 190 A LYS 190 A ILE 148 A ILE 148 A PHE 149 A PHE 149 A GLY 109 A GLY 109 A GLN 112 A GLN 112 A PHE 207 A PHE 207 A VAL 210 A VAL 210 BINDING SITE FOR CHAIN I OF PEPTIDIC INHIBITOR Software 12 A GLN 19 A GLN 19 12 1_555 A GLY 23 A GLY 23 12 1_555 A SER 24 A SER 24 12 1_555 A CYS 25 A CYS 25 12 1_555 A TRP 26 A TRP 26 12 1_555 A GLY 65 A GLY 65 12 1_555 A GLY 66 A GLY 66 12 1_555 A TYR 67 A TYR 67 12 1_555 A ARG 111 A ARG 111 12 2_574 A VAL 133 A VAL 133 12 1_555 A ASP 158 A ASP 158 12 1_555 A HIS 159 A HIS 159 12 1_555 19 P 21 21 21