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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF PRAPE1
Keywords TETRAHEDRAL DODECAMER, HYDROLASE
Experiment X-ray diffraction
Number of Models  1


   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  

PDB   5JH9     released     available     available     Quaternary Structure Server  


Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   VACUOLAR AMINOPEPTIDASE 1  A 475 3639 0
2  Protein   VACUOLAR AMINOPEPTIDASE 1  B 477 3660 0
3  Protein   VACUOLAR AMINOPEPTIDASE 1  C 473 3652 0
4  Protein   VACUOLAR AMINOPEPTIDASE 1  D 475 3668 0
5  Ligand   VACUOLAR AMINOPEPTIDASE 1  A 4 0 12
6  Ligand   VACUOLAR AMINOPEPTIDASE 1  B 4 0 12
7  Ligand   VACUOLAR AMINOPEPTIDASE 1  C 4 0 12
8  Ligand   VACUOLAR AMINOPEPTIDASE 1  D 4 0 12
9 Water     819 0 819
total       2735 14619 867

Proteins
Unit 1 LYS33 GLU34 LYS35 LYS36 GLU37 ASN38 GLU39 ASN40 SER41 TRP42 CYS43 ILE44 LEU45 GLU46 HIS47 ASN48 TYR49 GLU50 ASP51 ILE52 ALA53 GLN54 GLU55 PHE56 ILE57 ASP58 PHE59 ILE60 TYR61 LYS62 ASN63 PRO64 THR65 THR66 TYR67 HIS68 VAL69 VAL70 SER71 PHE72 PHE73 ALA74 GLU75 LEU76 LEU77 ASP78 LYS79 HIS80 ASN81 PHE82 LYS83 TYR84 LEU85 SER86 GLU87 LYS88 SER89 ASN90 TRP91 GLN92 ASP93 SER94 ILE95 GLY96 GLU97 ASP98 GLY99 GLY100 LYS101 PHE102 TYR103 THR104 ILE105 ARG106 ASN107 GLY108 THR109 ASN110 LEU111 SER112 ALA113 PHE114 ILE115 LEU116 GLY117 LYS118 ASN119 TRP120 ARG121 ALA122 GLU123 LYS124 GLY125 VAL126 GLY127 VAL128 ILE129 GLY130 SER131 HIS132 VAL133 ASP134 ALA135 LEU136 THR137 VAL138 LYS139 LEU140 LYS141 PRO142 VAL143 SER144 PHE145 LYS146 ASP147 THR148 ALA149 GLU150 GLY151 TYR152 GLY153 ARG154 ILE155 ALA156 VAL157 ALA158 PRO159 TYR160 GLY161 GLY162 THR163 LEU164 ASN165 GLU166 LEU167 TRP168 LEU169 ASP170 ARG171 ASP172 LEU173 GLY174 ILE175 GLY176 GLY177 ARG178 LEU179 LEU180 TYR181 LYS182 LYS183 LYS184 GLY185 THR186 ASN187 GLU188 ILE189 LYS190 SER191 ALA192 LEU193 VAL194 ASP195 SER196 THR197 PRO198 LEU199 PRO200 VAL201 CYS202 ARG203 ILE204 PRO205 SER206 LEU207 ALA208 PRO209 HIS210 PHE211 GLY212 LYS213 PRO214 ALA215 GLU216 GLY217 PRO218 PHE219 ASP220 LYS221 GLU222 ASP223 GLN224 THR225 ILE226 PRO227 VAL228 ILE229 GLY230 PHE231 PRO232 THR233 PRO234 GLU240 PRO241 PRO242 THR243 ASP244 ASP245 GLU246 LYS247 LYS248 SER249 PRO250 LEU251 PHE252 GLY253 LYS254 HIS255 CYS256 ILE257 HIS258 LEU259 LEU260 ARG261 TYR262 VAL263 ALA264 LYS265 LEU266 ALA267 GLY268 VAL269 GLU270 VAL271 SER272 GLU273 LEU274 ILE275 GLN276 MET277 ASP278 LEU279 ASP280 LEU281 PHE282 ASP283 VAL284 GLN285 LYS286 GLY287 THR288 ILE289 GLY290 GLY291 ILE292 GLY293 LYS294 HIS295 PHE296 LEU297 PHE298 ALA299 PRO300 ARG301 LEU302 ASP303 ASP304 ARG305 LEU306 CYS307 SER308 PHE309 ALA310 ALA311 MET312 ILE313 ALA314 LEU315 ILE316 CYS317 TYR318 ALA319 LYS320 ASP321 VAL322 ASN323 THR324 GLU325 GLU326 SER327 ASP328 LEU329 PHE330 SER331 THR332 VAL333 THR334 LEU335 TYR336 ASP337 ASN338 GLU339 GLU340 ILE341 GLY342 SER343 LEU344 THR345 ARG346 GLN347 GLY348 ALA349 LYS350 GLY351 GLY352 LEU353 LEU354 GLU355 SER356 VAL357 VAL358 GLU359 ARG360 SER361 SER362 SER363 ALA364 PHE365 THR366 LYS367 LYS368 PRO369 VAL370 ASP371 LEU372 HIS373 THR374 VAL375 TRP376 ALA377 ASN378 SER379 ILE380 ILE381 LEU382 SER383 ALA384 ASP385 VAL386 ASN387 HIS388 LEU389 TYR390 ASN391 PRO392 ASN393 PHE394 PRO395 GLU396 VAL397 TYR398 LEU399 LYS400 ASN401 HIS402 PHE403 PRO404 VAL405 PRO406 ASN407 VAL408 GLY409 ILE410 THR411 LEU412 SER413 LEU414 ASP415 PRO416 ASN417 GLY418 HIS419 MET420 ALA421 THR422 ASP423 VAL424 VAL425 GLY426 THR427 ALA428 LEU429 VAL430 GLU431 GLU432 LEU433 ALA434 ARG435 ARG436 ASN437 GLY438 ASP439 LYS440 VAL441 GLN442 TYR443 PHE444 GLN445 ILE446 LYS447 ASN448 ASN449 SER450 ARG451 SER452 GLY453 GLY454 THR455 ILE456 GLY457 PRO458 SER459 LEU460 ALA461 SER462 GLN463 THR464 GLY465 ALA466 ARG467 THR468 ILE469 ASP470 LEU471 GLY472 ILE473 ALA474 GLN475 LEU476 SER477 MET478 HIS479 SER480 ILE481 ARG482 ALA483 ALA484 THR485 GLY486 SER487 LYS488 ASP489 VAL490 GLY491 LEU492 GLY493 VAL494 LYS495 PHE496 PHE497 ASN498 GLY499 PHE500 PHE501 LYS502 HIS503 TRP504 ARG505 SER506 VAL507 TYR508 ASP509 GLU510 PHE511 GLY512
Unit 2 GLU31 GLU32 LYS33 GLU34 LYS35 LYS36 GLU37 ASN38 GLU39 ASN40 SER41 TRP42 CYS43 ILE44 LEU45 GLU46 HIS47 ASN48 TYR49 GLU50 ASP51 ILE52 ALA53 GLN54 GLU55 PHE56 ILE57 ASP58 PHE59 ILE60 TYR61 LYS62 ASN63 PRO64 THR65 THR66 TYR67 HIS68 VAL69 VAL70 SER71 PHE72 PHE73 ALA74 GLU75 LEU76 LEU77 ASP78 LYS79 HIS80 ASN81 PHE82 LYS83 TYR84 LEU85 SER86 GLU87 LYS88 SER89 ASN90 TRP91 GLN92 ASP93 SER94 ILE95 GLY96 GLU97 ASP98 GLY99 GLY100 LYS101 PHE102 TYR103 THR104 ILE105 ARG106 ASN107 GLY108 THR109 ASN110 LEU111 SER112 ALA113 PHE114 ILE115 LEU116 GLY117 LYS118 ASN119 TRP120 ARG121 ALA122 GLU123 LYS124 GLY125 VAL126 GLY127 VAL128 ILE129 GLY130 SER131 HIS132 VAL133 ASP134 ALA135 LEU136 THR137 VAL138 LYS139 LEU140 LYS141 PRO142 VAL143 SER144 PHE145 LYS146 ASP147 THR148 ALA149 GLU150 GLY151 TYR152 GLY153 ARG154 ILE155 ALA156 VAL157 ALA158 PRO159 TYR160 GLY161 GLY162 THR163 LEU164 ASN165 GLU166 LEU167 TRP168 LEU169 ASP170 ARG171 ASP172 LEU173 GLY174 ILE175 GLY176 GLY177 ARG178 LEU179 LEU180 TYR181 LYS182 LYS183 LYS184 GLY185 THR186 ASN187 GLU188 ILE189 LYS190 SER191 ALA192 LEU193 VAL194 ASP195 SER196 THR197 PRO198 LEU199 PRO200 VAL201 CYS202 ARG203 ILE204 PRO205 SER206 LEU207 ALA208 PRO209 HIS210 PHE211 GLY212 LYS213 PRO214 ALA215 GLU216 GLY217 PRO218 PHE219 ASP220 LYS221 GLU222 ASP223 GLN224 THR225 ILE226 PRO227 VAL228 ILE229 GLY230 PHE231 PRO232 THR233 PRO234 GLU240 PRO241 PRO242 THR243 ASP244 ASP245 GLU246 LYS247 LYS248 SER249 PRO250 LEU251 PHE252 GLY253 LYS254 HIS255 CYS256 ILE257 HIS258 LEU259 LEU260 ARG261 TYR262 VAL263 ALA264 LYS265 LEU266 ALA267 GLY268 VAL269 GLU270 VAL271 SER272 GLU273 LEU274 ILE275 GLN276 MET277 ASP278 LEU279 ASP280 LEU281 PHE282 ASP283 VAL284 GLN285 LYS286 GLY287 THR288 ILE289 GLY290 GLY291 ILE292 GLY293 LYS294 HIS295 PHE296 LEU297 PHE298 ALA299 PRO300 ARG301 LEU302 ASP303 ASP304 ARG305 LEU306 CYS307 SER308 PHE309 ALA310 ALA311 MET312 ILE313 ALA314 LEU315 ILE316 CYS317 TYR318 ALA319 LYS320 ASP321 VAL322 ASN323 THR324 GLU325 GLU326 SER327 ASP328 LEU329 PHE330 SER331 THR332 VAL333 THR334 LEU335 TYR336 ASP337 ASN338 GLU339 GLU340 ILE341 GLY342 SER343 LEU344 THR345 ARG346 GLN347 GLY348 ALA349 LYS350 GLY351 GLY352 LEU353 LEU354 GLU355 SER356 VAL357 VAL358 GLU359 ARG360 SER361 SER362 SER363 ALA364 PHE365 THR366 LYS367 LYS368 PRO369 VAL370 ASP371 LEU372 HIS373 THR374 VAL375 TRP376 ALA377 ASN378 SER379 ILE380 ILE381 LEU382 SER383 ALA384 ASP385 VAL386 ASN387 HIS388 LEU389 TYR390 ASN391 PRO392 ASN393 PHE394 PRO395 GLU396 VAL397 TYR398 LEU399 LYS400 ASN401 HIS402 PHE403 PRO404 VAL405 PRO406 ASN407 VAL408 GLY409 ILE410 THR411 LEU412 SER413 LEU414 ASP415 PRO416 ASN417 GLY418 HIS419 MET420 ALA421 THR422 ASP423 VAL424 VAL425 GLY426 THR427 ALA428 LEU429 VAL430 GLU431 GLU432 LEU433 ALA434 ARG435 ARG436 ASN437 GLY438 ASP439 LYS440 VAL441 GLN442 TYR443 PHE444 GLN445 ILE446 LYS447 ASN448 ASN449 SER450 ARG451 SER452 GLY453 GLY454 THR455 ILE456 GLY457 PRO458 SER459 LEU460 ALA461 SER462 GLN463 THR464 GLY465 ALA466 ARG467 THR468 ILE469 ASP470 LEU471 GLY472 ILE473 ALA474 GLN475 LEU476 SER477 MET478 HIS479 SER480 ILE481 ARG482 ALA483 ALA484 THR485 GLY486 SER487 LYS488 ASP489 VAL490 GLY491 LEU492 GLY493 VAL494 LYS495 PHE496 PHE497 ASN498 GLY499 PHE500 PHE501 LYS502 HIS503 TRP504 ARG505 SER506 VAL507 TYR508 ASP509 GLU510 PHE511 GLY512
Unit 3 LYS35 LYS36 GLU37 ASN38 GLU39 ASN40 SER41 TRP42 CYS43 ILE44 LEU45 GLU46 HIS47 ASN48 TYR49 GLU50 ASP51 ILE52 ALA53 GLN54 GLU55 PHE56 ILE57 ASP58 PHE59 ILE60 TYR61 LYS62 ASN63 PRO64 THR65 THR66 TYR67 HIS68 VAL69 VAL70 SER71 PHE72 PHE73 ALA74 GLU75 LEU76 LEU77 ASP78 LYS79 HIS80 ASN81 PHE82 LYS83 TYR84 LEU85 SER86 GLU87 LYS88 SER89 ASN90 TRP91 GLN92 ASP93 SER94 ILE95 GLY96 GLU97 ASP98 GLY99 GLY100 LYS101 PHE102 TYR103 THR104 ILE105 ARG106 ASN107 GLY108 THR109 ASN110 LEU111 SER112 ALA113 PHE114 ILE115 LEU116 GLY117 LYS118 ASN119 TRP120 ARG121 ALA122 GLU123 LYS124 GLY125 VAL126 GLY127 VAL128 ILE129 GLY130 SER131 HIS132 VAL133 ASP134 ALA135 LEU136 THR137 VAL138 LYS139 LEU140 LYS141 PRO142 VAL143 SER144 PHE145 LYS146 ASP147 THR148 ALA149 GLU150 GLY151 TYR152 GLY153 ARG154 ILE155 ALA156 VAL157 ALA158 PRO159 TYR160 GLY161 GLY162 THR163 LEU164 ASN165 GLU166 LEU167 TRP168 LEU169 ASP170 ARG171 ASP172 LEU173 GLY174 ILE175 GLY176 GLY177 ARG178 LEU179 LEU180 TYR181 LYS182 LYS183 LYS184 GLY185 THR186 ASN187 GLU188 ILE189 LYS190 SER191 ALA192 LEU193 VAL194 ASP195 SER196 THR197 PRO198 LEU199 PRO200 VAL201 CYS202 ARG203 ILE204 PRO205 SER206 LEU207 ALA208 PRO209 HIS210 PHE211 GLY212 LYS213 PRO214 ALA215 GLU216 GLY217 PRO218 PHE219 ASP220 LYS221 GLU222 ASP223 GLN224 THR225 ILE226 PRO227 VAL228 ILE229 GLY230 PHE231 PRO232 THR233 PRO234 GLU240 PRO241 PRO242 THR243 ASP244 ASP245 GLU246 LYS247 LYS248 SER249 PRO250 LEU251 PHE252 GLY253 LYS254 HIS255 CYS256 ILE257 HIS258 LEU259 LEU260 ARG261 TYR262 VAL263 ALA264 LYS265 LEU266 ALA267 GLY268 VAL269 GLU270 VAL271 SER272 GLU273 LEU274 ILE275 GLN276 MET277 ASP278 LEU279 ASP280 LEU281 PHE282 ASP283 VAL284 GLN285 LYS286 GLY287 THR288 ILE289 GLY290 GLY291 ILE292 GLY293 LYS294 HIS295 PHE296 LEU297 PHE298 ALA299 PRO300 ARG301 LEU302 ASP303 ASP304 ARG305 LEU306 CYS307 SER308 PHE309 ALA310 ALA311 MET312 ILE313 ALA314 LEU315 ILE316 CYS317 TYR318 ALA319 LYS320 ASP321 VAL322 ASN323 THR324 GLU325 GLU326 SER327 ASP328 LEU329 PHE330 SER331 THR332 VAL333 THR334 LEU335 TYR336 ASP337 ASN338 GLU339 GLU340 ILE341 GLY342 SER343 LEU344 THR345 ARG346 GLN347 GLY348 ALA349 LYS350 GLY351 GLY352 LEU353 LEU354 GLU355 SER356 VAL357 VAL358 GLU359 ARG360 SER361 SER362 SER363 ALA364 PHE365 THR366 LYS367 LYS368 PRO369 VAL370 ASP371 LEU372 HIS373 THR374 VAL375 TRP376 ALA377 ASN378 SER379 ILE380 ILE381 LEU382 SER383 ALA384 ASP385 VAL386 ASN387 HIS388 LEU389 TYR390 ASN391 PRO392 ASN393 PHE394 PRO395 GLU396 VAL397 TYR398 LEU399 LYS400 ASN401 HIS402 PHE403 PRO404 VAL405 PRO406 ASN407 VAL408 GLY409 ILE410 THR411 LEU412 SER413 LEU414 ASP415 PRO416 ASN417 GLY418 HIS419 MET420 ALA421 THR422 ASP423 VAL424 VAL425 GLY426 THR427 ALA428 LEU429 VAL430 GLU431 GLU432 LEU433 ALA434 ARG435 ARG436 ASN437 GLY438 ASP439 LYS440 VAL441 GLN442 TYR443 PHE444 GLN445 ILE446 LYS447 ASN448 ASN449 SER450 ARG451 SER452 GLY453 GLY454 THR455 ILE456 GLY457 PRO458 SER459 LEU460 ALA461 SER462 GLN463 THR464 GLY465 ALA466 ARG467 THR468 ILE469 ASP470 LEU471 GLY472 ILE473 ALA474 GLN475 LEU476 SER477 MET478 HIS479 SER480 ILE481 ARG482 ALA483 ALA484 THR485 GLY486 SER487 LYS488 ASP489 VAL490 GLY491 LEU492 GLY493 VAL494 LYS495 PHE496 PHE497 ASN498 GLY499 PHE500 PHE501 LYS502 HIS503 TRP504 ARG505 SER506 VAL507 TYR508 ASP509 GLU510 PHE511 GLY512
Unit 4 LYS35 LYS36 GLU37 ASN38 GLU39 ASN40 SER41 TRP42 CYS43 ILE44 LEU45 GLU46 HIS47 ASN48 TYR49 GLU50 ASP51 ILE52 ALA53 GLN54 GLU55 PHE56 ILE57 ASP58 PHE59 ILE60 TYR61 LYS62 ASN63 PRO64 THR65 THR66 TYR67 HIS68 VAL69 VAL70 SER71 PHE72 PHE73 ALA74 GLU75 LEU76 LEU77 ASP78 LYS79 HIS80 ASN81 PHE82 LYS83 TYR84 LEU85 SER86 GLU87 LYS88 SER89 ASN90 TRP91 GLN92 ASP93 SER94 ILE95 GLY96 GLU97 ASP98 GLY99 GLY100 LYS101 PHE102 TYR103 THR104 ILE105 ARG106 ASN107 GLY108 THR109 ASN110 LEU111 SER112 ALA113 PHE114 ILE115 LEU116 GLY117 LYS118 ASN119 TRP120 ARG121 ALA122 GLU123 LYS124 GLY125 VAL126 GLY127 VAL128 ILE129 GLY130 SER131 HIS132 VAL133 ASP134 ALA135 LEU136 THR137 VAL138 LYS139 LEU140 LYS141 PRO142 VAL143 SER144 PHE145 LYS146 ASP147 THR148 ALA149 GLU150 GLY151 TYR152 GLY153 ARG154 ILE155 ALA156 VAL157 ALA158 PRO159 TYR160 GLY161 GLY162 THR163 LEU164 ASN165 GLU166 LEU167 TRP168 LEU169 ASP170 ARG171 ASP172 LEU173 GLY174 ILE175 GLY176 GLY177 ARG178 LEU179 LEU180 TYR181 LYS182 LYS183 LYS184 GLY185 THR186 ASN187 GLU188 ILE189 LYS190 SER191 ALA192 LEU193 VAL194 ASP195 SER196 THR197 PRO198 LEU199 PRO200 VAL201 CYS202 ARG203 ILE204 PRO205 SER206 LEU207 ALA208 PRO209 HIS210 PHE211 GLY212 LYS213 PRO214 ALA215 GLU216 GLY217 PRO218 PHE219 ASP220 LYS221 GLU222 ASP223 GLN224 THR225 ILE226 PRO227 VAL228 ILE229 GLY230 PHE231 PRO232 THR233 PRO234 ASP235 ASN239 GLU240 PRO241 PRO242 THR243 ASP244 ASP245 GLU246 LYS247 LYS248 SER249 PRO250 LEU251 PHE252 GLY253 LYS254 HIS255 CYS256 ILE257 HIS258 LEU259 LEU260 ARG261 TYR262 VAL263 ALA264 LYS265 LEU266 ALA267 GLY268 VAL269 GLU270 VAL271 SER272 GLU273 LEU274 ILE275 GLN276 MET277 ASP278 LEU279 ASP280 LEU281 PHE282 ASP283 VAL284 GLN285 LYS286 GLY287 THR288 ILE289 GLY290 GLY291 ILE292 GLY293 LYS294 HIS295 PHE296 LEU297 PHE298 ALA299 PRO300 ARG301 LEU302 ASP303 ASP304 ARG305 LEU306 CYS307 SER308 PHE309 ALA310 ALA311 MET312 ILE313 ALA314 LEU315 ILE316 CYS317 TYR318 ALA319 LYS320 ASP321 VAL322 ASN323 THR324 GLU325 GLU326 SER327 ASP328 LEU329 PHE330 SER331 THR332 VAL333 THR334 LEU335 TYR336 ASP337 ASN338 GLU339 GLU340 ILE341 GLY342 SER343 LEU344 THR345 ARG346 GLN347 GLY348 ALA349 LYS350 GLY351 GLY352 LEU353 LEU354 GLU355 SER356 VAL357 VAL358 GLU359 ARG360 SER361 SER362 SER363 ALA364 PHE365 THR366 LYS367 LYS368 PRO369 VAL370 ASP371 LEU372 HIS373 THR374 VAL375 TRP376 ALA377 ASN378 SER379 ILE380 ILE381 LEU382 SER383 ALA384 ASP385 VAL386 ASN387 HIS388 LEU389 TYR390 ASN391 PRO392 ASN393 PHE394 PRO395 GLU396 VAL397 TYR398 LEU399 LYS400 ASN401 HIS402 PHE403 PRO404 VAL405 PRO406 ASN407 VAL408 GLY409 ILE410 THR411 LEU412 SER413 LEU414 ASP415 PRO416 ASN417 GLY418 HIS419 MET420 ALA421 THR422 ASP423 VAL424 VAL425 GLY426 THR427 ALA428 LEU429 VAL430 GLU431 GLU432 LEU433 ALA434 ARG435 ARG436 ASN437 GLY438 ASP439 LYS440 VAL441 GLN442 TYR443 PHE444 GLN445 ILE446 LYS447 ASN448 ASN449 SER450 ARG451 SER452 GLY453 GLY454 THR455 ILE456 GLY457 PRO458 SER459 LEU460 ALA461 SER462 GLN463 THR464 GLY465 ALA466 ARG467 THR468 ILE469 ASP470 LEU471 GLY472 ILE473 ALA474 GLN475 LEU476 SER477 MET478 HIS479 SER480 ILE481 ARG482 ALA483 ALA484 THR485 GLY486 SER487 LYS488 ASP489 VAL490 GLY491 LEU492 GLY493 VAL494 LYS495 PHE496 PHE497 ASN498 GLY499 PHE500 PHE501 LYS502 HIS503 TRP504 ARG505 SER506 VAL507 TYR508 ASP509 GLU510 PHE511 GLY512

Ligands
Unit 5 ZN601 ZN602 CAC603 CAC604
Unit 6 ZN601 ZN602 CAC603 CAC604
Unit 7 ZN601 ZN602 CAC603 CAC604
Unit 8 ZN601 ZN602 CAC603 CAC604

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany