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Sequence, Chains, Asymmetric and Biological Units

Title INSIGHTS INTO THE UBIQUITIN TRANSFER CASCADE FROM THE REFINED STRUCTURE OF THE ACTIVATING ENZYME FOR NEDD8
Keywords UBIQUITIN, NEDD8, E1, APPBP1, UBA3, SIGNALING PROTEIN
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   1YOV     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   AMYLOID PROTEIN-BINDING PROTEIN 1  A 529 4208 0
2  Protein   UBIQUITIN-ACTIVATING ENZYME E1C  B 397 3089 0
3  Protein   AMYLOID PROTEIN-BINDING PROTEIN 1  C 526 4183 0
4  Protein   UBIQUITIN-ACTIVATING ENZYME E1C  D 382 2972 0
5  Ligand   UBIQUITIN-ACTIVATING ENZYME E1C  B 1 0 1
6  Ligand   UBIQUITIN-ACTIVATING ENZYME E1C  D 1 0 1
7 Water     150 0 150
total       1986 14452 152
Proteins
Unit 1 LYS6 LEU7 LEU8 LYS9 GLU10 GLN11 LYS12 TYR13 ASP14 ARG15 GLN16 LEU17 ARG18 LEU19 TRP20 GLY21 ASP22 HIS23 GLY24 GLN25 GLU26 ALA27 LEU28 GLU29 SER30 ALA31 HIS32 VAL33 CYS34 LEU35 ILE36 ASN37 ALA38 THR39 ALA40 THR41 GLY42 THR43 GLU44 ILE45 LEU46 LYS47 ASN48 LEU49 VAL50 LEU51 PRO52 GLY53 ILE54 GLY55 SER56 PHE57 THR58 ILE59 ILE60 ASP61 GLY62 ASN63 GLN64 VAL65 SER66 GLY67 GLU68 ASP69 ALA70 GLY71 ASN72 ASN73 PHE74 PHE75 LEU76 GLN77 ARG78 SER79 SER80 ILE81 GLY82 LYS83 ASN84 ARG85 ALA86 GLU87 ALA88 ALA89 MET90 GLU91 PHE92 LEU93 GLN94 GLU95 LEU96 ASN97 SER98 ASP99 VAL100 SER101 GLY102 SER103 PHE104 VAL105 GLU106 GLU107 SER108 PRO109 GLU110 ASN111 LEU112 LEU113 ASP114 ASN115 ASP116 PRO117 SER118 PHE119 PHE120 CYS121 ARG122 PHE123 THR124 VAL125 VAL126 VAL127 ALA128 THR129 GLN130 LEU131 PRO132 GLU133 SER134 THR135 SER136 LEU137 ARG138 LEU139 ALA140 ASP141 VAL142 LEU143 TRP144 ASN145 SER146 GLN147 ILE148 PRO149 LEU150 LEU151 ILE152 CYS153 ARG154 THR155 TYR156 GLY157 LEU158 VAL159 GLY160 TYR161 MET162 ARG163 ILE164 ILE165 ILE166 LYS167 GLU168 HIS169 PRO170 VAL171 ILE172 GLU173 SER174 HIS175 PRO176 ASP177 ASN178 ALA179 LEU180 GLU181 ASP182 LEU183 ARG184 LEU185 ASP186 LYS187 PRO188 PHE189 PRO190 GLU191 LEU192 ARG193 GLU194 HIS195 PHE196 GLN197 SER198 TYR199 ASP200 LEU201 ASP202 HIS203 MET204 GLU205 LYS206 LYS207 ASP208 HIS209 SER210 HIS211 THR212 PRO213 TRP214 ILE215 VAL216 ILE217 ILE218 ALA219 LYS220 TYR221 LEU222 ALA223 GLN224 TRP225 TYR226 SER227 GLU228 THR229 ASN230 GLY231 ARG232 ILE233 PRO234 LYS235 THR236 TYR237 LYS238 GLU239 LYS240 GLU241 ASP242 PHE243 ARG244 ASP245 LEU246 ILE247 ARG248 GLN249 GLY250 ILE251 LEU252 LYS253 ASN254 GLU255 ASN256 GLY257 ALA258 PRO259 GLU260 ASP261 GLU262 GLU263 ASN264 PHE265 GLU266 GLU267 ALA268 ILE269 LYS270 ASN271 VAL272 ASN273 THR274 ALA275 LEU276 ASN277 THR278 THR279 GLN280 ILE281 PRO282 SER283 SER284 ILE285 GLU286 ASP287 ILE288 PHE289 ASN290 ASP291 ASP292 ARG293 CYS294 ILE295 ASN296 ILE297 THR298 LYS299 GLN300 THR301 PRO302 SER303 PHE304 TRP305 ILE306 LEU307 ALA308 ARG309 ALA310 LEU311 LYS312 GLU313 PHE314 VAL315 ALA316 LYS317 GLU318 GLY319 GLN320 GLY321 ASN322 LEU323 PRO324 VAL325 ARG326 GLY327 THR328 ILE329 PRO330 ASP331 MET332 ILE333 ALA334 ASP335 SER336 GLY337 LYS338 TYR339 ILE340 LYS341 LEU342 GLN343 ASN344 VAL345 TYR346 ARG347 GLU348 LYS349 ALA350 LYS351 LYS352 ASP353 ALA354 ALA355 ALA356 VAL357 GLY358 ASN359 HIS360 VAL361 ALA362 LYS363 LEU364 LEU365 GLN366 SER367 ILE368 GLY369 GLN370 ALA371 PRO372 GLU373 SER374 ILE375 SER376 GLU377 LYS378 GLU379 LEU380 LYS381 LEU382 LEU383 CYS384 SER385 ASN386 SER387 ALA388 PHE389 LEU390 ARG391 VAL392 VAL393 ARG394 CYS395 ARG396 SER397 LEU398 ALA399 GLU400 GLU401 TYR402 GLY403 LEU404 ASP405 THR406 ILE407 ASN408 LYS409 ASP410 GLU411 ILE412 ILE413 SER414 SER415 MET416 ASP417 ASN418 PRO419 ASP420 ASN421 GLU422 ILE423 VAL424 LEU425 TYR426 LEU427 MET428 LEU429 ARG430 ALA431 VAL432 ASP433 ARG434 PHE435 HIS436 LYS437 GLN438 GLN439 GLY440 ARG441 TYR442 PRO443 GLY444 VAL445 SER446 ASN447 TYR448 GLN449 VAL450 GLU451 GLU452 ASP453 ILE454 GLY455 LYS456 LEU457 LYS458 SER459 CYS460 LEU461 THR462 GLY463 PHE464 LEU465 GLN466 GLU467 TYR468 GLY469 LEU470 SER471 VAL472 MET473 VAL474 LYS475 ASP476 ASP477 TYR478 VAL479 HIS480 GLU481 PHE482 CYS483 ARG484 TYR485 GLY486 ALA487 ALA488 GLU489 PRO490 HIS491 THR492 ILE493 ALA494 ALA495 PHE496 LEU497 GLY498 GLY499 ALA500 ALA501 ALA502 GLN503 GLU504 VAL505 ILE506 LYS507 ILE508 ILE509 THR510 LYS511 GLN512 PHE513 VAL514 ILE515 PHE516 ASN517 ASN518 THR519 TYR520 ILE521 TYR522 SER523 GLY524 MET525 SER526 GLN527 THR528 SER529 ALA530 THR531 PHE532 GLN533 LEU534
Unit 2 ASP12 TRP13 GLU14 GLY15 ARG16 TRP17 ASN18 HIS19 VAL20 LYS21 LYS22 PHE23 LEU24 GLU25 ARG26 SER27 GLY28 PRO29 PHE30 THR31 HIS32 PRO33 ASP34 PHE35 GLU36 PRO37 SER38 THR39 GLU40 SER41 LEU42 GLN43 PHE44 LEU45 LEU46 ASP47 THR48 CYS49 LYS50 VAL51 LEU52 VAL53 ILE54 GLY55 ALA56 GLY57 GLY58 LEU59 GLY60 CYS61 GLU62 LEU63 LEU64 LYS65 ASN66 LEU67 ALA68 LEU69 SER70 GLY71 PHE72 ARG73 GLN74 ILE75 HIS76 VAL77 ILE78 ASP79 MET80 ASP81 THR82 ILE83 ASP84 VAL85 SER86 ASN87 LEU88 ASN89 ARG90 GLN91 PHE92 LEU93 PHE94 ARG95 PRO96 LYS97 ASP98 ILE99 GLY100 ARG101 PRO102 LYS103 ALA104 GLU105 VAL106 ALA107 ALA108 GLU109 PHE110 LEU111 ASN112 ASP113 ARG114 VAL115 PRO116 ASN117 CYS118 ASN119 VAL120 VAL121 PRO122 HIS123 PHE124 ASN125 LYS126 ILE127 GLN128 ASP129 PHE130 ASN131 ASP132 THR133 PHE134 TYR135 ARG136 GLN137 PHE138 HIS139 ILE140 ILE141 VAL142 CYS143 GLY144 LEU145 ASP146 SER147 ILE148 ILE149 ALA150 ARG151 ARG152 TRP153 ILE154 ASN155 GLY156 MET157 LEU158 ILE159 SER160 LEU161 LEU162 ASN163 TYR164 GLU165 ASP166 GLY167 VAL168 LEU169 ASP170 PRO171 SER172 SER173 ILE174 VAL175 PRO176 LEU177 ILE178 ASP179 GLY180 GLY181 THR182 GLU183 GLY184 PHE185 LYS186 GLY187 ASN188 ALA189 ARG190 VAL191 ILE192 LEU193 PRO194 GLY195 MET196 THR197 ALA198 CYS199 ILE200 GLU201 CYS202 THR203 LEU204 GLU205 LEU206 TYR207 PRO208 PRO209 GLN210 VAL211 ASN212 PHE213 PRO214 MET215 CYS216 THR217 ILE218 ALA219 SER220 MET221 PRO222 ARG223 LEU224 PRO225 GLU226 HIS227 CYS228 ILE229 GLU230 TYR231 VAL232 ARG233 MET234 LEU235 GLN236 TRP237 PRO238 LYS239 GLU240 GLN241 PRO242 PHE243 GLY244 GLU245 GLY246 VAL247 PRO248 LEU249 ASP250 GLY251 ASP252 ASP253 PRO254 GLU255 HIS256 ILE257 GLN258 TRP259 ILE260 PHE261 GLN262 LYS263 SER264 LEU265 GLU266 ARG267 ALA268 SER269 GLN270 TYR271 ASN272 ILE273 ARG274 GLY275 VAL276 THR277 TYR278 ARG279 LEU280 THR281 GLN282 GLY283 VAL284 VAL285 LYS286 ARG287 ILE288 ILE289 PRO290 ALA291 VAL292 ALA293 SER294 THR295 ASN296 ALA297 VAL298 ILE299 ALA300 ALA301 VAL302 CYS303 ALA304 THR305 GLU306 VAL307 PHE308 LYS309 ILE310 ALA311 THR312 SER313 ALA314 TYR315 ILE316 PRO317 LEU318 ASN319 ASN320 TYR321 LEU322 VAL323 PHE324 ASN325 ASP326 VAL327 ASP328 GLY329 LEU330 TYR331 THR332 TYR333 THR334 PHE335 GLU336 ALA337 GLU338 ARG339 LYS340 GLU341 ASN342 CYS343 PRO344 ALA345 CYS346 SER347 GLN348 LEU349 PRO350 GLN351 ASN352 ILE353 GLN354 LEU361 GLN362 GLU363 VAL364 LEU365 ASP366 TYR367 LEU368 THR369 ASN370 SER371 ALA372 SER373 LEU374 GLN375 MET376 LYS377 SER378 PRO379 ALA380 ILE381 THR382 ALA383 THR384 ARG390 THR391 LEU392 TYR393 LEU394 GLN395 SER396 GLU401 GLU402 ARG403 THR404 ARG405 PRO406 ASN407 LEU408 LEU423 ALA424 VAL425 ALA426 ASP427 VAL428 THR429 THR430 PRO431 GLN432 THR433 VAL434 LEU435 PHE436 LYS437
Unit 3 LYS9 GLU10 GLN11 LYS12 TYR13 ASP14 ARG15 GLN16 LEU17 ARG18 LEU19 TRP20 GLY21 ASP22 HIS23 GLY24 GLN25 GLU26 ALA27 LEU28 GLU29 SER30 ALA31 HIS32 VAL33 CYS34 LEU35 ILE36 ASN37 ALA38 THR39 ALA40 THR41 GLY42 THR43 GLU44 ILE45 LEU46 LYS47 ASN48 LEU49 VAL50 LEU51 PRO52 GLY53 ILE54 GLY55 SER56 PHE57 THR58 ILE59 ILE60 ASP61 GLY62 ASN63 GLN64 VAL65 SER66 GLY67 GLU68 ASP69 ALA70 GLY71 ASN72 ASN73 PHE74 PHE75 LEU76 GLN77 ARG78 SER79 SER80 ILE81 GLY82 LYS83 ASN84 ARG85 ALA86 GLU87 ALA88 ALA89 MET90 GLU91 PHE92 LEU93 GLN94 GLU95 LEU96 ASN97 SER98 ASP99 VAL100 SER101 GLY102 SER103 PHE104 VAL105 GLU106 GLU107 SER108 PRO109 GLU110 ASN111 LEU112 LEU113 ASP114 ASN115 ASP116 PRO117 SER118 PHE119 PHE120 CYS121 ARG122 PHE123 THR124 VAL125 VAL126 VAL127 ALA128 THR129 GLN130 LEU131 PRO132 GLU133 SER134 THR135 SER136 LEU137 ARG138 LEU139 ALA140 ASP141 VAL142 LEU143 TRP144 ASN145 SER146 GLN147 ILE148 PRO149 LEU150 LEU151 ILE152 CYS153 ARG154 THR155 TYR156 GLY157 LEU158 VAL159 GLY160 TYR161 MET162 ARG163 ILE164 ILE165 ILE166 LYS167 GLU168 HIS169 PRO170 VAL171 ILE172 GLU173 SER174 HIS175 PRO176 ASP177 ASN178 ALA179 LEU180 GLU181 ASP182 LEU183 ARG184 LEU185 ASP186 LYS187 PRO188 PHE189 PRO190 GLU191 LEU192 ARG193 GLU194 HIS195 PHE196 GLN197 SER198 TYR199 ASP200 LEU201 ASP202 HIS203 MET204 GLU205 LYS206 LYS207 ASP208 HIS209 SER210 HIS211 THR212 PRO213 TRP214 ILE215 VAL216 ILE217 ILE218 ALA219 LYS220 TYR221 LEU222 ALA223 GLN224 TRP225 TYR226 SER227 GLU228 THR229 ASN230 GLY231 ARG232 ILE233 PRO234 LYS235 THR236 TYR237 LYS238 GLU239 LYS240 GLU241 ASP242 PHE243 ARG244 ASP245 LEU246 ILE247 ARG248 GLN249 GLY250 ILE251 LEU252 LYS253 ASN254 GLU255 ASN256 GLY257 ALA258 PRO259 GLU260 ASP261 GLU262 GLU263 ASN264 PHE265 GLU266 GLU267 ALA268 ILE269 LYS270 ASN271 VAL272 ASN273 THR274 ALA275 LEU276 ASN277 THR278 THR279 GLN280 ILE281 PRO282 SER283 SER284 ILE285 GLU286 ASP287 ILE288 PHE289 ASN290 ASP291 ASP292 ARG293 CYS294 ILE295 ASN296 ILE297 THR298 LYS299 GLN300 THR301 PRO302 SER303 PHE304 TRP305 ILE306 LEU307 ALA308 ARG309 ALA310 LEU311 LYS312 GLU313 PHE314 VAL315 ALA316 LYS317 GLU318 GLY319 GLN320 GLY321 ASN322 LEU323 PRO324 VAL325 ARG326 GLY327 THR328 ILE329 PRO330 ASP331 MET332 ILE333 ALA334 ASP335 SER336 GLY337 LYS338 TYR339 ILE340 LYS341 LEU342 GLN343 ASN344 VAL345 TYR346 ARG347 GLU348 LYS349 ALA350 LYS351 LYS352 ASP353 ALA354 ALA355 ALA356 VAL357 GLY358 ASN359 HIS360 VAL361 ALA362 LYS363 LEU364 LEU365 GLN366 SER367 ILE368 GLY369 GLN370 ALA371 PRO372 GLU373 SER374 ILE375 SER376 GLU377 LYS378 GLU379 LEU380 LYS381 LEU382 LEU383 CYS384 SER385 ASN386 SER387 ALA388 PHE389 LEU390 ARG391 VAL392 VAL393 ARG394 CYS395 ARG396 SER397 LEU398 ALA399 GLU400 GLU401 TYR402 GLY403 LEU404 ASP405 THR406 ILE407 ASN408 LYS409 ASP410 GLU411 ILE412 ILE413 SER414 SER415 MET416 ASP417 ASN418 PRO419 ASP420 ASN421 GLU422 ILE423 VAL424 LEU425 TYR426 LEU427 MET428 LEU429 ARG430 ALA431 VAL432 ASP433 ARG434 PHE435 HIS436 LYS437 GLN438 GLN439 GLY440 ARG441 TYR442 PRO443 GLY444 VAL445 SER446 ASN447 TYR448 GLN449 VAL450 GLU451 GLU452 ASP453 ILE454 GLY455 LYS456 LEU457 LYS458 SER459 CYS460 LEU461 THR462 GLY463 PHE464 LEU465 GLN466 GLU467 TYR468 GLY469 LEU470 SER471 VAL472 MET473 VAL474 LYS475 ASP476 ASP477 TYR478 VAL479 HIS480 GLU481 PHE482 CYS483 ARG484 TYR485 GLY486 ALA487 ALA488 GLU489 PRO490 HIS491 THR492 ILE493 ALA494 ALA495 PHE496 LEU497 GLY498 GLY499 ALA500 ALA501 ALA502 GLN503 GLU504 VAL505 ILE506 LYS507 ILE508 ILE509 THR510 LYS511 GLN512 PHE513 VAL514 ILE515 PHE516 ASN517 ASN518 THR519 TYR520 ILE521 TYR522 SER523 GLY524 MET525 SER526 GLN527 THR528 SER529 ALA530 THR531 PHE532 GLN533 LEU534
Unit 4 HIS19 VAL20 LYS21 LYS22 PHE23 LEU24 GLU25 ARG26 SER27 GLY28 PRO29 PHE30 THR31 HIS32 PRO33 ASP34 PHE35 GLU36 PRO37 SER38 THR39 GLU40 SER41 LEU42 GLN43 PHE44 LEU45 LEU46 ASP47 THR48 CYS49 LYS50 VAL51 LEU52 VAL53 ILE54 GLY55 ALA56 GLY57 GLY58 LEU59 GLY60 CYS61 GLU62 LEU63 LEU64 LYS65 ASN66 LEU67 ALA68 LEU69 SER70 GLY71 PHE72 ARG73 GLN74 ILE75 HIS76 VAL77 ILE78 ASP79 MET80 ASP81 THR82 ILE83 ASP84 VAL85 SER86 ASN87 LEU88 ASN89 ARG90 GLN91 PHE92 LEU93 PHE94 ARG95 PRO96 LYS97 ASP98 ILE99 GLY100 ARG101 PRO102 LYS103 ALA104 GLU105 VAL106 ALA107 ALA108 GLU109 PHE110 LEU111 ASN112 ASP113 ARG114 VAL115 PRO116 ASN117 CYS118 ASN119 VAL120 VAL121 PRO122 HIS123 PHE124 ASN125 LYS126 ILE127 GLN128 ASP129 PHE130 ASN131 ASP132 THR133 PHE134 TYR135 ARG136 GLN137 PHE138 HIS139 ILE140 ILE141 VAL142 CYS143 GLY144 LEU145 ASP146 SER147 ILE148 ILE149 ALA150 ARG151 ARG152 TRP153 ILE154 ASN155 GLY156 MET157 LEU158 ILE159 SER160 LEU161 LEU162 ASN163 TYR164 GLU165 ASP166 GLY167 VAL168 LEU169 ASP170 PRO171 SER172 SER173 ILE174 VAL175 PRO176 LEU177 ILE178 ASP179 GLY180 GLY181 THR182 GLU183 GLY184 PHE185 LYS186 GLY187 ASN188 ALA189 ARG190 VAL191 ILE192 LEU193 PRO194 GLY195 MET196 THR197 ALA198 CYS199 ILE200 GLU201 CYS202 THR203 LEU204 GLU205 LEU206 TYR207 PRO208 PRO209 GLN210 VAL211 ASN212 PHE213 PRO214 MET215 CYS216 THR217 ILE218 ALA219 SER220 MET221 PRO222 ARG223 LEU224 PRO225 GLU226 HIS227 CYS228 ILE229 GLU230 TYR231 VAL232 ARG233 MET234 LEU235 GLN236 TRP237 PRO238 LYS239 GLU240 GLN241 PRO242 PHE243 GLY244 GLU245 GLY246 VAL247 PRO248 LEU249 ASP250 GLY251 ASP252 ASP253 PRO254 GLU255 HIS256 ILE257 GLN258 TRP259 ILE260 PHE261 GLN262 LYS263 SER264 LEU265 GLU266 ARG267 ALA268 SER269 GLN270 TYR271 ASN272 ILE273 ARG274 GLY275 VAL276 THR277 TYR278 ARG279 LEU280 THR281 GLN282 GLY283 VAL284 VAL285 LYS286 ARG287 ILE288 ILE289 PRO290 ALA291 VAL292 ALA293 SER294 THR295 ASN296 ALA297 VAL298 ILE299 ALA300 ALA301 VAL302 CYS303 ALA304 THR305 GLU306 VAL307 PHE308 LYS309 ILE310 ALA311 THR312 SER313 ALA314 TYR315 ILE316 PRO317 LEU318 ASN319 ASN320 TYR321 LEU322 VAL323 PHE324 ASN325 ASP326 VAL327 ASP328 GLY329 LEU330 TYR331 THR332 TYR333 THR334 PHE335 GLU336 ALA337 GLU338 ARG339 LYS340 GLU341 ASN342 CYS343 PRO344 ALA345 CYS346 SER347 GLN348 LEU349 PRO350 GLN351 ASN352 ILE353 GLN354 LEU361 GLN362 GLU363 VAL364 LEU365 ASP366 TYR367 LEU368 THR369 ASN370 SER371 ALA372 SER373 LEU374 GLN375 MET376 LYS377 SER378 PRO379 ALA380 ILE381 THR382 ASN389 ARG390 THR391 LEU392 TYR393 LEU394 GLN395 SER396 THR398 SER399 ILE400 GLU401 VAL425 ALA426 ASP427 VAL428 THR429 THR430 PRO431 GLN432 THR433 VAL434 LEU435 PHE436
Ligands
Unit 5 ZN443
Unit 6 ZN443
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany