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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF PEMBROLIZUMAB, A FULL LENGTH IGG4 ANTIB
Keywords CANCER, ANTIBODY, SUBCLASSES, IGG4, MELANOMA, IMMUNE SYSTEM
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   5DK3     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   LIGHT CHAIN  A 218 1668 0
2  Protein   HEAVY CHAIN  B 441 3344 0
3  Protein   LIGHT CHAIN  F 218 1638 0
4  Protein   HEAVY CHAIN  G 438 3350 0
5  Ligand    C 7 0 89
6  Ligand    D 7 0 85
7  Ligand    E 2 0 23
8  Ligand    H 2 0 23
9  Ligand    I 2 0 23
10  Ligand   LIGHT CHAIN  A 1 0 5
11  Ligand   HEAVY CHAIN  B 4 0 20
12 Water     481 0 481
total       1821 10000 749
Proteins
Unit 1 GLU1 ILE2 VAL3 LEU4 THR5 GLN6 SER7 PRO8 ALA9 THR10 LEU11 SER12 LEU13 SER14 PRO15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 LYS27 GLY28 VAL29 SER30 THR31 SER32 GLY33 TYR34 SER35 TYR36 LEU37 HIS38 TRP39 TYR40 GLN41 GLN42 LYS43 PRO44 GLY45 GLN46 ALA47 PRO48 ARG49 LEU50 LEU51 ILE52 TYR53 LEU54 ALA55 SER56 TYR57 LEU58 GLU59 SER60 GLY61 VAL62 PRO63 ALA64 ARG65 PHE66 SER67 GLY68 SER69 GLY70 SER71 GLY72 THR73 ASP74 PHE75 THR76 LEU77 THR78 ILE79 SER80 SER81 LEU82 GLU83 PRO84 GLU85 ASP86 PHE87 ALA88 VAL89 TYR90 TYR91 CYS92 GLN93 HIS94 SER95 ARG96 ASP97 LEU98 PRO99 LEU100 THR101 PHE102 GLY103 GLY104 GLY105 THR106 LYS107 VAL108 GLU109 ILE110 LYS111 ARG112 THR113 VAL114 ALA115 ALA116 PRO117 SER118 VAL119 PHE120 ILE121 PHE122 PRO123 PRO124 SER125 ASP126 GLU127 GLN128 LEU129 LYS130 SER131 GLY132 THR133 ALA134 SER135 VAL136 VAL137 CYS138 LEU139 LEU140 ASN141 ASN142 PHE143 TYR144 PRO145 ARG146 GLU147 ALA148 LYS149 VAL150 GLN151 TRP152 LYS153 VAL154 ASP155 ASN156 ALA157 LEU158 GLN159 SER160 GLY161 ASN162 SER163 GLN164 GLU165 SER166 VAL167 THR168 GLU169 GLN170 ASP171 SER172 LYS173 ASP174 SER175 THR176 TYR177 SER178 LEU179 SER180 SER181 THR182 LEU183 THR184 LEU185 SER186 LYS187 ALA188 ASP189 TYR190 GLU191 LYS192 HIS193 LYS194 VAL195 TYR196 ALA197 CYS198 GLU199 VAL200 THR201 HIS202 GLN203 GLY204 LEU205 SER206 SER207 PRO208 VAL209 THR210 LYS211 SER212 PHE213 ASN214 ARG215 GLY216 GLU217 CYS218
Unit 2 GLN1 VAL2 GLN3 LEU4 VAL5 GLN6 SER7 GLY8 VAL9 GLU10 VAL11 LYS12 LYS13 PRO14 GLY15 ALA16 SER17 VAL18 LYS19 VAL20 SER21 CYS22 LYS23 ALA24 SER25 GLY26 TYR27 THR28 PHE29 THR30 ASN31 TYR32 TYR33 MET34 TYR35 TRP36 VAL37 ARG38 GLN39 ALA40 PRO41 GLY42 GLN43 GLY44 LEU45 GLU46 TRP47 MET48 GLY49 GLY50 ILE51 ASN52 PRO53 SER54 ASN55 GLY56 GLY57 THR58 ASN59 PHE60 ASN61 GLU62 LYS63 PHE64 LYS65 ASN66 ARG67 VAL68 THR69 LEU70 THR71 THR72 ASP73 SER74 SER75 THR76 THR77 THR78 ALA79 TYR80 MET81 GLU82 LEU83 LYS84 SER85 LEU86 GLN87 PHE88 ASP89 ASP90 THR91 ALA92 VAL93 TYR94 TYR95 CYS96 ALA97 ARG98 ARG99 ASP100 TYR101 ARG102 PHE103 ASP104 MET105 GLY106 PHE107 ASP108 TYR109 TRP110 GLY111 GLN112 GLY113 THR114 THR115 VAL116 THR117 VAL118 SER119 SER120 ALA121 SER122 THR123 LYS124 GLY125 PRO126 SER127 VAL128 PHE129 PRO130 LEU131 ALA132 PRO133 CYS134 SER135 ARG136 SER137 THR138 SER139 GLU140 SER141 THR142 ALA143 ALA144 LEU145 GLY146 CYS147 LEU148 VAL149 LYS150 ASP151 TYR152 PHE153 PRO154 GLU155 PRO156 VAL157 THR158 VAL159 SER160 TRP161 ASN162 SER163 GLY164 ALA165 LEU166 THR167 SER168 GLY169 VAL170 HIS171 THR172 PHE173 PRO174 ALA175 VAL176 LEU177 GLN178 SER179 SER180 GLY181 LEU182 TYR183 SER184 LEU185 SER186 SER187 VAL188 VAL189 THR190 VAL191 PRO192 SER193 SER194 SER195 LEU196 GLY197 THR198 LYS199 THR200 TYR201 THR202 CYS203 ASN204 VAL205 ASP206 HIS207 LYS208 PRO209 SER210 ASN211 THR212 LYS213 VAL214 ASP215 LYS216 ARG217 VAL218 GLU219 SER220 LYS221 TYR222 GLY223 PRO224 PRO225 CYS226 PRO227 PRO228 CYS229 GLU233 PHE234 LEU235 GLY236 GLY237 PRO238 SER239 VAL240 PHE241 LEU242 PHE243 PRO244 PRO245 LYS246 PRO247 LYS248 ASP249 THR250 LEU251 MET252 ILE253 SER254 ARG255 THR256 PRO257 GLU258 VAL259 THR260 CYS261 VAL262 VAL263 VAL264 ASP265 VAL266 SER267 GLN268 GLU269 ASP270 PRO271 GLU272 VAL273 GLN274 PHE275 ASN276 TRP277 TYR278 VAL279 ASP280 GLY281 VAL282 GLU283 VAL284 HIS285 ASN286 ALA287 LYS288 THR289 LYS290 PRO291 ARG292 GLU293 GLU294 GLN295 PHE296 ASN297 SER298 THR299 TYR300 ARG301 VAL302 VAL303 SER304 VAL305 LEU306 THR307 VAL308 LEU309 HIS310 GLN311 ASP312 TRP313 LEU314 ASN315 GLY316 LYS317 GLU318 TYR319 LYS320 CYS321 LYS322 VAL323 SER324 ASN325 LYS326 GLY327 LEU328 PRO329 SER330 SER331 ILE332 GLU333 LYS334 THR335 ILE336 SER337 LYS338 ALA339 LYS340 GLY341 GLN342 PRO343 ARG344 GLU345 PRO346 GLN347 VAL348 TYR349 THR350 LEU351 PRO352 PRO353 SER354 GLN355 GLU356 GLU357 MET358 THR359 LYS360 ASN361 GLN362 VAL363 SER364 LEU365 THR366 CYS367 LEU368 VAL369 LYS370 GLY371 PHE372 TYR373 PRO374 SER375 ASP376 ILE377 ALA378 VAL379 GLU380 TRP381 GLU382 SER383 ASN384 GLY385 GLN386 PRO387 GLU388 ASN389 ASN390 TYR391 LYS392 THR393 THR394 PRO395 PRO396 VAL397 LEU398 ASP399 SER400 ASP401 GLY402 SER403 PHE404 PHE405 LEU406 TYR407 SER408 ARG409 LEU410 THR411 VAL412 ASP413 LYS414 SER415 ARG416 TRP417 GLN418 GLN419 GLY420 ASN421 VAL422 PHE423 SER424 CYS425 SER426 VAL427 MET428 HIS429 GLU430 ALA431 LEU432 HIS433 ASN434 HIS435 TYR436 THR437 GLN438 LYS439 SER440 LEU441 SER442 LEU443 SER444
Unit 3 GLU1 ILE2 VAL3 LEU4 THR5 GLN6 SER7 PRO8 ALA9 THR10 LEU11 SER12 LEU13 SER14 PRO15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 LYS27 GLY28 VAL29 SER30 THR31 SER32 GLY33 TYR34 SER35 TYR36 LEU37 HIS38 TRP39 TYR40 GLN41 GLN42 LYS43 PRO44 GLY45 GLN46 ALA47 PRO48 ARG49 LEU50 LEU51 ILE52 TYR53 LEU54 ALA55 SER56 TYR57 LEU58 GLU59 SER60 GLY61 VAL62 PRO63 ALA64 ARG65 PHE66 SER67 GLY68 SER69 GLY70 SER71 GLY72 THR73 ASP74 PHE75 THR76 LEU77 THR78 ILE79 SER80 SER81 LEU82 GLU83 PRO84 GLU85 ASP86 PHE87 ALA88 VAL89 TYR90 TYR91 CYS92 GLN93 HIS94 SER95 ARG96 ASP97 LEU98 PRO99 LEU100 THR101 PHE102 GLY103 GLY104 GLY105 THR106 LYS107 VAL108 GLU109 ILE110 LYS111 ARG112 THR113 VAL114 ALA115 ALA116 PRO117 SER118 VAL119 PHE120 ILE121 PHE122 PRO123 PRO124 SER125 ASP126 GLU127 GLN128 LEU129 LYS130 SER131 GLY132 THR133 ALA134 SER135 VAL136 VAL137 CYS138 LEU139 LEU140 ASN141 ASN142 PHE143 TYR144 PRO145 ARG146 GLU147 ALA148 LYS149 VAL150 GLN151 TRP152 LYS153 VAL154 ASP155 ASN156 ALA157 LEU158 GLN159 SER160 GLY161 ASN162 SER163 GLN164 GLU165 SER166 VAL167 THR168 GLU169 GLN170 ASP171 SER172 LYS173 ASP174 SER175 THR176 TYR177 SER178 LEU179 SER180 SER181 THR182 LEU183 THR184 LEU185 SER186 LYS187 ALA188 ASP189 TYR190 GLU191 LYS192 HIS193 LYS194 VAL195 TYR196 ALA197 CYS198 GLU199 VAL200 THR201 HIS202 GLN203 GLY204 LEU205 SER206 SER207 PRO208 VAL209 THR210 LYS211 SER212 PHE213 ASN214 ARG215 GLY216 GLU217 CYS218
Unit 4 GLN1 VAL2 GLN3 LEU4 VAL5 GLN6 SER7 GLY8 VAL9 GLU10 VAL11 LYS12 LYS13 PRO14 GLY15 ALA16 SER17 VAL18 LYS19 VAL20 SER21 CYS22 LYS23 ALA24 SER25 GLY26 TYR27 THR28 PHE29 THR30 ASN31 TYR32 TYR33 MET34 TYR35 TRP36 VAL37 ARG38 GLN39 ALA40 PRO41 GLY42 GLN43 GLY44 LEU45 GLU46 TRP47 MET48 GLY49 GLY50 ILE51 ASN52 PRO53 SER54 ASN55 GLY56 GLY57 THR58 ASN59 PHE60 ASN61 GLU62 LYS63 PHE64 LYS65 ASN66 ARG67 VAL68 THR69 LEU70 THR71 THR72 ASP73 SER74 SER75 THR76 THR77 THR78 ALA79 TYR80 MET81 GLU82 LEU83 LYS84 SER85 LEU86 GLN87 PHE88 ASP89 ASP90 THR91 ALA92 VAL93 TYR94 TYR95 CYS96 ALA97 ARG98 ARG99 ASP100 TYR101 ARG102 PHE103 ASP104 MET105 GLY106 PHE107 ASP108 TYR109 TRP110 GLY111 GLN112 GLY113 THR114 THR115 VAL116 THR117 VAL118 SER119 SER120 ALA121 SER122 THR123 LYS124 GLY125 PRO126 SER127 VAL128 PHE129 PRO130 LEU131 ALA132 PRO133 CYS134 SER135 ARG136 SER137 THR138 SER139 GLU140 SER141 THR142 ALA143 ALA144 LEU145 GLY146 CYS147 LEU148 VAL149 LYS150 ASP151 TYR152 PHE153 PRO154 GLU155 PRO156 VAL157 THR158 VAL159 SER160 TRP161 ASN162 SER163 GLY164 ALA165 LEU166 THR167 SER168 GLY169 VAL170 HIS171 THR172 PHE173 PRO174 ALA175 VAL176 LEU177 GLN178 SER179 SER180 GLY181 LEU182 TYR183 SER184 LEU185 SER186 SER187 VAL188 VAL189 THR190 VAL191 PRO192 SER193 SER194 SER195 LEU196 GLY197 THR198 LYS199 THR200 TYR201 THR202 CYS203 ASN204 VAL205 ASP206 HIS207 LYS208 PRO209 SER210 ASN211 THR212 LYS213 VAL214 ASP215 LYS216 ARG217 VAL218 GLU219 SER220 LYS221 TYR222 GLY223 PRO224 PRO225 CYS226 PRO227 PRO228 CYS229 GLY236 GLY237 PRO238 SER239 VAL240 PHE241 LEU242 PHE243 PRO244 PRO245 LYS246 PRO247 LYS248 ASP249 THR250 LEU251 MET252 ILE253 SER254 ARG255 THR256 PRO257 GLU258 VAL259 THR260 CYS261 VAL262 VAL263 VAL264 ASP265 VAL266 SER267 GLN268 GLU269 ASP270 PRO271 GLU272 VAL273 GLN274 PHE275 ASN276 TRP277 TYR278 VAL279 ASP280 GLY281 VAL282 GLU283 VAL284 HIS285 ASN286 ALA287 LYS288 THR289 LYS290 PRO291 ARG292 GLU293 GLU294 GLN295 PHE296 ASN297 SER298 THR299 TYR300 ARG301 VAL302 VAL303 SER304 VAL305 LEU306 THR307 VAL308 LEU309 HIS310 GLN311 ASP312 TRP313 LEU314 ASN315 GLY316 LYS317 GLU318 TYR319 LYS320 CYS321 LYS322 VAL323 SER324 ASN325 LYS326 GLY327 LEU328 PRO329 SER330 SER331 ILE332 GLU333 LYS334 THR335 ILE336 SER337 LYS338 ALA339 LYS340 GLY341 GLN342 PRO343 ARG344 GLU345 PRO346 GLN347 VAL348 TYR349 THR350 LEU351 PRO352 PRO353 SER354 GLN355 GLU356 GLU357 MET358 THR359 LYS360 ASN361 GLN362 VAL363 SER364 LEU365 THR366 CYS367 LEU368 VAL369 LYS370 GLY371 PHE372 TYR373 PRO374 SER375 ASP376 ILE377 ALA378 VAL379 GLU380 TRP381 GLU382 SER383 ASN384 GLY385 GLN386 PRO387 GLU388 ASN389 ASN390 TYR391 LYS392 THR393 THR394 PRO395 PRO396 VAL397 LEU398 ASP399 SER400 ASP401 GLY402 SER403 PHE404 PHE405 LEU406 TYR407 SER408 ARG409 LEU410 THR411 VAL412 ASP413 LYS414 SER415 ARG416 TRP417 GLN418 GLN419 GLY420 ASN421 VAL422 PHE423 SER424 CYS425 SER426 VAL427 MET428 HIS429 GLU430 ALA431 LEU432 HIS433 ASN434 HIS435 TYR436 THR437 GLN438 LYS439 SER440 LEU441 SER442 LEU443 SER444
Ligands
Unit 5 NAG1 NAG2 BMA3 MAN4 NAG5 MAN6 NAG7
Unit 6 NAG1 NAG2 BMA3 MAN4 NAG5 MAN6 FUC7
Unit 7 GLC1 FRU2
Unit 8 GLC1 FRU2
Unit 9 GLC1 FRU2
Unit 10 SO4301
Unit 11 SO4501 SO4502 SO4503 SO4504
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany