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Sequence, Chains, Asymmetric and Biological Units

Title POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXA
Keywords VIRUS COAT PROTEIN, OLIGOSACCHARIDE BINDING, VIRUS ASSEMBLY, ACID, VIRAL PROTEIN
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   1VPS     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   POLYOMAVIRUS VP1 PENTAMER  A 285 2220 0
2  Protein   POLYOMAVIRUS VP1 PENTAMER  B 289 2254 0
3  Protein   POLYOMAVIRUS VP1 PENTAMER  C 285 2220 0
4  Protein   POLYOMAVIRUS VP1 PENTAMER  D 285 2220 0
5  Protein   POLYOMAVIRUS VP1 PENTAMER  E 285 2220 0
6  Ligand    F 4 0 66
7  Ligand    G 4 0 66
8  Ligand    H 4 0 66
9  Ligand    I 4 0 66
10  Ligand    J 4 0 66
11 Water     2127 0 2127
total       3576 11134 2457
Proteins
Unit 1 GLY32 GLY33 MET34 GLU35 VAL36 LEU37 ASP38 LEU39 VAL40 THR41 GLY42 PRO43 ASP44 SER45 VAL46 THR47 GLU48 ILE49 GLU50 ALA51 PHE52 LEU53 ASN54 PRO55 ARG56 MET57 GLY58 GLN59 PRO60 PRO61 THR62 PRO63 GLU64 SER65 LEU66 THR67 GLU68 GLY69 GLY70 GLN71 TYR72 TYR73 GLY74 TRP75 SER76 ARG77 GLY78 ILE79 ASN80 LEU81 ALA82 THR83 SER84 ASP85 THR86 GLU87 ASP88 SER89 PRO90 GLY91 ASN92 ASN93 THR94 LEU95 PRO96 THR97 TRP98 SER99 MET100 ALA101 LYS102 LEU103 GLN104 LEU105 PRO106 MET107 LEU108 ASN109 GLU110 ASP111 LEU112 THR113 CYS114 ASP115 THR116 LEU117 GLN118 MET119 TRP120 GLU121 ALA122 VAL123 SER124 VAL125 LYS126 THR127 GLU128 VAL129 VAL130 GLY131 SER132 GLY133 SER134 LEU135 LEU136 ASP137 VAL138 HIS139 GLY140 PHE141 ASN142 LYS143 PRO144 THR145 ASP146 THR147 VAL148 ASN149 THR150 LYS151 GLY152 ILE153 SER154 THR155 PRO156 VAL157 GLU158 GLY159 SER160 GLN161 TYR162 HIS163 VAL164 PHE165 ALA166 VAL167 GLY168 GLY169 GLU170 PRO171 LEU172 ASP173 LEU174 GLN175 GLY176 LEU177 VAL178 THR179 ASP180 ALA181 ARG182 THR183 LYS184 TYR185 LYS186 GLU187 GLU188 GLY189 VAL190 VAL191 THR192 ILE193 LYS194 THR195 ILE196 THR197 LYS198 LYS199 ASP200 MET201 VAL202 ASN203 LYS204 ASP205 GLN206 VAL207 LEU208 ASN209 PRO210 ILE211 SER212 LYS213 ALA214 LYS215 LEU216 ASP217 LYS218 ASP219 GLY220 MET221 TYR222 PRO223 VAL224 GLU225 ILE226 TRP227 HIS228 PRO229 ASP230 PRO231 ALA232 LYS233 ASN234 GLU235 ASN236 THR237 ARG238 TYR239 PHE240 GLY241 ASN242 TYR243 THR244 GLY245 GLY246 THR247 THR248 THR249 PRO250 PRO251 VAL252 LEU253 GLN254 PHE255 THR256 ASN257 THR258 LEU259 THR260 THR261 VAL262 LEU263 LEU264 ASP265 GLU266 ASN267 GLY268 VAL269 GLY270 PRO271 LEU272 CYS273 LYS274 GLY275 GLU276 GLY277 LEU278 TYR279 LEU280 SER281 CYS282 VAL283 ASP284 ILE285 MET286 GLY287 TRP288 ARG289 VAL290 THR291 ARG292 ASN293 TYR294 ASP295 VAL296 HIS297 HIS298 TRP299 ARG300 GLY301 LEU302 PRO303 ARG304 TYR305 PHE306 LYS307 ILE308 THR309 LEU310 ARG311 LYS312 ARG313 TRP314 VAL315 LYS316
Unit 2 GLY32 GLY33 MET34 GLU35 VAL36 LEU37 ASP38 LEU39 VAL40 THR41 GLY42 PRO43 ASP44 SER45 VAL46 THR47 GLU48 ILE49 GLU50 ALA51 PHE52 LEU53 ASN54 PRO55 ARG56 MET57 GLY58 GLN59 PRO60 PRO61 THR62 PRO63 GLU64 SER65 LEU66 THR67 GLU68 GLY69 GLY70 GLN71 TYR72 TYR73 GLY74 TRP75 SER76 ARG77 GLY78 ILE79 ASN80 LEU81 ALA82 THR83 SER84 ASP85 THR86 GLU87 ASP88 SER89 PRO90 GLY91 ASN92 ASN93 THR94 LEU95 PRO96 THR97 TRP98 SER99 MET100 ALA101 LYS102 LEU103 GLN104 LEU105 PRO106 MET107 LEU108 ASN109 GLU110 ASP111 LEU112 THR113 CYS114 ASP115 THR116 LEU117 GLN118 MET119 TRP120 GLU121 ALA122 VAL123 SER124 VAL125 LYS126 THR127 GLU128 VAL129 VAL130 GLY131 SER132 GLY133 SER134 LEU135 LEU136 ASP137 VAL138 HIS139 GLY140 PHE141 ASN142 LYS143 PRO144 THR145 ASP146 THR147 VAL148 ASN149 THR150 LYS151 GLY152 ILE153 SER154 THR155 PRO156 VAL157 GLU158 GLY159 SER160 GLN161 TYR162 HIS163 VAL164 PHE165 ALA166 VAL167 GLY168 GLY169 GLU170 PRO171 LEU172 ASP173 LEU174 GLN175 GLY176 LEU177 VAL178 THR179 ASP180 ALA181 ARG182 THR183 LYS184 TYR185 LYS186 GLU187 GLU188 GLY189 VAL190 VAL191 THR192 ILE193 LYS194 THR195 ILE196 THR197 LYS198 LYS199 ASP200 MET201 VAL202 ASN203 LYS204 ASP205 GLN206 VAL207 LEU208 ASN209 PRO210 ILE211 SER212 LYS213 ALA214 LYS215 LEU216 ASP217 LYS218 ASP219 GLY220 MET221 TYR222 PRO223 VAL224 GLU225 ILE226 TRP227 HIS228 PRO229 ASP230 PRO231 ALA232 LYS233 ASN234 GLU235 ASN236 THR237 ARG238 TYR239 PHE240 GLY241 ASN242 TYR243 THR244 GLY245 GLY246 THR247 THR248 THR249 PRO250 PRO251 VAL252 LEU253 GLN254 PHE255 THR256 ASN257 THR258 LEU259 THR260 THR261 VAL262 LEU263 LEU264 ASP265 GLU266 ASN267 GLY268 VAL269 GLY270 PRO271 LEU272 CYS273 LYS274 GLY275 GLU276 GLY277 LEU278 TYR279 LEU280 SER281 CYS282 VAL283 ASP284 ILE285 MET286 GLY287 TRP288 ARG289 VAL290 THR291 ARG292 ASN293 TYR294 ASP295 VAL296 HIS297 HIS298 TRP299 ARG300 GLY301 LEU302 PRO303 ARG304 TYR305 PHE306 LYS307 ILE308 THR309 LEU310 ARG311 LYS312 ARG313 TRP314 VAL315 LYS316 ASN317 PRO318 TYR319 PRO320
Unit 3 GLY32 GLY33 MET34 GLU35 VAL36 LEU37 ASP38 LEU39 VAL40 THR41 GLY42 PRO43 ASP44 SER45 VAL46 THR47 GLU48 ILE49 GLU50 ALA51 PHE52 LEU53 ASN54 PRO55 ARG56 MET57 GLY58 GLN59 PRO60 PRO61 THR62 PRO63 GLU64 SER65 LEU66 THR67 GLU68 GLY69 GLY70 GLN71 TYR72 TYR73 GLY74 TRP75 SER76 ARG77 GLY78 ILE79 ASN80 LEU81 ALA82 THR83 SER84 ASP85 THR86 GLU87 ASP88 SER89 PRO90 GLY91 ASN92 ASN93 THR94 LEU95 PRO96 THR97 TRP98 SER99 MET100 ALA101 LYS102 LEU103 GLN104 LEU105 PRO106 MET107 LEU108 ASN109 GLU110 ASP111 LEU112 THR113 CYS114 ASP115 THR116 LEU117 GLN118 MET119 TRP120 GLU121 ALA122 VAL123 SER124 VAL125 LYS126 THR127 GLU128 VAL129 VAL130 GLY131 SER132 GLY133 SER134 LEU135 LEU136 ASP137 VAL138 HIS139 GLY140 PHE141 ASN142 LYS143 PRO144 THR145 ASP146 THR147 VAL148 ASN149 THR150 LYS151 GLY152 ILE153 SER154 THR155 PRO156 VAL157 GLU158 GLY159 SER160 GLN161 TYR162 HIS163 VAL164 PHE165 ALA166 VAL167 GLY168 GLY169 GLU170 PRO171 LEU172 ASP173 LEU174 GLN175 GLY176 LEU177 VAL178 THR179 ASP180 ALA181 ARG182 THR183 LYS184 TYR185 LYS186 GLU187 GLU188 GLY189 VAL190 VAL191 THR192 ILE193 LYS194 THR195 ILE196 THR197 LYS198 LYS199 ASP200 MET201 VAL202 ASN203 LYS204 ASP205 GLN206 VAL207 LEU208 ASN209 PRO210 ILE211 SER212 LYS213 ALA214 LYS215 LEU216 ASP217 LYS218 ASP219 GLY220 MET221 TYR222 PRO223 VAL224 GLU225 ILE226 TRP227 HIS228 PRO229 ASP230 PRO231 ALA232 LYS233 ASN234 GLU235 ASN236 THR237 ARG238 TYR239 PHE240 GLY241 ASN242 TYR243 THR244 GLY245 GLY246 THR247 THR248 THR249 PRO250 PRO251 VAL252 LEU253 GLN254 PHE255 THR256 ASN257 THR258 LEU259 THR260 THR261 VAL262 LEU263 LEU264 ASP265 GLU266 ASN267 GLY268 VAL269 GLY270 PRO271 LEU272 CYS273 LYS274 GLY275 GLU276 GLY277 LEU278 TYR279 LEU280 SER281 CYS282 VAL283 ASP284 ILE285 MET286 GLY287 TRP288 ARG289 VAL290 THR291 ARG292 ASN293 TYR294 ASP295 VAL296 HIS297 HIS298 TRP299 ARG300 GLY301 LEU302 PRO303 ARG304 TYR305 PHE306 LYS307 ILE308 THR309 LEU310 ARG311 LYS312 ARG313 TRP314 VAL315 LYS316
Unit 4 GLY32 GLY33 MET34 GLU35 VAL36 LEU37 ASP38 LEU39 VAL40 THR41 GLY42 PRO43 ASP44 SER45 VAL46 THR47 GLU48 ILE49 GLU50 ALA51 PHE52 LEU53 ASN54 PRO55 ARG56 MET57 GLY58 GLN59 PRO60 PRO61 THR62 PRO63 GLU64 SER65 LEU66 THR67 GLU68 GLY69 GLY70 GLN71 TYR72 TYR73 GLY74 TRP75 SER76 ARG77 GLY78 ILE79 ASN80 LEU81 ALA82 THR83 SER84 ASP85 THR86 GLU87 ASP88 SER89 PRO90 GLY91 ASN92 ASN93 THR94 LEU95 PRO96 THR97 TRP98 SER99 MET100 ALA101 LYS102 LEU103 GLN104 LEU105 PRO106 MET107 LEU108 ASN109 GLU110 ASP111 LEU112 THR113 CYS114 ASP115 THR116 LEU117 GLN118 MET119 TRP120 GLU121 ALA122 VAL123 SER124 VAL125 LYS126 THR127 GLU128 VAL129 VAL130 GLY131 SER132 GLY133 SER134 LEU135 LEU136 ASP137 VAL138 HIS139 GLY140 PHE141 ASN142 LYS143 PRO144 THR145 ASP146 THR147 VAL148 ASN149 THR150 LYS151 GLY152 ILE153 SER154 THR155 PRO156 VAL157 GLU158 GLY159 SER160 GLN161 TYR162 HIS163 VAL164 PHE165 ALA166 VAL167 GLY168 GLY169 GLU170 PRO171 LEU172 ASP173 LEU174 GLN175 GLY176 LEU177 VAL178 THR179 ASP180 ALA181 ARG182 THR183 LYS184 TYR185 LYS186 GLU187 GLU188 GLY189 VAL190 VAL191 THR192 ILE193 LYS194 THR195 ILE196 THR197 LYS198 LYS199 ASP200 MET201 VAL202 ASN203 LYS204 ASP205 GLN206 VAL207 LEU208 ASN209 PRO210 ILE211 SER212 LYS213 ALA214 LYS215 LEU216 ASP217 LYS218 ASP219 GLY220 MET221 TYR222 PRO223 VAL224 GLU225 ILE226 TRP227 HIS228 PRO229 ASP230 PRO231 ALA232 LYS233 ASN234 GLU235 ASN236 THR237 ARG238 TYR239 PHE240 GLY241 ASN242 TYR243 THR244 GLY245 GLY246 THR247 THR248 THR249 PRO250 PRO251 VAL252 LEU253 GLN254 PHE255 THR256 ASN257 THR258 LEU259 THR260 THR261 VAL262 LEU263 LEU264 ASP265 GLU266 ASN267 GLY268 VAL269 GLY270 PRO271 LEU272 CYS273 LYS274 GLY275 GLU276 GLY277 LEU278 TYR279 LEU280 SER281 CYS282 VAL283 ASP284 ILE285 MET286 GLY287 TRP288 ARG289 VAL290 THR291 ARG292 ASN293 TYR294 ASP295 VAL296 HIS297 HIS298 TRP299 ARG300 GLY301 LEU302 PRO303 ARG304 TYR305 PHE306 LYS307 ILE308 THR309 LEU310 ARG311 LYS312 ARG313 TRP314 VAL315 LYS316
Unit 5 GLY32 GLY33 MET34 GLU35 VAL36 LEU37 ASP38 LEU39 VAL40 THR41 GLY42 PRO43 ASP44 SER45 VAL46 THR47 GLU48 ILE49 GLU50 ALA51 PHE52 LEU53 ASN54 PRO55 ARG56 MET57 GLY58 GLN59 PRO60 PRO61 THR62 PRO63 GLU64 SER65 LEU66 THR67 GLU68 GLY69 GLY70 GLN71 TYR72 TYR73 GLY74 TRP75 SER76 ARG77 GLY78 ILE79 ASN80 LEU81 ALA82 THR83 SER84 ASP85 THR86 GLU87 ASP88 SER89 PRO90 GLY91 ASN92 ASN93 THR94 LEU95 PRO96 THR97 TRP98 SER99 MET100 ALA101 LYS102 LEU103 GLN104 LEU105 PRO106 MET107 LEU108 ASN109 GLU110 ASP111 LEU112 THR113 CYS114 ASP115 THR116 LEU117 GLN118 MET119 TRP120 GLU121 ALA122 VAL123 SER124 VAL125 LYS126 THR127 GLU128 VAL129 VAL130 GLY131 SER132 GLY133 SER134 LEU135 LEU136 ASP137 VAL138 HIS139 GLY140 PHE141 ASN142 LYS143 PRO144 THR145 ASP146 THR147 VAL148 ASN149 THR150 LYS151 GLY152 ILE153 SER154 THR155 PRO156 VAL157 GLU158 GLY159 SER160 GLN161 TYR162 HIS163 VAL164 PHE165 ALA166 VAL167 GLY168 GLY169 GLU170 PRO171 LEU172 ASP173 LEU174 GLN175 GLY176 LEU177 VAL178 THR179 ASP180 ALA181 ARG182 THR183 LYS184 TYR185 LYS186 GLU187 GLU188 GLY189 VAL190 VAL191 THR192 ILE193 LYS194 THR195 ILE196 THR197 LYS198 LYS199 ASP200 MET201 VAL202 ASN203 LYS204 ASP205 GLN206 VAL207 LEU208 ASN209 PRO210 ILE211 SER212 LYS213 ALA214 LYS215 LEU216 ASP217 LYS218 ASP219 GLY220 MET221 TYR222 PRO223 VAL224 GLU225 ILE226 TRP227 HIS228 PRO229 ASP230 PRO231 ALA232 LYS233 ASN234 GLU235 ASN236 THR237 ARG238 TYR239 PHE240 GLY241 ASN242 TYR243 THR244 GLY245 GLY246 THR247 THR248 THR249 PRO250 PRO251 VAL252 LEU253 GLN254 PHE255 THR256 ASN257 THR258 LEU259 THR260 THR261 VAL262 LEU263 LEU264 ASP265 GLU266 ASN267 GLY268 VAL269 GLY270 PRO271 LEU272 CYS273 LYS274 GLY275 GLU276 GLY277 LEU278 TYR279 LEU280 SER281 CYS282 VAL283 ASP284 ILE285 MET286 GLY287 TRP288 ARG289 VAL290 THR291 ARG292 ASN293 TYR294 ASP295 VAL296 HIS297 HIS298 TRP299 ARG300 GLY301 LEU302 PRO303 ARG304 TYR305 PHE306 LYS307 ILE308 THR309 LEU310 ARG311 LYS312 ARG313 TRP314 VAL315 LYS316
Ligands
Unit 6 NAG1 GAL2 SIA3 SIA4
Unit 7 NAG1 GAL2 SIA3 SIA4
Unit 8 NAG1 GAL2 SIA3 SIA4
Unit 9 NAG1 GAL2 SIA3 SIA4
Unit 10 NAG1 GAL2 SIA3 SIA4
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany