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Sequence, Chains, Asymmetric and Biological Units

Title BK POLYOMAVIRUS VP1 PENTAMER IN COMPLEX WITH GD3 OLIGOSACCHA
Keywords ANTIPARALLEL BETA SANDWICH, JELLY-ROLL TOPOLOGY, VIRAL PROTE POLYOMAVIRUS, RECEPTOR-SWITCHING, GLYCAN RECEPTOR, VIRUS MA CAPSID PROTEIN, ATTACHMENT TO HOST-CELL SURFACE RECEPTORS
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   4MJ0     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   VP1 CAPSID PROTEIN  A 265 2028 0
2  Protein   VP1 CAPSID PROTEIN  B 263 2004 0
3  Protein   VP1 CAPSID PROTEIN  C 247 1891 0
4  Protein   VP1 CAPSID PROTEIN  D 267 2048 0
5  Protein   VP1 CAPSID PROTEIN  E 264 2037 0
6  Ligand    F 4 0 63
7  Ligand    G 2 0 41
8  Ligand    H 3 0 52
9  Ligand    I 2 0 41
10  Ligand   VP1 CAPSID PROTEIN  A 2 0 7
11  Ligand   VP1 CAPSID PROTEIN  B 3 0 13
12  Ligand   VP1 CAPSID PROTEIN  C 2 0 7
13  Ligand   VP1 CAPSID PROTEIN  D 2 0 7
14  Ligand   VP1 CAPSID PROTEIN  E 3 0 13
15 Water     1280 0 1280
total       2609 10008 1524
Proteins
Unit 1 VAL32 GLU33 VAL34 LEU35 GLU36 VAL37 LYS38 THR39 GLY40 VAL41 ASP42 ALA43 ILE44 THR45 GLU46 VAL47 GLU48 CYS49 PHE50 LEU51 ASN52 PRO53 GLU54 MET55 GLY56 ASP57 PRO58 ASP59 GLU60 ASN61 LEU62 ARG63 GLY64 PHE65 SER66 LEU67 LYS68 LEU69 SER70 ALA71 GLU72 ASN73 ASP74 PHE75 SER76 SER77 ASP78 SER79 PRO80 GLU81 ARG82 LYS83 MET84 LEU85 PRO86 CYS87 TYR88 SER89 THR90 ALA91 ARG92 ILE93 PRO94 LEU95 PRO96 ASN97 LEU98 ASN99 GLU100 ASP101 LEU102 THR103 CYS104 GLY105 ASN106 LEU107 LEU108 MET109 TRP110 GLU111 ALA112 VAL113 THR114 VAL115 GLN116 THR117 GLU118 VAL119 ILE120 GLY121 ILE122 THR123 SER124 MET125 LEU126 ASN127 LEU128 HIS129 ALA130 GLY131 SER132 GLN133 LYS134 VAL135 HIS136 GLU137 HIS138 GLY139 GLY140 GLY141 LYS142 PRO143 ILE144 GLN145 GLY146 SER147 ASN148 PHE149 HIS150 PHE151 PHE152 ALA153 VAL154 GLY155 GLY156 ASP157 PRO158 LEU159 GLU160 MET161 GLN162 GLY163 VAL164 LEU165 MET166 ASN167 TYR168 ARG169 THR170 LYS171 TYR172 PRO173 ASP174 GLY175 THR176 ILE177 THR178 PRO179 LYS180 ASN181 PRO182 THR183 ALA184 GLN185 SER186 GLN187 VAL188 MET189 ASN190 THR191 ASP192 HIS193 LYS194 ALA195 TYR196 LEU197 ASP198 LYS199 ASN200 ASN201 ALA202 TYR203 PRO204 VAL205 GLU206 CYS207 TRP208 VAL209 PRO210 ASP211 PRO212 SER213 ARG214 ASN215 GLU216 ASN217 THR218 ARG219 TYR220 PHE221 GLY222 THR223 PHE224 THR225 GLY226 GLY227 GLU228 ASN229 VAL230 PRO231 PRO232 VAL233 LEU234 HIS235 VAL236 THR237 ASN238 THR239 ALA240 THR241 THR242 VAL243 LEU244 LEU245 ASP246 GLU247 GLN248 GLY249 VAL250 GLY251 PRO252 LEU253 CYS254 LYS255 ALA256 ASP257 SER258 LEU259 TYR260 VAL261 SER262 ALA263 ALA264 ASP265 ILE266 CYS267 GLY268 LEU269 PHE270 THR271 ASN272 SER273 SER274 GLY275 THR276 GLN277 GLN278 TRP279 ARG280 GLY281 LEU282 ALA283 ARG284 TYR285 PHE286 LYS287 ILE288 ARG289 LEU290 ARG291 LYS292 ARG293 SER294 VAL295 LYS296
Unit 2 GLU33 VAL34 LEU35 GLU36 VAL37 LYS38 THR39 ASP42 ALA43 ILE44 THR45 GLU46 VAL47 GLU48 CYS49 PHE50 LEU51 ASN52 PRO53 GLU54 MET55 GLY56 ASP57 PRO58 ASP59 GLU60 ASN61 LEU62 ARG63 GLY64 PHE65 SER66 LEU67 LYS68 LEU69 SER70 ALA71 GLU72 ASN73 ASP74 PHE75 SER76 SER77 ASP78 SER79 PRO80 GLU81 ARG82 LYS83 MET84 LEU85 PRO86 CYS87 TYR88 SER89 THR90 ALA91 ARG92 ILE93 PRO94 LEU95 PRO96 ASN97 LEU98 ASN99 GLU100 ASP101 LEU102 THR103 CYS104 GLY105 ASN106 LEU107 LEU108 MET109 TRP110 GLU111 ALA112 VAL113 THR114 VAL115 GLN116 THR117 GLU118 VAL119 ILE120 GLY121 ILE122 THR123 SER124 MET125 LEU126 ASN127 LEU128 HIS129 ALA130 GLY131 SER132 GLN133 LYS134 VAL135 HIS136 GLU137 HIS138 GLY139 GLY140 GLY141 LYS142 PRO143 ILE144 GLN145 GLY146 SER147 ASN148 PHE149 HIS150 PHE151 PHE152 ALA153 VAL154 GLY155 GLY156 ASP157 PRO158 LEU159 GLU160 MET161 GLN162 GLY163 VAL164 LEU165 MET166 ASN167 TYR168 ARG169 THR170 LYS171 TYR172 PRO173 ASP174 GLY175 THR176 ILE177 THR178 PRO179 LYS180 ASN181 PRO182 THR183 ALA184 GLN185 SER186 GLN187 VAL188 MET189 ASN190 THR191 ASP192 HIS193 LYS194 ALA195 TYR196 LEU197 ASP198 LYS199 ASN200 ASN201 ALA202 TYR203 PRO204 VAL205 GLU206 CYS207 TRP208 VAL209 PRO210 ASP211 PRO212 SER213 ARG214 ASN215 GLU216 ASN217 THR218 ARG219 TYR220 PHE221 GLY222 THR223 PHE224 THR225 GLY226 GLY227 GLU228 ASN229 VAL230 PRO231 PRO232 VAL233 LEU234 HIS235 VAL236 THR237 ASN238 THR239 ALA240 THR241 THR242 VAL243 LEU244 LEU245 ASP246 GLU247 GLN248 GLY249 VAL250 GLY251 PRO252 LEU253 CYS254 LYS255 ALA256 ASP257 SER258 LEU259 TYR260 VAL261 SER262 ALA263 ALA264 ASP265 ILE266 CYS267 GLY268 LEU269 PHE270 THR271 ASN272 SER273 SER274 GLY275 THR276 GLN277 GLN278 TRP279 ARG280 GLY281 LEU282 ALA283 ARG284 TYR285 PHE286 LYS287 ILE288 ARG289 LEU290 ARG291 LYS292 ARG293 SER294 VAL295 LYS296 ASN297
Unit 3 VAL34 LEU35 GLU36 VAL37 ILE44 THR45 GLU46 VAL47 GLU48 CYS49 PHE50 LEU51 ASN52 PRO53 GLU54 MET55 GLY56 ASP57 PRO58 ASP59 GLU60 ASN61 LEU62 ARG63 GLY64 PHE65 SER66 LEU67 LYS68 LEU69 SER70 ALA71 GLU72 ASN73 ASP74 PHE75 SER76 SER77 ASP78 SER79 PRO80 GLU81 ARG82 LYS83 MET84 LEU85 PRO86 CYS87 TYR88 SER89 THR90 ALA91 ARG92 ILE93 PRO94 LEU95 PRO96 ASN97 LEU107 LEU108 MET109 TRP110 GLU111 ALA112 VAL113 THR114 VAL115 GLN116 THR117 GLU118 VAL119 ILE120 GLY121 ILE122 THR123 SER124 MET125 LEU126 ASN127 LEU128 HIS129 ALA130 GLY131 SER132 GLN133 LYS134 VAL135 HIS136 GLU137 HIS138 GLY139 GLY140 GLY141 LYS142 PRO143 ILE144 GLN145 GLY146 SER147 ASN148 PHE149 HIS150 PHE151 PHE152 ALA153 VAL154 GLY155 GLY156 ASP157 PRO158 LEU159 GLU160 MET161 GLN162 GLY163 VAL164 LEU165 MET166 ASN167 TYR168 ARG169 THR170 LYS171 TYR172 PRO173 ASP174 GLY175 THR176 ILE177 THR178 PRO179 LYS180 ASN181 PRO182 THR183 ALA184 GLN185 SER186 GLN187 VAL188 MET189 ASN190 THR191 ASP192 HIS193 LYS194 ALA195 TYR196 LEU197 ASP198 LYS199 ASN200 ASN201 ALA202 TYR203 PRO204 VAL205 GLU206 CYS207 TRP208 VAL209 PRO210 ASP211 PRO212 SER213 ARG214 ASN215 GLU216 ASN217 THR218 ARG219 TYR220 PHE221 GLY222 THR223 PHE224 THR225 GLY226 GLY227 GLU228 ASN229 VAL230 PRO231 PRO232 VAL233 LEU234 HIS235 VAL236 THR237 ASN238 THR239 ALA240 THR241 THR242 VAL243 LEU244 LEU245 ASP246 GLU247 GLN248 GLY249 VAL250 GLY251 PRO252 LEU253 CYS254 LYS255 ALA256 ASP257 SER258 LEU259 TYR260 VAL261 SER262 ALA263 ALA264 ASP265 ILE266 CYS267 GLY268 LEU269 PHE270 THR271 ASN272 SER273 SER274 GLY275 THR276 GLN277 GLN278 TRP279 ARG280 GLY281 LEU282 ALA283 ARG284 TYR285 PHE286 LYS287 ILE288 ARG289 LEU290 ARG291 LYS292 ARG293 SER294 VAL295
Unit 4 VAL32 GLU33 VAL34 LEU35 GLU36 VAL37 LYS38 THR39 GLY40 VAL41 ASP42 ALA43 ILE44 THR45 GLU46 VAL47 GLU48 CYS49 PHE50 LEU51 ASN52 PRO53 GLU54 MET55 GLY56 ASP57 PRO58 ASP59 GLU60 ASN61 LEU62 ARG63 GLY64 PHE65 SER66 LEU67 LYS68 LEU69 SER70 ALA71 GLU72 ASN73 ASP74 PHE75 SER76 SER77 ASP78 SER79 PRO80 GLU81 ARG82 LYS83 MET84 LEU85 PRO86 CYS87 TYR88 SER89 THR90 ALA91 ARG92 ILE93 PRO94 LEU95 PRO96 ASN97 LEU98 ASN99 GLU100 ASP101 LEU102 THR103 CYS104 GLY105 ASN106 LEU107 LEU108 MET109 TRP110 GLU111 ALA112 VAL113 THR114 VAL115 GLN116 THR117 GLU118 VAL119 ILE120 GLY121 ILE122 THR123 SER124 MET125 LEU126 ASN127 LEU128 HIS129 ALA130 GLY131 SER132 GLN133 LYS134 VAL135 HIS136 GLU137 HIS138 GLY139 GLY140 GLY141 LYS142 PRO143 ILE144 GLN145 GLY146 SER147 ASN148 PHE149 HIS150 PHE151 PHE152 ALA153 VAL154 GLY155 GLY156 ASP157 PRO158 LEU159 GLU160 MET161 GLN162 GLY163 VAL164 LEU165 MET166 ASN167 TYR168 ARG169 THR170 LYS171 TYR172 PRO173 ASP174 GLY175 THR176 ILE177 THR178 PRO179 LYS180 ASN181 PRO182 THR183 ALA184 GLN185 SER186 GLN187 VAL188 MET189 ASN190 THR191 ASP192 HIS193 LYS194 ALA195 TYR196 LEU197 ASP198 LYS199 ASN200 ASN201 ALA202 TYR203 PRO204 VAL205 GLU206 CYS207 TRP208 VAL209 PRO210 ASP211 PRO212 SER213 ARG214 ASN215 GLU216 ASN217 THR218 ARG219 TYR220 PHE221 GLY222 THR223 PHE224 THR225 GLY226 GLY227 GLU228 ASN229 VAL230 PRO231 PRO232 VAL233 LEU234 HIS235 VAL236 THR237 ASN238 THR239 ALA240 THR241 THR242 VAL243 LEU244 LEU245 ASP246 GLU247 GLN248 GLY249 VAL250 GLY251 PRO252 LEU253 CYS254 LYS255 ALA256 ASP257 SER258 LEU259 TYR260 VAL261 SER262 ALA263 ALA264 ASP265 ILE266 CYS267 GLY268 LEU269 PHE270 THR271 ASN272 SER273 SER274 GLY275 THR276 GLN277 GLN278 TRP279 ARG280 GLY281 LEU282 ALA283 ARG284 TYR285 PHE286 LYS287 ILE288 ARG289 LEU290 ARG291 LYS292 ARG293 SER294 VAL295 LYS296 ASN297 PRO298
Unit 5 VAL32 GLU33 VAL34 LEU35 GLU36 VAL37 LYS38 THR39 GLY40 ILE44 THR45 GLU46 VAL47 GLU48 CYS49 PHE50 LEU51 ASN52 PRO53 GLU54 MET55 GLY56 ASP57 PRO58 ASP59 GLU60 ASN61 LEU62 ARG63 GLY64 PHE65 SER66 LEU67 LYS68 LEU69 SER70 ALA71 GLU72 ASN73 ASP74 PHE75 SER76 SER77 ASP78 SER79 PRO80 GLU81 ARG82 LYS83 MET84 LEU85 PRO86 CYS87 TYR88 SER89 THR90 ALA91 ARG92 ILE93 PRO94 LEU95 PRO96 ASN97 LEU98 ASN99 GLU100 ASP101 LEU102 THR103 CYS104 GLY105 ASN106 LEU107 LEU108 MET109 TRP110 GLU111 ALA112 VAL113 THR114 VAL115 GLN116 THR117 GLU118 VAL119 ILE120 GLY121 ILE122 THR123 SER124 MET125 LEU126 ASN127 LEU128 HIS129 ALA130 GLY131 SER132 GLN133 LYS134 VAL135 HIS136 GLU137 HIS138 GLY139 GLY140 GLY141 LYS142 PRO143 ILE144 GLN145 GLY146 SER147 ASN148 PHE149 HIS150 PHE151 PHE152 ALA153 VAL154 GLY155 GLY156 ASP157 PRO158 LEU159 GLU160 MET161 GLN162 GLY163 VAL164 LEU165 MET166 ASN167 TYR168 ARG169 THR170 LYS171 TYR172 PRO173 ASP174 GLY175 THR176 ILE177 THR178 PRO179 LYS180 ASN181 PRO182 THR183 ALA184 GLN185 SER186 GLN187 VAL188 MET189 ASN190 THR191 ASP192 HIS193 LYS194 ALA195 TYR196 LEU197 ASP198 LYS199 ASN200 ASN201 ALA202 TYR203 PRO204 VAL205 GLU206 CYS207 TRP208 VAL209 PRO210 ASP211 PRO212 SER213 ARG214 ASN215 GLU216 ASN217 THR218 ARG219 TYR220 PHE221 GLY222 THR223 PHE224 THR225 GLY226 GLY227 GLU228 ASN229 VAL230 PRO231 PRO232 VAL233 LEU234 HIS235 VAL236 THR237 ASN238 THR239 ALA240 THR241 THR242 VAL243 LEU244 LEU245 ASP246 GLU247 GLN248 GLY249 VAL250 GLY251 PRO252 LEU253 CYS254 LYS255 ALA256 ASP257 SER258 LEU259 TYR260 VAL261 SER262 ALA263 ALA264 ASP265 ILE266 CYS267 GLY268 LEU269 PHE270 THR271 ASN272 SER273 SER274 GLY275 THR276 GLN277 GLN278 TRP279 ARG280 GLY281 LEU282 ALA283 ARG284 TYR285 PHE286 LYS287 ILE288 ARG289 LEU290 ARG291 LYS292 ARG293 SER294 VAL295 LYS296 ASN297 PRO298
Ligands
Unit 6 BGC1 GAL2 SIA3 SIA4
Unit 7 SIA1 SIA2
Unit 8 GAL1 SIA2 SIA3
Unit 9 SIA1 SIA2
Unit 10 GOL405 CL406
Unit 11 GOL403 GOL404 CL405
Unit 12 GOL404 CL405
Unit 13 GOL403 CL404
Unit 14 GOL401 GOL402 CL403
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany