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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURE OF HIV-1 GP120 (CORE WITH V3) IN COMPLEX WITH CD4- SITE ANTIBODY F105
Keywords HIV, GP120, CD4 BINDING SITE ANTIBODY, F105, IMMUNE EVASION, APOPTOSIS, CELL MEMBRANE, CLEAVAGE ON PAIR OF BASIC RESIDUE DISULFIDE BOND, ENVELOPE PROTEIN, FUSION PROTEIN, GLYCOPROT HOST-VIRUS INTERACTION, LIPOPROTEIN, MEMBRANE, PALMITATE, TRANSMEMBRANE, VIRAL IMMUNOEVASION, VIRION, STRUCTURAL PROT IMMUNE SYSTEM COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3HI1     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   GLYCOPROTEIN 120  G 289 2276 0
2  Protein   F105 LIGHT CHAIN  L 215 1651 0
3  Protein   F105 HEAVY CHAIN  H 225 1680 0
4  Protein   GLYCOPROTEIN 120  J 289 2276 0
5  Protein   F105 LIGHT CHAIN  A 215 1651 0
6  Protein   F105 HEAVY CHAIN  B 225 1680 0
7  Ligand   GLYCOPROTEIN 120  G 13 0 182
8  Ligand   GLYCOPROTEIN 120  J 14 0 196
9 Water     77 0 78
total       1562 11214 456
Proteins
Unit 1 THR90 GLU91 ASN92 PHE93 ASN94 MET95 TRP96 LYS97 ASN98 ASN99 MET100 VAL101 GLU102 GLN103 MET104 HIS105 GLU106 ASP107 ILE108 ILE109 SER110 LEU111 TRP112 ASP113 GLN114 SER115 LEU116 LYS117 PRO118 CYS119 VAL120 LYS121 LEU122 THR123 GLY124 GLY198 SER199 VAL200 ILE201 THR202 GLN203 ALA204 CYS205 PRO206 LYS207 VAL208 SER209 PHE210 GLU211 PRO212 ILE213 PRO214 ILE215 HIS216 TYR217 CYS218 ALA219 PRO220 ALA221 GLY222 PHE223 ALA224 ILE225 LEU226 LYS227 CYS228 ASN229 ASP230 LYS231 LYS232 PHE233 ASN234 GLY235 THR236 GLY237 PRO238 CYS239 THR240 ASN241 VAL242 SER243 THR244 VAL245 GLN246 CYS247 THR248 HIS249 GLY250 ILE251 ARG252 PRO253 VAL254 VAL255 SER256 THR257 GLN258 LEU259 LEU260 LEU261 ASN262 GLY263 SER264 LEU265 ALA266 GLU267 GLU268 GLU269 ILE270 VAL271 ILE272 ARG273 SER274 GLU275 ASN276 PHE277 THR278 ASN279 ASN280 ALA281 LYS282 THR283 ILE284 ILE285 VAL286 GLN287 LEU288 ASN289 GLU290 SER291 VAL292 VAL293 ILE294 ASN295 CYS296 THR297 ARG298 PRO299 ASN300 ASN301 ARG327 GLN328 ALA329 HIS330 CYS331 ASN332 LEU333 SER334 LYS335 THR336 GLN337 TRP338 GLU339 ASN340 THR341 LEU342 GLU343 GLN344 ILE345 ALA346 ILE347 LYS348 LEU349 LYS350 GLU351 GLN352 PHE353 GLY354 ASN355 ASN356 LYS357 THR358 ILE359 ILE360 PHE361 ASN362 PRO363 SER364 SER365 GLY366 GLY367 ASP368 PRO369 GLU370 ILE371 VAL372 THR373 HIS374 SER375 PHE376 ASN377 CYS378 GLY379 GLY380 GLU381 PHE382 PHE383 TYR384 CYS385 ASN386 SER387 THR388 GLN389 LEU390 PHE391 THR392 TRP393 ASN394 ASP395 ARG412 ASN413 ILE414 THR415 LEU416 PRO417 CYS418 ARG419 ILE420 LYS421 GLN422 ILE423 ILE424 ASN425 MET426 TRP427 GLN428 GLU429 VAL430 GLY431 LYS432 ALA433 MET434 TYR435 ALA436 PRO437 PRO438 ILE439 ARG440 GLY441 GLN442 ILE443 ARG444 CYS445 SER446 SER447 ASN448 ILE449 THR450 GLY451 LEU452 LEU453 LEU454 THR455 ARG456 ASP457 GLY458 GLY459 LYS460 ASP461 THR462 ASN463 GLY464 THR465 GLU466 ILE467 PHE468 ARG469 PRO470 GLY471 GLY472 GLY473 ASP474 MET475 ARG476 ASP477 ASN478 TRP479 ARG480 SER481 GLU482 LEU483 TYR484 LYS485 TYR486 LYS487 VAL488 VAL489 LYS490 ILE491 GLU492
Unit 2 GLU1 ILE2 VAL3 LEU4 THR5 GLN6 SER7 PRO8 GLY9 THR10 LEU11 SER12 LEU13 SER14 ALA15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 GLN27 SER27A VAL28 SER29 SER30 ARG31 TYR32 LEU33 ALA34 TRP35 TYR36 GLN37 GLN38 LYS39 PRO40 GLY41 GLN42 ALA43 PRO44 ARG45 LEU46 LEU47 ILE48 TYR49 GLY50 ALA51 SER52 SER53 ARG54 ALA55 THR56 GLY57 ILE58 PRO59 ASP60 ARG61 PHE62 SER63 GLY64 SER65 GLY66 SER67 GLY68 THR69 ASP70 PHE71 THR72 LEU73 THR74 ILE75 SER76 ARG77 VAL78 GLU79 PRO80 GLU81 ASP82 PHE83 ALA84 VAL85 TYR86 TYR87 CYS88 GLN89 GLN90 TYR91 ASP92 ASN93 SER94 VAL95 CYS96 THR97 PHE98 GLY99 GLN100 GLY101 THR102 LYS103 LEU104 GLU105 ILE106 LYS107 ARG108 THR109 VAL110 ALA111 ALA112 PRO113 SER114 VAL115 PHE116 ILE117 PHE118 PRO119 PRO120 SER121 ASP122 GLU123 GLN124 LEU125 LYS126 SER127 GLY128 THR129 ALA130 SER131 VAL132 VAL133 CYS134 LEU135 LEU136 ASN137 ASN138 PHE139 TYR140 PRO141 ARG142 GLU143 ALA144 LYS145 VAL146 GLN147 TRP148 LYS149 VAL150 ASP151 ASN152 ALA153 LEU154 GLN155 SER156 GLY157 ASN158 SER159 GLN160 GLU161 SER162 VAL163 THR164 GLU165 GLN166 ASP167 SER168 LYS169 ASP170 SER171 THR172 TYR173 SER174 LEU175 SER176 SER177 THR178 LEU179 THR180 LEU181 SER182 LYS183 ALA184 ASP185 TYR186 GLU187 LYS188 HIS189 LYS190 VAL191 TYR192 ALA193 CYS194 GLU195 VAL196 THR197 HIS198 GLN199 GLY200 LEU201 SER202 SER203 PRO204 VAL205 THR206 LYS207 SER208 PHE209 ASN210 ARG211 GLY212 GLU213 CYS214
Unit 3 GLN1 VAL2 GLN3 LEU4 GLN5 GLU6 SER7 GLY8 PRO9 GLY10 LEU11 VAL12 LYS13 PRO14 SER15 GLU16 THR17 LEU18 SER19 LEU20 THR21 CYS22 THR23 VAL24 SER25 GLY26 GLY27 SER28 ILE29 SER30 SER31 HIS32 TYR33 TRP34 SER35 TRP36 ILE37 ARG38 GLN39 SER40 PRO41 GLY42 LYS43 GLY44 LEU45 GLN46 TRP47 ILE48 GLY49 TYR50 ILE51 TYR52 TYR53 SER54 GLY55 SER56 THR57 ASN58 TYR59 SER60 PRO61 SER62 LEU63 LYS64 SER65 ARG66 VAL67 THR68 ILE69 SER70 VAL71 GLU72 THR73 ALA74 LYS75 ASN76 GLN77 PHE78 SER79 LEU80 LYS81 LEU82 THR82A SER82B MET82C THR83 ALA84 ALA85 ASP86 THR87 ALA88 VAL89 TYR90 TYR91 CYS92 ALA93 ARG94 GLY95 PRO96 VAL97 PRO98 ALA99 VAL100 PHE100A TYR100B GLY100C ASP100D TYR100E ARG100F LEU100G ASP101 PRO102 TRP103 GLY104 GLN105 GLY106 THR107 LEU108 VAL109 THR110 VAL111 SER112 SER113 ALA114 SER115 THR116 LYS117 GLY118 PRO119 SER120 VAL121 PHE122 PRO123 LEU124 ALA125 PRO126 SER127 SER128 LYS129 SER130 THR131 SER132 GLY133 GLY134 THR135 ALA136 ALA137 LEU138 GLY139 CYS140 LEU141 VAL142 LYS143 ASP144 TYR145 PHE146 PRO147 GLU148 PRO149 VAL150 THR151 VAL152 SER153 TRP154 ASN155 SER156 GLY157 ALA158 LEU159 THR160 SER161 GLY162 VAL163 HIS164 THR165 PHE166 PRO167 ALA168 VAL169 LEU170 GLN171 SER172 SER173 GLY174 LEU175 TYR176 SER177 LEU178 SER179 SER180 VAL181 VAL182 THR183 VAL184 PRO185 SER186 SER187 SER188 LEU189 GLY190 THR191 GLN192 THR193 TYR194 ILE195 CYS196 ASN197 VAL198 ASN199 HIS200 LYS201 PRO202 SER203 ASN204 THR205 LYS206 VAL207 ASP208 LYS209 LYS210 VAL211 GLU212 PRO213 LYS214 SER215
Unit 4 THR90 GLU91 ASN92 PHE93 ASN94 MET95 TRP96 LYS97 ASN98 ASN99 MET100 VAL101 GLU102 GLN103 MET104 HIS105 GLU106 ASP107 ILE108 ILE109 SER110 LEU111 TRP112 ASP113 GLN114 SER115 LEU116 LYS117 PRO118 CYS119 VAL120 LYS121 LEU122 THR123 GLY124 GLY198 SER199 VAL200 ILE201 THR202 GLN203 ALA204 CYS205 PRO206 LYS207 VAL208 SER209 PHE210 GLU211 PRO212 ILE213 PRO214 ILE215 HIS216 TYR217 CYS218 ALA219 PRO220 ALA221 GLY222 PHE223 ALA224 ILE225 LEU226 LYS227 CYS228 ASN229 ASP230 LYS231 LYS232 PHE233 ASN234 GLY235 THR236 GLY237 PRO238 CYS239 THR240 ASN241 VAL242 SER243 THR244 VAL245 GLN246 CYS247 THR248 HIS249 GLY250 ILE251 ARG252 PRO253 VAL254 VAL255 SER256 THR257 GLN258 LEU259 LEU260 LEU261 ASN262 GLY263 SER264 LEU265 ALA266 GLU267 GLU268 GLU269 ILE270 VAL271 ILE272 ARG273 SER274 GLU275 ASN276 PHE277 THR278 ASN279 ASN280 ALA281 LYS282 THR283 ILE284 ILE285 VAL286 GLN287 LEU288 ASN289 GLU290 SER291 VAL292 VAL293 ILE294 ASN295 CYS296 THR297 ARG298 PRO299 ASN300 ASN301 ARG327 GLN328 ALA329 HIS330 CYS331 ASN332 LEU333 SER334 LYS335 THR336 GLN337 TRP338 GLU339 ASN340 THR341 LEU342 GLU343 GLN344 ILE345 ALA346 ILE347 LYS348 LEU349 LYS350 GLU351 GLN352 PHE353 GLY354 ASN355 ASN356 LYS357 THR358 ILE359 ILE360 PHE361 ASN362 PRO363 SER364 SER365 GLY366 GLY367 ASP368 PRO369 GLU370 ILE371 VAL372 THR373 HIS374 SER375 PHE376 ASN377 CYS378 GLY379 GLY380 GLU381 PHE382 PHE383 TYR384 CYS385 ASN386 SER387 THR388 GLN389 LEU390 PHE391 THR392 TRP393 ASN394 ASP395 ARG412 ASN413 ILE414 THR415 LEU416 PRO417 CYS418 ARG419 ILE420 LYS421 GLN422 ILE423 ILE424 ASN425 MET426 TRP427 GLN428 GLU429 VAL430 GLY431 LYS432 ALA433 MET434 TYR435 ALA436 PRO437 PRO438 ILE439 ARG440 GLY441 GLN442 ILE443 ARG444 CYS445 SER446 SER447 ASN448 ILE449 THR450 GLY451 LEU452 LEU453 LEU454 THR455 ARG456 ASP457 GLY458 GLY459 LYS460 ASP461 THR462 ASN463 GLY464 THR465 GLU466 ILE467 PHE468 ARG469 PRO470 GLY471 GLY472 GLY473 ASP474 MET475 ARG476 ASP477 ASN478 TRP479 ARG480 SER481 GLU482 LEU483 TYR484 LYS485 TYR486 LYS487 VAL488 VAL489 LYS490 ILE491 GLU492
Unit 5 GLU1 ILE2 VAL3 LEU4 THR5 GLN6 SER7 PRO8 GLY9 THR10 LEU11 SER12 LEU13 SER14 ALA15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 GLN27 SER27A VAL28 SER29 SER30 ARG31 TYR32 LEU33 ALA34 TRP35 TYR36 GLN37 GLN38 LYS39 PRO40 GLY41 GLN42 ALA43 PRO44 ARG45 LEU46 LEU47 ILE48 TYR49 GLY50 ALA51 SER52 SER53 ARG54 ALA55 THR56 GLY57 ILE58 PRO59 ASP60 ARG61 PHE62 SER63 GLY64 SER65 GLY66 SER67 GLY68 THR69 ASP70 PHE71 THR72 LEU73 THR74 ILE75 SER76 ARG77 VAL78 GLU79 PRO80 GLU81 ASP82 PHE83 ALA84 VAL85 TYR86 TYR87 CYS88 GLN89 GLN90 TYR91 ASP92 ASN93 SER94 VAL95 CYS96 THR97 PHE98 GLY99 GLN100 GLY101 THR102 LYS103 LEU104 GLU105 ILE106 LYS107 ARG108 THR109 VAL110 ALA111 ALA112 PRO113 SER114 VAL115 PHE116 ILE117 PHE118 PRO119 PRO120 SER121 ASP122 GLU123 GLN124 LEU125 LYS126 SER127 GLY128 THR129 ALA130 SER131 VAL132 VAL133 CYS134 LEU135 LEU136 ASN137 ASN138 PHE139 TYR140 PRO141 ARG142 GLU143 ALA144 LYS145 VAL146 GLN147 TRP148 LYS149 VAL150 ASP151 ASN152 ALA153 LEU154 GLN155 SER156 GLY157 ASN158 SER159 GLN160 GLU161 SER162 VAL163 THR164 GLU165 GLN166 ASP167 SER168 LYS169 ASP170 SER171 THR172 TYR173 SER174 LEU175 SER176 SER177 THR178 LEU179 THR180 LEU181 SER182 LYS183 ALA184 ASP185 TYR186 GLU187 LYS188 HIS189 LYS190 VAL191 TYR192 ALA193 CYS194 GLU195 VAL196 THR197 HIS198 GLN199 GLY200 LEU201 SER202 SER203 PRO204 VAL205 THR206 LYS207 SER208 PHE209 ASN210 ARG211 GLY212 GLU213 CYS214
Unit 6 GLN1 VAL2 GLN3 LEU4 GLN5 GLU6 SER7 GLY8 PRO9 GLY10 LEU11 VAL12 LYS13 PRO14 SER15 GLU16 THR17 LEU18 SER19 LEU20 THR21 CYS22 THR23 VAL24 SER25 GLY26 GLY27 SER28 ILE29 SER30 SER31 HIS32 TYR33 TRP34 SER35 TRP36 ILE37 ARG38 GLN39 SER40 PRO41 GLY42 LYS43 GLY44 LEU45 GLN46 TRP47 ILE48 GLY49 TYR50 ILE51 TYR52 TYR53 SER54 GLY55 SER56 THR57 ASN58 TYR59 SER60 PRO61 SER62 LEU63 LYS64 SER65 ARG66 VAL67 THR68 ILE69 SER70 VAL71 GLU72 THR73 ALA74 LYS75 ASN76 GLN77 PHE78 SER79 LEU80 LYS81 LEU82 THR82A SER82B MET82C THR83 ALA84 ALA85 ASP86 THR87 ALA88 VAL89 TYR90 TYR91 CYS92 ALA93 ARG94 GLY95 PRO96 VAL97 PRO98 ALA99 VAL100 PHE100A TYR100B GLY100C ASP100D TYR100E ARG100F LEU100G ASP101 PRO102 TRP103 GLY104 GLN105 GLY106 THR107 LEU108 VAL109 THR110 VAL111 SER112 SER113 ALA114 SER115 THR116 LYS117 GLY118 PRO119 SER120 VAL121 PHE122 PRO123 LEU124 ALA125 PRO126 SER127 SER128 LYS129 SER130 THR131 SER132 GLY133 GLY134 THR135 ALA136 ALA137 LEU138 GLY139 CYS140 LEU141 VAL142 LYS143 ASP144 TYR145 PHE146 PRO147 GLU148 PRO149 VAL150 THR151 VAL152 SER153 TRP154 ASN155 SER156 GLY157 ALA158 LEU159 THR160 SER161 GLY162 VAL163 HIS164 THR165 PHE166 PRO167 ALA168 VAL169 LEU170 GLN171 SER172 SER173 GLY174 LEU175 TYR176 SER177 LEU178 SER179 SER180 VAL181 VAL182 THR183 VAL184 PRO185 SER186 SER187 SER188 LEU189 GLY190 THR191 GLN192 THR193 TYR194 ILE195 CYS196 ASN197 VAL198 ASN199 HIS200 LYS201 PRO202 SER203 ASN204 THR205 LYS206 VAL207 ASP208 LYS209 LYS210 VAL211 GLU212 PRO213 LYS214 SER215
Ligands
Unit 7 NAG734 NAG741 NAG762 NAG776 NAG789 NAG795 NAG801 NAG832 NAG856 NAG886 NAG894 NAG948 NAG963
Unit 8 NAG734 NAG741 NAG762 NAG776 NAG789 NAG795 NAG801 NAG832 NAG856 NAG886 NAG894 NAG913 NAG948 NAG963
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany