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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF CD4M47, A SCORPION-TOXIN MIMIC OF CD4, WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 A 17B
Keywords HIV-1, GP120, YU2, SCORPION TOXIN, CD4 MIMIC, CD4M47, ANTIBO PROTEIN-IMMUNE SYSTEM COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2I5Y     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  G 302 2348 0
2  Protein   ANTIBODY 17B LIGHT CHAIN  L 214 1647 0
3  Protein   ANTIBODY 17B HEAVY CHAIN  H 224 1688 0
4  Protein   CD4M47, SCORPION-TOXIN MIMIC OF CD4  M 27 170 37
5  Protein   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  P 300 2332 0
6  Protein   ANTIBODY 17B LIGHT CHAIN  Q 214 1647 0
7  Protein   ANTIBODY 17B HEAVY CHAIN  R 223 1684 0
8  Protein   CD4M47, SCORPION-TOXIN MIMIC OF CD4  S 27 170 37
9  Ligand   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  G 8 0 112
10  Ligand   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  P 8 0 112
11 Water     549 0 549
total       2096 11686 847
Proteins
Unit 1 SER82 GLU83 VAL84 LYS85 LEU86 GLU87 ASN88 VAL89 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 PRO124 LEU125 CYS126 VAL127 GLY128 ALA129 GLY194 SER195 CYS196 ASN197 THR198 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 GLY298 ALA299 GLY329 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 ASP1 ILE2 VAL3 MET4 THR5 GLN6 SER7 PRO8 ALA9 THR10 LEU11 SER12 VAL13 SER14 PRO15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 GLU27 SER28 VAL29 SER30 SER31 ASP32 LEU33 ALA34 TRP35 TYR36 GLN37 GLN38 LYS39 PRO40 GLY41 GLN42 ALA43 PRO44 ARG45 LEU46 LEU47 ILE48 TYR49 GLY50 ALA51 SER52 THR53 ARG54 ALA55 THR56 GLY57 VAL58 PRO59 ALA60 ARG61 PHE62 SER63 GLY64 SER65 GLY66 SER67 GLY68 ALA69 GLU70 PHE71 THR72 LEU73 THR74 ILE75 SER76 SER77 LEU78 GLN79 SER80 GLU81 ASP82 PHE83 ALA84 VAL85 TYR86 TYR87 CYS88 GLN89 GLN90 TYR91 ASN92 ASN93 TRP94 PRO95 PRO95A ARG95B TYR96 THR97 PHE98 GLY99 GLN100 GLY101 THR102 ARG103 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
Unit 3 GLU1 VAL2 GLN3 LEU4 VAL5 GLU6 SER7 GLY8 ALA9 GLU10 VAL11 LYS12 LYS13 PRO14 GLY15 SER16 SER17 VAL18 LYS19 VAL20 SER21 CYS22 LYS23 ALA24 SER25 GLY26 ASP27 THR28 PHE29 ILE30 ARG31 TYR32 SER33 PHE34 THR35 TRP36 VAL37 ARG38 GLN39 ALA40 PRO41 GLY42 GLN43 GLY44 LEU45 GLU46 TRP47 MET48 GLY49 ARG50 ILE51 ILE52 THR52A ILE53 LEU54 ASP55 VAL56 ALA57 HIS58 TYR59 ALA60 PRO61 HIS62 LEU63 GLN64 GLY65 ARG66 VAL67 THR68 ILE69 THR70 ALA71 ASP72 LYS73 SER74 THR75 SER76 THR77 VAL78 TYR79 LEU80 GLU81 LEU82 ARG82A ASN82B LEU82C ARG83 SER84 ASP85 ASP86 THR87 ALA88 VAL89 TYR90 PHE91 CYS92 ALA93 GLY94 VAL95 TYR96 GLU97 GLY98 GLU99 ALA100 ASP100A GLU100B GLY100C GLU100D TYR100E ASP100F ASN100G ASN100H GLY100I PHE100J LEU100K LYS101 HIS102 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 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
Unit 4 MPT1 ASN2 LEU3 HIS4 PHE5 CYS6 GLN7 LEU8 ARG9 CYS10 LYS11 SER12 LEU13 GLY14 LEU15 LEU16 GLY17 ARG18 CYS19 ALA20 DPR21 THR22 BIF23 CYS24 ALA25 CYS26 VLM27
Unit 5 SER82 GLU83 VAL84 LYS85 LEU86 GLU87 ASN88 VAL89 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 PRO124 LEU125 CYS126 VAL127 GLY128 ALA129 GLY194 SER195 CYS196 ASN197 THR198 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 GLY298 ALA299 GLY329 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 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 6 ASP1 ILE2 VAL3 MET4 THR5 GLN6 SER7 PRO8 ALA9 THR10 LEU11 SER12 VAL13 SER14 PRO15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 GLU27 SER28 VAL29 SER30 SER31 ASP32 LEU33 ALA34 TRP35 TYR36 GLN37 GLN38 LYS39 PRO40 GLY41 GLN42 ALA43 PRO44 ARG45 LEU46 LEU47 ILE48 TYR49 GLY50 ALA51 SER52 THR53 ARG54 ALA55 THR56 GLY57 VAL58 PRO59 ALA60 ARG61 PHE62 SER63 GLY64 SER65 GLY66 SER67 GLY68 ALA69 GLU70 PHE71 THR72 LEU73 THR74 ILE75 SER76 SER77 LEU78 GLN79 SER80 GLU81 ASP82 PHE83 ALA84 VAL85 TYR86 TYR87 CYS88 GLN89 GLN90 TYR91 ASN92 ASN93 TRP94 PRO95 PRO95A ARG95B TYR96 THR97 PHE98 GLY99 GLN100 GLY101 THR102 ARG103 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
Unit 7 GLU1 VAL2 GLN3 LEU4 VAL5 GLU6 SER7 GLY8 ALA9 GLU10 VAL11 LYS12 LYS13 PRO14 GLY15 SER16 SER17 VAL18 LYS19 VAL20 SER21 CYS22 LYS23 ALA24 SER25 GLY26 ASP27 THR28 PHE29 ILE30 ARG31 TYR32 SER33 PHE34 THR35 TRP36 VAL37 ARG38 GLN39 ALA40 PRO41 GLY42 GLN43 GLY44 LEU45 GLU46 TRP47 MET48 GLY49 ARG50 ILE51 ILE52 THR52A ILE53 LEU54 ASP55 VAL56 ALA57 HIS58 TYR59 ALA60 PRO61 HIS62 LEU63 GLN64 GLY65 ARG66 VAL67 THR68 ILE69 THR70 ALA71 ASP72 LYS73 SER74 THR75 SER76 THR77 VAL78 TYR79 LEU80 GLU81 LEU82 ARG82A ASN82B LEU82C ARG83 SER84 ASP85 ASP86 THR87 ALA88 VAL89 TYR90 PHE91 CYS92 ALA93 GLY94 VAL95 TYR96 GLU97 GLY98 GLU99 ALA100 ASP100A GLU100B GLY100C GLU100D TYR100E ASP100F ASN100G ASN100H GLY100I PHE100J LEU100K LYS101 HIS102 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 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
Unit 8 MPT1 ASN2 LEU3 HIS4 PHE5 CYS6 GLN7 LEU8 ARG9 CYS10 LYS11 SER12 LEU13 GLY14 LEU15 LEU16 GLY17 ARG18 CYS19 ALA20 DPR21 THR22 BIF23 CYS24 ALA25 CYS26 VLM27
Ligands
Unit 9 NAG588 NAG734 NAG741 NAG762 NAG776 NAG789 NAG795 NAG886
Unit 10 NAG588 NAG734 NAG741 NAG762 NAG776 NAG789 NAG795 NAG886
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany