4DKRA

Crystal structure of clade a/e 93th057 hiv-1 gp120 core in complex with aws-i-169
Total Genus 96
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
96
sequence length
353
structure length
339
Chain Sequence
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCINGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors.
pubmed doi rcsb
molecule tags Viral protein/inhibitor
source organism Human immunodeficiency virus type 1
molecule keywords HIV-1 gp120 core
total genus 96
structure length 339
sequence length 353
chains with identical sequence C
ec nomenclature
pdb deposition date 2012-02-03
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.170.40.20 Mainly Beta Beta Complex HIV Envelope Protein Gp120; Chain G Human immunodeficiency virus 1, Gp160, envelope glycoprotein 4dkrA01
4YFLE 4LSUG 4YDKG 4JPWG 4LSVG 4RWYA 3SE9G 2NXYA 3JWOA 5FA2A 2B4CG 4YDIG 5TE6G 2I60G 4LSSG 4OLZG 5CAYG 4JZZA 4R2GA 2NY3A 3U7YG 5CD5A 3TIHA 2NY5G 5TE7G 2NY6A 4DVWA 4DVRG 2NXZA 4RFOG 2NY1A 3SE8G 4YDLA 4XNYG 1GC1G 2NY0A 4DKOA 4I53A 4XMPG 3TGRA 2NY4A 3IDYA 5F4RA 4I54A 4DKVA 2I5YG 1G9NG 4RFNA 4DVXA 3TGTA 4RX4E 4XVSG 5KJRG 4JDTG 4DKUA 4JM2E 4R4NA 4OLXG 3NGBA 4JZWA 2BF1A 4P9HG 4R4FA 4KA2A 4S1RG 4LSQG 4RZ8A 4YDJG 3JWDA 5FECC 4JKPG 4YE4G 1YYMG 4H8WG 3LQAG 5F4LA 1YYLG 3RJQA 4LSTG 2NY2A 4J6RG 4OLYG 5I9QA 4JPVG 4OLVG 4XVTG 4S1SG 3HI1G 4DKQA 4OLUG 5F96G 5F4UA 4S1QG 4LSPG 2NY7G 4OLWG 4JB9G 1G9MG 4OM0G 1RZJG 3IDXG 4DVVA 5F9WA 4DVSA 3TGQA 5IGXG 4XNZA 1RZKG 4LAJA 4DVTA 5T33G 4DKRA 4K0AA 5TE4G 4DKPA 3FUSA 3TGSA 2QADA 5F9OG 4LSRG 5F4PA 4OM1G
chains in the Genus database with same CATH superfamily
4YFLE 4LSUG 4YDKG 4JPWG 4LSVG 4RWYA 3SE9G 2NXYA 3JWOA 5FA2A 2B4CG 4YDIG 5TE6G 2I60G 4LSSG 4OLZG 5CAYG 4JZZA 4R2GA 2NY3A 3U7YG 5CD5A 3TIHA 2NY5G 5TE7G 2NY6A 4DVWA 4DVRG 2NXZA 4RFOG 2NY1A 3SE8G 4YDLA 4XNYG 1GC1G 2NY0A 4DKOA 4I53A 4XMPG 3TGRA 2NY4A 3IDYA 5F4RA 4I54A 4DKVA 2I5YG 1G9NG 4RFNA 4DVXA 3TGTA 4RX4E 4XVSG 5KJRG 4JDTG 4DKUA 4JM2E 4R4NA 4OLXG 3NGBA 4JZWA 2BF1A 4P9HG 4R4FA 4KA2A 4S1RG 4LSQG 4RZ8A 4YDJG 3JWDA 5FECC 4JKPG 4YE4G 1YYMG 4H8WG 3LQAG 5F4LA 1YYLG 3RJQA 4LSTG 2NY2A 4J6RG 4OLYG 5I9QA 4JPVG 4OLVG 4XVTG 4S1SG 3HI1G 4DKQA 4OLUG 5F96G 5F4UA 4S1QG 4LSPG 2NY7G 4OLWG 4JB9G 1G9MG 4OM0G 1RZJG 3IDXG 4DVVA 5F9WA 4DVSA 3TGQA 5IGXG 4XNZA 1RZKG 4LAJA 4DVTA 5T33G 4DKRA 4K0AA 5TE4G 4DKPA 3FUSA 3TGSA 2QADA 5F9OG 4LSRG 5F4PA 4OM1G
chains in the Genus database with same CATH topology
4YFLE 4LSUG 4YDKG 4JPWG 4LSVG 4RWYA 3SE9G 2NXYA 3JWOA 5FA2A 2B4CG 4YDIG 5TE6G 2I60G 4LSSG 4OLZG 5CAYG 4JZZA 4R2GA 2NY3A 3U7YG 5CD5A 3TIHA 2NY5G 5TE7G 2NY6A 4DVWA 4DVRG 2NXZA 4RFOG 2NY1A 3SE8G 4YDLA 4XNYG 1GC1G 2NY0A 4DKOA 4I53A 4XMPG 3TGRA 2NY4A 3IDYA 5F4RA 4I54A 4DKVA 2I5YG 1G9NG 4RFNA 4DVXA 3TGTA 4RX4E 4XVSG 5KJRG 4JDTG 4DKUA 4JM2E 4R4NA 4OLXG 3NGBA 4JZWA 2BF1A 4P9HG 4R4FA 4KA2A 4S1RG 4LSQG 4RZ8A 4YDJG 3JWDA 5FECC 4JKPG 4YE4G 1YYMG 4H8WG 3LQAG 5F4LA 1YYLG 3RJQA 4LSTG 2NY2A 4J6RG 4OLYG 5I9QA 4JPVG 4OLVG 4XVTG 4S1SG 3HI1G 4DKQA 4OLUG 5F96G 5F4UA 4S1QG 4LSPG 2NY7G 4OLWG 4JB9G 1G9MG 4OM0G 1RZJG 3IDXG 4DVVA 5F9WA 4DVSA 3TGQA 5IGXG 4XNZA 1RZKG 4LAJA 4DVTA 5T33G 4DKRA 4K0AA 5TE4G 4DKPA 3FUSA 3TGSA 2QADA 5F9OG 4LSRG 5F4PA 4OM1G
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4YFL E;  4LSU G;  4YDK G;  4JPW G;  4LSV G;  4RWY A;  3SE9 G;  2NXY A;  3JWO A;  5FA2 A;  2B4C G;  4YDI G;  5TE6 G;  2I60 G;  4LSS G;  4OLZ G;  5CAY G;  4JZZ A;  4R2G A;  2NY3 A;  3U7Y G;  5CD5 A;  3TIH A;  2NY5 G;  5TE7 G;  2NY6 A;  4DVW A;  4DVR G;  2NXZ A;  4RFO G;  2NY1 A;  3SE8 G;  4YDL A;  4XNY G;  1GC1 G;  2NY0 A;  4DKO A;  4I53 A;  4XMP G;  3TGR A;  2NY4 A;  3IDY A;  5F4R A;  4I54 A;  4DKV A;  2I5Y G;  1G9N G;  4RFN A;  4DVX A;  3TGT A;  4RX4 E;  4XVS G;  5KJR G;  4JDT G;  4DKU A;  4JM2 E;  4R4N A;  4OLX G;  3NGB A;  4JZW A;  2BF1 A;  4P9H G;  4R4F A;  4KA2 A;  4S1R G;  4LSQ G;  4RZ8 A;  4YDJ G;  3JWD A;  5FEC C;  4JKP G;  4YE4 G;  1YYM G;  4H8W G;  3LQA G;  5F4L A;  1YYL G;  3RJQ A;  4LST G;  2NY2 A;  4J6R G;  4OLY G;  5I9Q A;  4JPV G;  4OLV G;  4XVT G;  4S1S G;  3HI1 G;  4DKQ A;  4OLU G;  5F96 G;  5F4U A;  4S1Q G;  4LSP G;  2NY7 G;  4OLW G;  4JB9 G;  1G9M G;  4OM0 G;  1RZJ G;  3IDX G;  4DVV A;  5F9W A;  4DVS A;  3TGQ A;  5IGX G;  4XNZ A;  1RZK G;  4LAJ A;  4DVT A;  5T33 G;  4DKR A;  4K0A A;  5TE4 G;  4DKP A;  3FUS A;  3TGS A;  2QAD A;  5F9O G;  4LSR G;  5F4P A;  4OM1 G; 
#chains in the Genus database with same CATH topology
 4YFL E;  4LSU G;  4YDK G;  4JPW G;  4LSV G;  4RWY A;  3SE9 G;  2NXY A;  3JWO A;  5FA2 A;  2B4C G;  4YDI G;  5TE6 G;  2I60 G;  4LSS G;  4OLZ G;  5CAY G;  4JZZ A;  4R2G A;  2NY3 A;  3U7Y G;  5CD5 A;  3TIH A;  2NY5 G;  5TE7 G;  2NY6 A;  4DVW A;  4DVR G;  2NXZ A;  4RFO G;  2NY1 A;  3SE8 G;  4YDL A;  4XNY G;  1GC1 G;  2NY0 A;  4DKO A;  4I53 A;  4XMP G;  3TGR A;  2NY4 A;  3IDY A;  5F4R A;  4I54 A;  4DKV A;  2I5Y G;  1G9N G;  4RFN A;  4DVX A;  3TGT A;  4RX4 E;  4XVS G;  5KJR G;  4JDT G;  4DKU A;  4JM2 E;  4R4N A;  4OLX G;  3NGB A;  4JZW A;  2BF1 A;  4P9H G;  4R4F A;  4KA2 A;  4S1R G;  4LSQ G;  4RZ8 A;  4YDJ G;  3JWD A;  5FEC C;  4JKP G;  4YE4 G;  1YYM G;  4H8W G;  3LQA G;  5F4L A;  1YYL G;  3RJQ A;  4LST G;  2NY2 A;  4J6R G;  4OLY G;  5I9Q A;  4JPV G;  4OLV G;  4XVT G;  4S1S G;  3HI1 G;  4DKQ A;  4OLU G;  5F96 G;  5F4U A;  4S1Q G;  4LSP G;  2NY7 G;  4OLW G;  4JB9 G;  1G9M G;  4OM0 G;  1RZJ G;  3IDX G;  4DVV A;  5F9W A;  4DVS A;  3TGQ A;  5IGX G;  4XNZ A;  1RZK G;  4LAJ A;  4DVT A;  5T33 G;  4DKR A;  4K0A A;  5TE4 G;  4DKP A;  3FUS A;  3TGS A;  2QAD A;  5F9O G;  4LSR G;  5F4P A;  4OM1 G; 
#chains in the Genus database with same CATH homology
 4YFL E;  4LSU G;  4YDK G;  4JPW G;  4LSV G;  4RWY A;  3SE9 G;  2NXY A;  3JWO A;  5FA2 A;  2B4C G;  4YDI G;  5TE6 G;  2I60 G;  4LSS G;  4OLZ G;  5CAY G;  4JZZ A;  4R2G A;  2NY3 A;  3U7Y G;  5CD5 A;  3TIH A;  2NY5 G;  5TE7 G;  2NY6 A;  4DVW A;  4DVR G;  2NXZ A;  4RFO G;  2NY1 A;  3SE8 G;  4YDL A;  4XNY G;  1GC1 G;  2NY0 A;  4DKO A;  4I53 A;  4XMP G;  3TGR A;  2NY4 A;  3IDY A;  5F4R A;  4I54 A;  4DKV A;  2I5Y G;  1G9N G;  4RFN A;  4DVX A;  3TGT A;  4RX4 E;  4XVS G;  5KJR G;  4JDT G;  4DKU A;  4JM2 E;  4R4N A;  4OLX G;  3NGB A;  4JZW A;  2BF1 A;  4P9H G;  4R4F A;  4KA2 A;  4S1R G;  4LSQ G;  4RZ8 A;  4YDJ G;  3JWD A;  5FEC C;  4JKP G;  4YE4 G;  1YYM G;  4H8W G;  3LQA G;  5F4L A;  1YYL G;  3RJQ A;  4LST G;  2NY2 A;  4J6R G;  4OLY G;  5I9Q A;  4JPV G;  4OLV G;  4XVT G;  4S1S G;  3HI1 G;  4DKQ A;  4OLU G;  5F96 G;  5F4U A;  4S1Q G;  4LSP G;  2NY7 G;  4OLW G;  4JB9 G;  1G9M G;  4OM0 G;  1RZJ G;  3IDX G;  4DVV A;  5F9W A;  4DVS A;  3TGQ A;  5IGX G;  4XNZ A;  1RZK G;  4LAJ A;  4DVT A;  5T33 G;  4DKR A;  4K0A A;  5TE4 G;  4DKP A;  3FUS A;  3TGS A;  2QAD A;  5F9O G;  4LSR G;  5F4P A;  4OM1 G; 
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similar chains in the Genus database (?% sequence similarity)
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#similar chains in the Genus database (?% sequence similarity)
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