PDB entry 1yyl

View 1yyl on RCSB PDB site
Description: crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b
Class: Viral protein/Immune system
Keywords: HIV-1, gp120, YU2, scorpion toxin, CD4 mimic, CD4M33, antibody, Viral protein-Immune system COMPLEX
Deposited on 2005-02-25, released 2005-05-03
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 2.75 Å
R-factor: 0.202
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961
      • linker (49-51)
      • linker (155-157)
    Domains in SCOPe 2.03: d1yylg_
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Domains in SCOPe 2.03: d1yylh1, d1yylh2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Domains in SCOPe 2.03: d1yyll1, d1yyll2
  • Chain 'M':
    Compound: CD4M33, scorpion-toxin mimic of CD4
    Species: synthetic, synthetic
    Domains in SCOPe 2.03: d1yylm1
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (158-312)
      • linker (49-51)
      • linker (155-157)
    Domains in SCOPe 2.03: d1yylp_
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Domains in SCOPe 2.03: d1yylq1, d1yylq2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Domains in SCOPe 2.03: d1yylr1, d1yylr2
  • Chain 'S':
    Compound: CD4M33, scorpion-toxin mimic of CD4
    Species: synthetic, synthetic
    Domains in SCOPe 2.03: d1yyls1
  • Heterogens: NAG, NDG, HOH

PDB Chain Sequences:

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >1yylG (G:)
    garsevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvit
    qacpkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqllln
    gslaeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklke
    qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
    ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
    rselykykvvkie
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yylG (G:)
    evklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqacp
    kvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsla
    eeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfgn
    nktiifnpssggdpeivthsfncggeffycnstqlftwndrnitlpcrikqiinmwqevg
    kamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvki
    e
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yylH (H:)
    evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
    aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
    gtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
    fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yylL (L:)
    divmtqspatlsvspgeratlscrasesvssdlawyqqkpgqaprlliygastratgvpa
    rfsgsgsgaeftltisslqsedfavyycqqynnwpprytfgqgtrleikrtvaapsvfif
    ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
    ltlskadyekhkvyacevthqglsspvtksfnrg
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yylM (M:)
    xnlhfcqlrckslgllgkcagsfcacx
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >1yylP (P:)
    garsevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvit
    qacpkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqllln
    gslaeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklke
    qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
    ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
    rselykykvvkie
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yylP (P:)
    evklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqacp
    kvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsla
    eeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfgn
    nktiifnpssggdpeivthsfncggeffycnstqlftwndrnitlpcrikqiinmwqevg
    kamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvki
    e
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yylQ (Q:)
    divmtqspatlsvspgeratlscrasesvssdlawyqqkpgqaprlliygastratgvpa
    rfsgsgsgaeftltisslqsedfavyycqqynnwpprytfgqgtrleikrtvaapsvfif
    ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
    ltlskadyekhkvyacevthqglsspvtksfnrg
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yylR (R:)
    evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
    aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
    gtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
    fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yylS (S:)
    xnlhfcqlrckslgllgkcagsfcacx