PDB entry 2i5y

View 2i5y on RCSB PDB site
Description: Crystal structure of CD4M47, 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, cd4m47, antibody, viral protein-immune system complex
Deposited on 2006-08-26, released 2006-10-10
The last revision prior to the SCOPe 2.06 freeze date was dated 2012-06-06, with a file datestamp of 2012-06-01.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: 0.214
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus [TaxId:12721]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
      • cloning artifact (3)
    • Uniprot P35961 (52-154)
      • linker (49-51)
    • Uniprot P35961 (158-312)
      • linker (155-157)
    Domains in SCOPe 2.06: d2i5yg2, d2i5yg3
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I5Y (0-228)
    Domains in SCOPe 2.06: d2i5yh1, d2i5yh2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I5Y (1-213)
    Domains in SCOPe 2.06: d2i5yl1, d2i5yl2
  • Chain 'M':
    Compound: cd4m47, scorpion-toxin mimic of cd4
    Species: synthetic, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I5Y (0-26)
    Domains in SCOPe 2.06: d2i5ym1
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus [TaxId:12721]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
      • cloning artifact (3)
    • Uniprot P35961 (52-154)
      • linker (49-51)
    • Uniprot P35961 (158-312)
      • linker (155-157)
    Domains in SCOPe 2.06: d2i5yp2, d2i5yp3
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I5Y (1-213)
    Domains in SCOPe 2.06: d2i5yq1, d2i5yq2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I5Y (0-228)
    Domains in SCOPe 2.06: d2i5yr1, d2i5yr2
  • Chain 'S':
    Compound: cd4m47, scorpion-toxin mimic of cd4
    Species: synthetic, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I5Y (0-26)
    Domains in SCOPe 2.06: d2i5ys1
  • Heterogens: NAG, NDG, HOH

PDB Chain Sequences:

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2i5yG (G:)
    garsevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvit
    qacpkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqllln
    gslaeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklke
    qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
    ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
    rselykykvvkie
    

    Sequence, based on observed residues (ATOM records): (download)
    >2i5yG (G:)
    sevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqac
    pkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsl
    aeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfg
    nnktiifnpssggdpeivthsfncggeffycnstqlftwndrnitlpcrikqiinmwqev
    gkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvk
    ie
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2i5yH (H:)
    evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
    aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
    gtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
    fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2i5yH (H:)
    evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
    aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
    gtlvtvssastkgpsvfplapsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
    qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2i5yL (L:)
    divmtqspatlsvspgeratlscrasesvssdlawyqqkpgqaprlliygastratgvpa
    rfsgsgsgaeftltisslqsedfavyycqqynnwpprytfgqgtrleikrtvaapsvfif
    ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
    ltlskadyekhkvyacevthqglsspvtksfnrg
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2i5yM (M:)
    xnlhfcqlrckslgllgrcaptfcacx
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >2i5yP (P:)
    garsevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvit
    qacpkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqllln
    gslaeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklke
    qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
    ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
    rselykykvvkie
    

    Sequence, based on observed residues (ATOM records): (download)
    >2i5yP (P:)
    sevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqac
    pkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsl
    aeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfg
    nnktiifnpssggdpeivthsfncggeffycnstqlftwrnitlpcrikqiinmwqevgk
    amyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvkie
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2i5yQ (Q:)
    divmtqspatlsvspgeratlscrasesvssdlawyqqkpgqaprlliygastratgvpa
    rfsgsgsgaeftltisslqsedfavyycqqynnwpprytfgqgtrleikrtvaapsvfif
    ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
    ltlskadyekhkvyacevthqglsspvtksfnrg
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >2i5yR (R:)
    evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
    aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
    gtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
    fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2i5yR (R:)
    evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
    aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
    gtlvtvssastkgpsvfplapsgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlq
    ssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2i5yS (S:)
    xnlhfcqlrckslgllgrcaptfcacx