PDB entry 1yym

View 1yym on RCSB PDB site
Description: crystal structure of F23, 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, F23, antibody
Deposited on 2005-02-25, released 2005-05-03
The last revision prior to the SCOP 1.73 freeze date was dated 2005-05-10, with a file datestamp of 2007-06-28.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: 0.209
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 type 1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961
      • linker (49-51)
      • linker (155-157)
    Domains in SCOP 1.73: d1yymg1
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d1yymh1, d1yymh2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d1yyml1, d1yyml2
  • Chain 'M':
    Compound: F23, scorpion-toxin mimic of CD4
    Species: synthetic, synthetic
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus type 1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (158-312)
      • linker (49-51)
      • linker (155-157)
    Domains in SCOP 1.73: d1yymp1
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d1yymq1, d1yymq2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d1yymr1, d1yymr2
  • Chain 'S':
    Compound: F23, scorpion-toxin mimic of CD4
    Species: synthetic, synthetic
  • Heterogens: NAG, NDG, EDO, IPA, HOH

PDB Chain Sequences:

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

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

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

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

  • Chain 'M':
    No sequence available.

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

    Sequence, based on observed residues (ATOM records): (download)
    >1yymP (P:)
    evklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqacp
    kvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsla
    eeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfgn
    nktiifnpssggdpeivthsfncggeffycnstqlftwrnitlpcrikqiinmwqevgka
    myappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvkie
    

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

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

  • Chain 'S':
    No sequence available.