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, Viral protein-Immune system COMPLEX
Deposited on 2005-02-25, released 2005-05-03
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1yymg_
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YYM
    Domains in SCOPe 2.08: d1yymh1, d1yymh2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YYM
    Domains in SCOPe 2.08: d1yyml1, d1yyml2
  • Chain 'M':
    Compound: F23, scorpion-toxin mimic of CD4
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YYM
    Domains in SCOPe 2.08: d1yymm1
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
      • linker (49-51)
    • Uniprot P35961 (52-154)
      • linker (155-157)
    • Uniprot P35961 (158-312)
    Domains in SCOPe 2.08: d1yymp_
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YYM (0-213)
    Domains in SCOPe 2.08: d1yymq1, d1yymq2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YYM (0-228)
    Domains in SCOPe 2.08: d1yymr1, d1yymr2
  • Chain 'S':
    Compound: F23, scorpion-toxin mimic of CD4
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YYM (0-26)
    Domains in SCOPe 2.08: d1yyms1
  • Heterogens: NAG, 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':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yymM (M:)
xnlhfcqlrckslgllgkcagsfcacx

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