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: virus/viral protein/immune system
Keywords: hiv-1, gp120, yu2, scorpion toxin, cd4 mimic, cd4m47, antibody
Deposited on 2006-08-26, released 2006-10-10
The last revision prior to the SCOP 1.73 freeze date was dated 2006-10-10, with a file datestamp of 2007-06-28.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: 0.214
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
      • cloning artifact (3)
      • linker (49-51)
      • linker (155-157)
    • Uniprot P35961 (52-154)
    • Uniprot P35961 (158-312)
    Domains in SCOP 1.73: d2i5yg1
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i5yh1, d2i5yh2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i5yl1, d2i5yl2
  • Chain 'M':
    Compound: cd4m47, scorpion-toxin mimic of cd4
    Species: synthetic, synthetic
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
      • cloning artifact (3)
      • linker (49-51)
      • linker (155-157)
    • Uniprot P35961 (52-154)
    • Uniprot P35961 (158-312)
    Domains in SCOP 1.73: d2i5yp1
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i5yq1, d2i5yq2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i5yr1, d2i5yr2
  • Chain 'S':
    Compound: cd4m47, scorpion-toxin mimic of cd4
    Species: synthetic, synthetic
  • 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':
    No sequence available.

  • 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':
    No sequence available.