PDB entry 2i60

View 2i60 on RCSB PDB site
Description: Crystal structure of [Phe23]M47, 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, [Phe23]M47, antibody, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Deposited on 2006-08-26, released 2006-10-10
The last revision prior to the SCOPe 2.05 freeze date was dated 2012-06-06, with a file datestamp of 2012-06-01.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: 0.215
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
    • Uniprot P35961 (52-154)
      • linker (49-51)
    • Uniprot P35961 (158-312)
      • linker (155-157)
    Domains in SCOPe 2.05: d2i60g_
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I60 (Start-228)
    Domains in SCOPe 2.05: d2i60h1, d2i60h2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I60 (0-213)
    Domains in SCOPe 2.05: d2i60l1, d2i60l2
  • Chain 'M':
    Compound: [phe23]m47, scorpion-toxin mimic of cd4
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I60 (0-26)
    Domains in SCOPe 2.05: d2i60m1
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    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 2.05: d2i60p_
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I60 (0-213)
    Domains in SCOPe 2.05: d2i60q1, d2i60q2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I60 (0-228)
    Domains in SCOPe 2.05: d2i60r1, d2i60r2
  • Chain 'S':
    Compound: [phe23]m47, scorpion-toxin mimic of cd4
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 2I60 (0-26)
    Domains in SCOPe 2.05: d2i60s1
  • Heterogens: NAG, NDG, IPA, HOH

PDB Chain Sequences:

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >2i60G (G:)
garsevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvit
qacpkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqllln
gslaeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklke
qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
rselykykvvkie

    Sequence, based on observed residues (ATOM records): (download) 
    >2i60G (G:)
evklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqacp
kvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsla
eeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfgn
nktiifnpssggdpeivthsfncggeffycnstqlftwndrnitlpcrikqiinmwqevg
kamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvki
e

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >2i60H (H:)
evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
gtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

    Sequence, based on observed residues (ATOM records): (download) 
    >2i60H (H:)
vqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahya
phlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgqg
tlvtvssastkgpsvfplapgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2i60L (L:)
divmtqspatlsvspgeratlscrasesvssdlawyqqkpgqaprlliygastratgvpa
rfsgsgsgaeftltisslqsedfavyycqqynnwpprytfgqgtrleikrtvaapsvfif
ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
ltlskadyekhkvyacevthqglsspvtksfnrg

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2i60M (M:)
xnlhfcqlrckslgllgrcaptfcacx

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >2i60P (P:)
garsevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvit
qacpkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqllln
gslaeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklke
qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
rselykykvvkie

    Sequence, based on observed residues (ATOM records): (download) 
    >2i60P (P:)
sevklenvtenfnmwknnmveqmhediislwdqslkpcvkltplcvgagscntsvitqac
pkvsfepipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngsl
aeeeivirsenftnnaktiivqlnesvvinctgaghcnlsktqwentleqiaiklkeqfg
nnktiifnpssggdpeivthsfncggeffycnstqlftwrnitlpcrikqiinmwqevgk
amyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnwrselykykvvkie

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2i60Q (Q:)
divmtqspatlsvspgeratlscrasesvssdlawyqqkpgqaprlliygastratgvpa
rfsgsgsgaeftltisslqsedfavyycqqynnwpprytfgqgtrleikrtvaapsvfif
ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
ltlskadyekhkvyacevthqglsspvtksfnrg

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >2i60R (R:)
evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
gtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvht
fpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

    Sequence, based on observed residues (ATOM records): (download) 
    >2i60R (R:)
evqlvesgaevkkpgssvkvsckasgdtfirysftwvrqapgqglewmgriitildvahy
aphlqgrvtitadkststvylelrnlrsddtavyfcagvyegeadegeydnngflkhwgq
gtlvtvssastkgpsvfplapgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2i60S (S:)
xnlhfcqlrckslgllgrcaptfcacx