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: virus/viral protein/immune system
Keywords: HIV-1, GP120, YU2, scorpion toxin, CD4 mimic, [Phe23]M47, 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: 2.4 Å
R-factor: 0.215
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (4-48)
      • linker (49-51)
      • linker (155-157)
    • Uniprot P35961 (52-154)
    • Uniprot P35961 (158-312)
    Domains in SCOP 1.73: d2i60g1
  • Chain 'H':
    Compound: Antibody 17B Heavy chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i60h1, d2i60h2
  • Chain 'L':
    Compound: Antibody 17B Light chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i60l1, d2i60l2
  • Chain 'M':
    Compound: [phe23]m47, scorpion-toxin mimic of cd4
    Species: synthetic, synthetic
  • Chain 'P':
    Compound: Exterior membrane glycoprotein(GP120)
    Species: Human immunodeficiency virus 1
    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: d2i60p1
  • Chain 'Q':
    Compound: Antibody 17B Light chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i60q1, d2i60q2
  • Chain 'R':
    Compound: Antibody 17B Heavy chain
    Species: HOMO SAPIENS
    Domains in SCOP 1.73: d2i60r1, d2i60r2
  • Chain 'S':
    Compound: [phe23]m47, scorpion-toxin mimic of cd4
    Species: synthetic, synthetic
  • 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':
    No sequence available.

  • 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':
    No sequence available.