PDB entry 4dvr

View 4dvr on RCSB PDB site
Description: Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
Class: immune system/transcription inhibitor
Keywords: HIV-1 gp120, CD4 binding site, NBD-557, IMMUNE SYSTEM-TRANSCRIPTION INHIBITOR complex
Deposited on 2012-02-23, released 2013-02-27
The last revision prior to the SCOPe 2.05 freeze date was dated 2014-12-17, with a file datestamp of 2014-12-12.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.233
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: glycoprotein gp120
    Species: Human immunodeficiency virus type 1 (isolate YU2) [TaxId:362651]
    Gene: env, HIV-1 Env
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (152-312)
      • linker (41-42)
    Domains in SCOPe 2.05: d4dvrg_
  • Chain 'H':
    Compound: Fab 48d heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4DVR (0-218)
    Domains in SCOPe 2.05: d4dvrh1, d4dvrh2
  • Chain 'L':
    Compound: Fab 48d light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4DVR (Start-211)
    Domains in SCOPe 2.05: d4dvrl1, d4dvrl2
  • Heterogens: NAG, 0LY, HOH

PDB Chain Sequences:

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4dvrG (G:)
    evklenvtenfnmwknnmveqmhediislwdqslkpcvkltggsvitqacpkvsfepipi
    hycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngslaeeeivirse
    nftnnaktiivqlnesvvinctrpnnggsgsggdirqahcnlsktqwentleqiaiklke
    qfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitlpcr
    ikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmrdnw
    rselykykvvkie
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dvrG (G:)
    tenfnmwknnmveqmhediislwdqslkpcvkltggsvitqacpkvsfepipihycapag
    failkcndkkfngtgpctnvstvqcthgirpvvstqlllngslaeeeivirsenftnnak
    tiivqlnesvvinctrpnngdirqahcnlsktqwentleqiaiklkeqfgnnktiifnps
    sggdpeivthsfncggeffycnstqlftwndtrnitlpcrikqiinmwqevgkamyappi
    rgqircssnitgllltrdngteifrpgggdmrdnwrselykykvvkie
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4dvrH (H:)
    evqlvqsgaevkkpgatvkisckasgytfsdfymywvrqapgkglewmglidpedadtmy
    aekfrgrvtitadtstdtgylelsslrsedtavyycaadpwelnafnvwgqgtlvsvssa
    stkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssg
    lyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvep
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >4dvrL (L:)
    diqmtqspssvsasvgdrvtitcrasqdistwlawyqqkpgkapklliyaastlqsgvps
    rfsgsgsgtdfsltinslqpedfatyycqqansfftfgggtkveikrtvaapsvfifpps
    deqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltl
    skadyekhklyacevthqglsspvtksfnrge
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dvrL (L:)
    iqmtqspssvsasvgdrvtitcrasqdistwlawyqqkpgkapklliyaastlqsgvpsr
    fsgsgsgtdfsltinslqpedfatyycqqansfftfgggtkveikrtvaapsvfifppsd
    eqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltls
    kadyekhklyacevthqglsspvtksfnrge