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 2.07 freeze date was dated 2017-05-31, with a file datestamp of 2017-05-26.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'G':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus type 1 group M subtype B (isolate YU-2) [TaxId:362651]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot P35961 (Start-40)
      • linker (41-42)
    • Uniprot P35961 (43-145)
    • Uniprot P35961 (152-312)
    Domains in SCOPe 2.07: 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 2.07: 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 2.07: 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