PDB entry 4d8d

View 4d8d on RCSB PDB site
Description: Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant
Class: transferase/protein binding
Keywords: signaling molecules, TRANSFERASE-PROTEIN BINDING complex
Deposited on 2012-01-10, released 2013-01-16
The last revision prior to the SCOPe 2.07 freeze date was dated 2013-01-16, with a file datestamp of 2013-01-11.
Experiment type: XRAY
Resolution: 2.52 Å
R-factor: 0.213
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Tyrosine-protein kinase Fyn
    Species: Homo sapiens [TaxId:9606]
    Gene: FYN, FYN TYROSINE KINASE
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06241 (Start-57)
      • engineered mutation (12)
    Domains in SCOPe 2.07: d4d8da_
  • Chain 'B':
    Compound: Protein Nef
    Species: Human immunodeficiency virus type 1 [TaxId:11686]
    Gene: nef
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4d8db_
  • Chain 'C':
    Compound: Tyrosine-protein kinase Fyn
    Species: Homo sapiens [TaxId:9606]
    Gene: FYN, FYN TYROSINE KINASE
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06241 (0-57)
      • engineered mutation (12)
    Domains in SCOPe 2.07: d4d8dc_
  • Chain 'D':
    Compound: Protein Nef
    Species: Human immunodeficiency virus type 1 [TaxId:11686]
    Gene: nef
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4d8dd_
  • Heterogens: GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4d8dA (A:)
vtlfvalydyeawteddlsfhkgekfqilnssegdwwearslttgetgyipsnyvapv

    Sequence, based on observed residues (ATOM records): (download) 
    >4d8dA (A:)
tlfvalydyeawteddlsfhkgekfqilnssegdwwearslttgetgyipsnyvapv

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4d8dB (B:)
gsleaqeeeevgfpvtpqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiy
htqgyfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpvslhgmdd
perevlewrfdsrlafhhvarelhpeyfknc

    Sequence, based on observed residues (ATOM records): (download) 
    >4d8dB (B:)
pvtpqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiyhtqgyfpdwqnyt
pgpgvrypltfgwcyklvpvevlewrfdsrlafhhvarelhpeyfk

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d8dC (C:)
vtlfvalydyeawteddlsfhkgekfqilnssegdwwearslttgetgyipsnyvapv

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4d8dD (D:)
gsleaqeeeevgfpvtpqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiy
htqgyfpdwqnytpgpgvrypltfgwcyklvpvepdkveeankgentsllhpvslhgmdd
perevlewrfdsrlafhhvarelhpeyfknc

    Sequence, based on observed residues (ATOM records): (download) 
    >4d8dD (D:)
vtpqvplrpmtykaavdlshflkekggleglihsqrrqdildlwiyhtqgyfpdwqnytp
gpgvrypltfgwcyklvpvevlewrfdsrlafhhvarelhpeyfk