1AVZ Complex (Myristylation Transferase) date Sep 23, 1997
title V-1 Nef Protein In Complex With Wild Type Fyn Sh3 Domain
authors S.Arold, P.Franken, C.Dumas
compound source
Molecule: Negative Factor
Chain: A, B
Fragment: Conserved Core Domain
Synonym: Nef, F-Protein
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Variant: Lai Isolate
Cell_line: Bl21
Gene: Hiv-1 Nef
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pgex-2t

Molecule: Fyn Tyrosine Kinase
Chain: C
Fragment: Src-Homology 3 Domain
Synonym: Sh3 Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Bl21
Gene: Fyn Tyrosine Kinase
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pgex-2t
symmetry Space Group: P 65 2 2
R_factor 0.220 R_Free 0.270
length a length b length c angle alpha angle beta angle gamma
108.200 108.200 223.700 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1AVV, 1EFN, 1KSW, 1QWF
A, B

Primary referenceThe crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling., Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C, Structure 1997 Oct 15;5(10):1361-72. PMID:9351809
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (1avz.pdb1.gz) 41 Kb
  • CSU: Contacts of Structural Units for 1AVZ
  • Likely Quarternary Molecular Structure file(s) for 1AVZ
  • Retrieve 1AVZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1AVZ from S2C, [Save to disk]
  • View 1AVZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1AVZ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1AVZ, from MSDmotif at EBI
  • Genome occurence of 1AVZ's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1avza_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1avzb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1avzc_, region C [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1avz_C] [1avz] [1avz_A] [1avz_B]
  • SWISS-PROT database: [P06241] [P03406]
  • Domain organization of [FYN_HUMAN] [NEF_HV1BR] by SWISSPFAM
  • Domain found in 1AVZ: [SH3 ] by SMART
  • Other resources with information on 1AVZ
  • Community annotation for 1AVZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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