4EXH

The crystal structure of xmrv protease complexed with acetyl-pepstatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibition of XMRV and HIV-1 proteases by pepstatin A and acetyl-pepstatin.

Matuz, K.Motyan, J.Li, M.Wlodawer, A.

(2012) Febs J. 279: 3276-3286

  • DOI: 10.1111/j.1742-4658.2012.08714.x

  • PubMed Abstract: 
  • The kinetic properties of two classical inhibitors of aspartic proteases (PRs), pepstatin A and acetyl-pepstatin, were compared in their interactions with HIV-1 and xenotropic murine leukemia virus related virus (XMRV) PRs. Both compounds are substan ...

    The kinetic properties of two classical inhibitors of aspartic proteases (PRs), pepstatin A and acetyl-pepstatin, were compared in their interactions with HIV-1 and xenotropic murine leukemia virus related virus (XMRV) PRs. Both compounds are substantially weaker inhibitors of XMRV PR than of HIV-1 PR. Previous kinetic and structural studies characterized HIV-1 PR-acetyl-pepstatin and XMRV PR-pepstatin A complexes and suggested dramatically different binding modes. Interaction energies were calculated for the possible binding modes and suggested a strong preference for the one-inhibitor binding mode for HIV-1 PR-acetyl-pepstatin and the two-inhibitor binding mode for XMRV PR-pepstatin A interactions. Comparison of the molecular models suggested that in the case of XMRV PR the relatively unfavorable interactions at S3' and the favorable interactions at S4 and S4' sites with the statine residues may shift the ground state binding towards the two-inhibitor binding mode, whereas the single molecule ground state binding of statines to the HIV-1 PR appear to be more favorable. The preferred single molecular binding to HIV-1 PR allows the formation of the transition state complex, represented by substantially better binding constants. Intriguingly, the crystal structure of the complex of acetyl-pepstatin with XMRV PR has shown a mixed type of binding: the unusual binding mode of two molecules of the inhibitor to the enzyme, in a mode very similar to the previously determined complex with pepstatin A, together with the classical binding mode found for HIV-1 PR. The structure is thus in good agreement with the very similar interaction energies calculated for the two types of binding.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative gag-pro-pol polyprotein
A, B
132DG-75 Murine leukemia virusMutation(s): 0 
Find proteins for Q9E7M1 (DG-75 Murine leukemia virus)
Go to UniProtKB:  Q9E7M1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACETYL-PEPSTATIN
J, M, P
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
M
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001057
Query on PRD_001057
MACETYL-PEPSTATINOligopeptide / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.314α = 90.00
b = 65.210β = 90.00
c = 69.468γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
MAR345data collection
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-30 
  • Released Date: 2012-08-01 
  • Deposition Author(s): Li, M., Wlodawer, A.

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2017-11-15
    Type: Advisory, Refinement description