2WHH

HIV-1 protease tethered dimer Q-product complex along with nucleophilic water molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Catalytic Water Co-Existing with a Product Peptide in the Active Site of HIV-1 Protease Revealed by X- Ray Structure Analysis.

Prashar, V.Bihani, S.Das, A.Ferrer, J.L.Hosur, M.V.

(2009) PLoS One 4: E7860

  • DOI: https://doi.org/10.1371/journal.pone.0007860
  • Primary Citation of Related Structures:  
    2WHH

  • PubMed Abstract: 

    It is known that HIV-1 protease is an important target for design of antiviral compounds in the treatment of Acquired Immuno Deficiency Syndrome (AIDS). In this context, understanding the catalytic mechanism of the enzyme is of crucial importance as transition state structure directs inhibitor design. Most mechanistic proposals invoke nucleophilic attack on the scissile peptide bond by a water molecule. But such a water molecule coexisting with any ligand in the active site has not been found so far in the crystal structures.


  • Organizational Affiliation

    Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POL PROTEIN203Human immunodeficiency virus 1Mutation(s): 1 
EC: 3.4.23.16
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.54α = 90
b = 62.54β = 90
c = 81.99γ = 120
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description