3KT2

Crystal Structure of N88D mutant HIV-1 Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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This is version 1.4 of the entry. See complete history


Literature

Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S.

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

(2009) Biochem Biophys Res Commun 389: 295-300

  • DOI: https://doi.org/10.1016/j.bbrc.2009.08.138
  • Primary Citation of Related Structures:  
    3KT2, 3KT5

  • PubMed Abstract: 

    Nelfinavir is an inhibitor of HIV-1 protease, and is used for treatment of patients suffering from HIV/AIDS. However, treatment results in drug resistant mutations in HIV-1 protease. N88D and N88S are two such mutations which occur in the non-active site region of the enzyme. We have determined crystal structures of unliganded N88D and N88S mutants of HIV-1 protease to resolution of 1.65A and 1.8A, respectively. These structures refined against synchrotron data lead to R-factors of 0.1859 and 0.1780, respectively. While structural effects of N88D are very subtle, the mutation N88S has caused a significant conformational change in D30, an active site residue crucial for substrate and inhibitor binding.


  • Organizational Affiliation

    Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease203HIV-1 M:B_HXB2RMutation(s): 4 
Gene Names: gag-pol
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: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.05α = 90
b = 62.05β = 90
c = 83.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2024-05-29
    Changes: Data collection