3DOX

X-ray structure of HIV-1 protease in situ product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray structure of HIV-1 protease in situ product complex

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

(2009) Proteins 74: 594-602

  • DOI: 10.1002/prot.22174
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • HIV-1 protease is an effective target for design of different types of drugs against AIDS. HIV-1 protease is also one of the few enzymes that can cleave substrates containing both proline and nonproline residues at the cleavage site. We report here t ...

    HIV-1 protease is an effective target for design of different types of drugs against AIDS. HIV-1 protease is also one of the few enzymes that can cleave substrates containing both proline and nonproline residues at the cleavage site. We report here the first structure of HIV-1 protease complexed with the product peptides SQNY and PIV derived by in situ cleavage of the oligopeptide substrate SQNYPIV, within the crystals. In the structure, refined against 2.0-A resolution synchrotron data, a carboxyl oxygen of SQNY is hydrogen-bonded with the N-terminal nitrogen atom of PIV. At the same time, this proline nitrogen atom does not form any hydrogen bond with catalytic aspartates. These two observations suggest that the protonation of scissile nitrogen, during peptide bond cleavage, is by a gem-hydroxyl of the tetrahedral intermediate rather than by a catalytic aspartic acid.


    Related Citations: 
    • 1.9 A x-ray study shows closed flap conformation in crystals of tethered HIV-1 PR
      Pillai, B., Kannan, K.K., Hosur, M.V.
      (2001) Proteins 43: 57
    • Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex
      Kumar, M., Prashar, V., Mahale, S., Hosur, M.V.
      (2005) Biochem J 389: 365
    • Rapid screening for HIV-1 protease inhibitor leads through X-ray diffraction
      Pillai, B., Kannan, K.K., Bhat, S.V., Hosur, M.V.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 594
    • Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates
      Das, A., Prashar, V., Mahale, S., Serre, L., Ferrer, J.-L., Hosur, M.V.
      (2006) Proc Natl Acad Sci U S A 103: 18464

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASEA203HIV-1 M:B_HXB2RMutation(s): 2 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A PEPTIDE SUBSTRATE-SQNYP4N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
A PEPTIDE SUBSTRATE-PIVQ3N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.38α = 90
b = 62.38β = 90
c = 82γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-09
    Changes: Advisory, Refinement description, Source and taxonomy