3DOX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 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

  • 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: 
    • 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.Usa 103: 18464
    • 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.,Sect.D 60: 594
    • 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


    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 PROTEASE
A
203Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A PEPTIDE SUBSTRATE-SQNY
P
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
A PEPTIDE SUBSTRATE-PIV
Q
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.380α = 90.00
b = 62.380β = 90.00
c = 82.000γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
CNSphasing
CNSrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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