Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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This is version 2.2 of the entry. See complete history


Domain flexibility in retroviral proteases: structural implications for drug resistant mutations.

Rose, R.B.Craik, C.S.Stroud, R.M.

(1998) Biochemistry 37: 2607-2621

  • DOI: https://doi.org/10.1021/bi9716074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Rigid body rotation of five domains and movements within their interfacial joints provide a rational context for understanding why HIV protease mutations that arise in drug resistant strains are often spatially removed from the drug or substrate binding sites. Domain motions associated with substrate binding in the retroviral HIV-1 and SIV proteases are identified and characterized. These motions are in addition to closure of the flaps and result from rotations of approximately 6-7 degrees at primarily hydrophobic interfaces. A crystal structure of unliganded SIV protease (incorporating the point mutation Ser 4 His to stabilize the protease against autolysis) was determined to 2.0 A resolution in a new space group, P3221. The structure is in the most "open" conformation of any retroviral protease so far examined, with six residues of the flaps disordered. Comparison of this and unliganded HIV structures, with their respective liganded structures by difference distance matrixes identifies five domains of the protease dimer that move as rigid bodies against one another: one terminal domain encompassing the N- and C-terminal beta sheet of the dimer, two core domains containing the catalytic aspartic acids, and two flap domains. The two core domains rotate toward each other on substrate binding, reshaping the binding pocket. We therefore show that, for enzymes, mutations at interdomain interfaces that favor the unliganded form of the target active site will increase the off-rate of the inhibitor, allowing the substrate greater access for catalysis. This offers a mechanism of resistance to competitive inhibitors, especially when the forward enzymatic reaction rate exceeds the rate of substrate dissociation.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California in San Francisco, San Francisco, California 94143-0448, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIV PROTEASE99Simian immunodeficiency virusMutation(s): 1 
Gene Names: SIV(MAC)239
Find proteins for P05896 (Simian immunodeficiency virus (isolate Mm142-83))
Explore P05896 
Go to UniProtKB:  P05896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05896
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.4α = 90
b = 45.4β = 90
c = 87.9γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 2.0: 2021-11-03
    Changes: Atomic model, Database references, Other
  • Version 2.1: 2024-02-07
    Changes: Data collection
  • Version 2.2: 2024-04-03
    Changes: Refinement description