Crystal structure of Rous sarcoma virus protease in complex with inhibitor

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Structural basis for specificity of retroviral proteases.

Wu, J.Adomat, J.M.Ridky, T.W.Louis, J.M.Leis, J.Harrison, R.W.Weber, I.T.

(1998) Biochemistry 37: 4518-4526

  • DOI: https://doi.org/10.1021/bi972183g
  • Primary Citation of Related Structures:  
    1A94, 1BAI

  • PubMed Abstract: 

    The Rous sarcoma virus (RSV) protease S9 variant has been engineered to exhibit high affinity for HIV-1 protease substrates and inhibitors in order to verify the residues deduced to be critical for the specificity differences. The variant has 9 substitutions (S38T, I42D, I44V, M73V, A100L, V104T, R105P, G106V, and S107N) of structurally equivalent residues from HIV-1 protease. Unlike the wild-type enzyme, RSV S9 protease hydrolyzes peptides representing the HIV-1 protease polyprotein cleavage sites. The crystal structure of RSV S9 protease with the inhibitor, Arg-Val-Leu-r-Phe-Glu-Ala-Nle-NH2, a reduced peptide analogue of the HIV-1 CA-p2 cleavage site, has been refined to an R factor of 0.175 at 2.4-A resolution. The structure shows flap residues that were not visible in the previous crystal structure of unliganded wild-type enzyme. Flap residues 64-76 are structurally similar to residues 47-59 of HIV-1 protease. However, residues 61-63 form unique loops at the base of the flaps. Mutational analysis indicates that these loop residues are essential for catalytic activity. Side chains of flap residues His 65 and Gln 63' make hydrogen bond interactions with the inhibitor P3 amide and P4' carbonyl oxygen, respectively. Other interactions of RSV S9 protease with the CA-p2 analogue are very similar to those observed in the crystal structure of HIV-1 protease with the same inhibitor. This is the first crystal structure of an avian retroviral protease in complex with an inhibitor, and it verifies our knowledge of the molecular basis for specificity differences between RSV and HIV-1 proteases.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107,

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
124Rous sarcoma virusMutation(s): 7 
Find proteins for P03322 (Rous sarcoma virus subgroup C (strain Prague))
Explore P03322 
Go to UniProtKB:  P03322
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03322
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0Q4

Download Ideal Coordinates CCD File 
C [auth A]N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide
C40 H70 N11 O8
Binding Affinity Annotations 
IDSourceBinding Affinity
0Q4 Binding MOAD:  1BAI Ki: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.61α = 90
b = 62.61β = 90
c = 132.15γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
R-AXISdata reduction
R-AXISdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary