Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 10.98 kDa 
• Atom Count: 780 
• Residue Count: 99 
• Unique protein chains: 1

2SAM

STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR

• DOI: 10.2210/pdb2SAM/pdb

• Classification: HYDROLASE(ACID PROTEASE)
• Organism(s): Simian immunodeficiency virus
• Mutation(s): No 


• Deposited: 1994-07-08 Released: 1994-10-15 
• Deposition Author(s): Rose, R.B., Rose, J.R., Salto, R., Craik, C.S., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor.

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

(1993) Biochemistry 32: 12498-12507

• PubMed: 8241141 
• DOI: 10.1021/bi00097a030
• Primary Citation of Related Structures:  
  2SAM


• PubMed Abstract: 
  

A variant of the simian immunodeficiency virus protease (SIV PR), covalently bound to the inhibitor 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), was crystallized. The structure of the inhibited complex was determined by X-ray crystallography to a resolution of 2.4 A and refined to an R factor of 19%. The variant, SIV PR S4H, was shown to diminish the rate of autolysis by at least 4-fold without affecting enzymatic parameters. The overall root mean square (rms) deviation of the alpha-carbons from the structure of HIV-1PR complexed with a peptidomimetic inhibitor (7HVP) was 1.16 A. The major differences are concentrated in three surface loops with rms differences between 1.2 and 2.1 A. For 60% of the molecule the rms deviation was only 0.6 A. The structure reveals one molecule of EPNP bound per protease dimer, a stoichiometry confirmed by mass spectral analysis. The epoxide moiety forms a covalent bond with either of the active site aspartic acids of the dimer, and the phenyl moiety occupies the P1 binding site. The EPNP nitro group interacts with Arg 8. This structure suggests a starting template for the design of nonpeptide-based irreversible inhibitors of the SIV and related HIV-1 and HIV-2 PRs.

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Organizational Affiliation: 

Department of Biochemistry, University of California at San Francisco 94143-0448.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIV PROTEASE	A	99	Simian immunodeficiency virus	Mutation(s): 0  Gene Names: pol EC: 2.7.7.49 (UniProt), 3.1.13.2 (UniProt), 3.1.26.13 (UniProt)
Find proteins for Q5QGH9 (Simian immunodeficiency virus) Explore Q5QGH9  Go to UniProtKB:  Q5QGH9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPN	A	3-(4-NITRO-PHENOXY)-PROPAN-1-OL C9 H11 N O4 XHRNQMMJGWBTBU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.7	α = 90
b = 32.2	β = 90
c = 96.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-07-08 
• Released Date: 1994-10-15 
Deposition Author(s): Rose, R.B., Rose, J.R., Salto, R., Craik, C.S., Stroud, R.M.

Revision History 

• Version 1.0: 1994-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other