Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29.20 kDa 
• Atom Count: 1912 
• Modelled Residue Count: 228 
• Deposited Residue Count: 264 
• Unique protein chains: 1

3SM2

The crystal structure of XMRV protease complexed with Amprenavir

• PDB DOI: 10.2210/pdb3SM2/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): DG-75 Murine leukemia virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-27 Released: 2011-10-12 
• Deposition Author(s): Li, M., Gustchina, A., Wlodawer, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Structural and biochemical characterization of the inhibitor complexes of xenotropic murine leukemia virus-related virus protease.

Li, M., Gustchina, A., Matuz, K., Tozser, J., Namwong, S., Goldfarb, N.E., Dunn, B.M., Wlodawer, A.

(2011) FEBS J 278: 4413-4424

• PubMed: 21951660 
• DOI: 10.1111/j.1742-4658.2011.08364.x
• Primary Citation of Related Structures:  
  3SLZ, 3SM1, 3SM2


• PubMed Abstract: 
  

Interactions between the protease (PR) encoded by the xenotropic murine leukemia virus-related virus and a number of potential inhibitors have been investigated by biochemical and structural techniques. It was observed that several inhibitors used clinically against HIV PR exhibit nanomolar or even subnanomolar values of K(i) , depending on the exact experimental conditions. Both TL-3, a universal inhibitor of retroviral PRs, and some inhibitors originally shown to inhibit plasmepsins were also quite potent, whereas inhibition by pepstatin A was considerably weaker. Crystal structures of the complexes of xenotropic murine leukemia virus-related virus PR with TL-3, amprenavir and pepstatin A were solved at high resolution and compared with the structures of complexes of these inhibitors with other retropepsins. Whereas TL-3 and amprenavir bound in a predictable manner, spanning the substrate-binding site of the enzyme, two molecules of pepstatin A bound simultaneously in an unprecedented manner, leaving the catalytic water molecule in place.

---

Organizational Affiliation: 

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gag-pro-pol polyprotein	A, B	132	DG-75 Murine leukemia virus	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt)
UniProt
Find proteins for Q9E7M1 (DG-75 Murine leukemia virus) Explore Q9E7M1  Go to UniProtKB:  Q9E7M1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
478	C [auth A]	{3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER C25 H35 N3 O6 S YMARZQAQMVYCKC-OEMFJLHTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
478	PDBBind:  3SM2	Ki: 0.2 (nM) from 1 assay(s)
	Binding MOAD:  3SM2	Ki: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.572	α = 90
b = 65.099	β = 90
c = 69.161	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-27 
• Released Date: 2011-10-12 
Deposition Author(s): Li, M., Gustchina, A., Wlodawer, A.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references