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 (software)

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.55 kDa 
• Atom Count: 7392 
• Residue Count: 920 
• Unique protein chains: 1

2WPO

HCMV protease inhibitor complex

• DOI: 10.2210/pdb2WPO/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human betaherpesvirus 5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-08-04 Released: 1999-08-04 
• Deposition Author(s): Tong, L., Qian, C., Massariol, M.-J., Deziel, R., Yoakim, C., Lagace, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.332 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease.

Tong, L., Qian, C., Massariol, M.J., Deziel, R., Yoakim, C., Lagace, L.

(1998) Nat Struct Biol 5: 819-826

• PubMed: 9731777 
• DOI: 10.1038/1860
• Primary Citation of Related Structures:  
  2WPO


• PubMed Abstract: 
  

Human cytomegalovirus (HCMV) protease belongs to a new class of serine proteases, with a unique polypeptide backbone fold. The crystal structure of the protease in complex with a peptidomimetic inhibitor (based on the natural substrates and covering the P4 to P1' positions) has been determined at 2.7 A resolution. The inhibitor is bound in an extended conformation, forming an anti-parallel beta-sheet with the protease. The P3 and P1 side chains are less accessible to solvent, whereas the P4 and P2 side chains are more exposed. The inhibitor binding mode shows significant similarity to those observed for peptidomimetic inhibitors or substrates of other classes of serine proteases (chymotrypsin and subtilisin). HCMV protease therefore represents example of convergent evolution. In addition, large conformational differences relative to the structure of the free enzyme are observed, which may be important for inhibitor binding.

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Related Citations: 

• A New Serine-Protease Fold Revealed by the Crystal Structure of Human Cytomegalovirus Protease
  Tong, L., Qian, C., Massariol, M.J., Bonneau, P.R., Cordingley, M.G., Lagace, L.
  (1996) Nature 383: 272

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Organizational Affiliation: 

Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN CYTOMEGALOVIRUS PROTEASE	A, B, C, D	256	Human betaherpesvirus 5	Mutation(s): 3  EC: 3.4.21 (PDB Primary Data), 3.4.21.97 (UniProt)
Find proteins for P16753 (Human cytomegalovirus (strain AD169)) Explore P16753  Go to UniProtKB:  P16753

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
01E	A, B, C, D	(2S)-2-(3,3-dimethylbutanoylamino)-N-[(2S)-1-[[(2S,3S)-3-hydroxy-4-[(4-iodophenyl)methylamino]-4-oxo-butan-2-yl]amino]- 1,4-dioxo-4-pyrrol-1-yl-butan-2-yl]-3,3-dimethyl-butanamide C31 H44 I N5 O6 DUBMDYQWHSIBPD-FBESYSLLSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000229 (01E)	A, B, C, D	BILC 821	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.332 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.8	α = 90
b = 53.4	β = 90
c = 212.4	γ = 90

Software Package:

Software Name	Purpose
REPLACE	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
REPLACE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-04 
• Released Date: 1999-08-04 
Deposition Author(s): Tong, L., Qian, C., Massariol, M.-J., Deziel, R., Yoakim, C., Lagace, L.

Revision History 

• Version 1.0: 1999-08-04
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other