Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.09 kDa 
• Atom Count: 7532 
• Residue Count: 880 
• Unique protein chains: 1

5E0I

Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution

• DOI: 10.2210/pdb5E0I/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepatitis B virus subtype adyw
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-09-28 Released: 2015-12-09 
• Deposition Author(s): Lukacs, C.M., Abendroth, J., Klumpp, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein.

Klumpp, K., Lam, A.M., Lukacs, C., Vogel, R., Ren, S., Espiritu, C., Baydo, R., Atkins, K., Abendroth, J., Liao, G., Efimov, A., Hartman, G., Flores, O.A.

(2015) Proc Natl Acad Sci U S A 112: 15196-15201

• PubMed: 26598693 
• DOI: 10.1073/pnas.1513803112
• Primary Citation of Related Structures:  
  5E0I


• PubMed Abstract: 
  

The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010-001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 °C. NVR-010-001-E2 binds at the dimer-dimer interface of the core proteins, forms a new interaction surface promoting protein-protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010-001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein-protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties.

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Organizational Affiliation: 

Novira Therapeutics, Doylestown, PA 18902;

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D, E, F	157	Hepatitis B virus subtype adyw	Mutation(s): 1  Gene Names: C
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)) Explore P03147  Go to UniProtKB:  P03147

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5J6	A, B, C, D, E, F	methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate C20 H18 Br F N4 O3 S RVCJKGYMRDZTJU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.6	α = 90
b = 88.17	β = 103.47
c = 102.25	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-28 
• Released Date: 2015-12-09 
Deposition Author(s): Lukacs, C.M., Abendroth, J., Klumpp, K.

Revision History 

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references