5LC0

Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor.

Lei, J.Hansen, G.Nitsche, C.Klein, C.D.Zhang, L.Hilgenfeld, R.

(2016) Science 353: 503-505

  • DOI: https://doi.org/10.1126/science.aag2419
  • Primary Citation of Related Structures:  
    5LC0

  • PubMed Abstract: 

    The ongoing Zika virus (ZIKV) outbreak is linked to severe neurological disorders. ZIKV relies on its NS2B/NS3 protease for polyprotein processing; hence, this enzyme is an attractive drug target. The 2.7 angstrom; crystal structure of ZIKV protease in complex with a peptidomimetic boronic acid inhibitor reveals a cyclic diester between the boronic acid and glycerol. The P2 4-aminomethylphenylalanine moiety of the inhibitor forms a salt-bridge with the nonconserved Asp(83) of NS2B; ion-pairing between Asp(83) and the P2 residue of the substrate likely accounts for the enzyme's high catalytic efficiency. The unusual dimer of the ZIKV protease:inhibitor complex seen in the crystal may provide a model for assemblies formed at high local concentrations of protease at the endoplasmatic reticulum membrane, the site of polyprotein processing.


  • Organizational Affiliation

    Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany. German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS2B-NS3 protease,NS2B-NS3 protease
A, B
230Zika virusMutation(s): 2 
UniProt
Find proteins for A0A140DLX4 (Zika virus)
Explore A0A140DLX4 
Go to UniProtKB:  A0A140DLX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140DLX4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6T8
Query on 6T8

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-((S)-3-(4-(aminomethyl)phenyl)-1-(((R)-4-guanidino-1-(5-hydroxy-1,3,2-dioxaborinan-2-yl)butyl)amino)-1-oxopropan-2-yl)benzamide
C25 H35 B N6 O5
DYKCMHQIYUDANF-VXKWHMMOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.808α = 90
b = 125.808β = 90
c = 73.461γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Center for Infection Research (DZIF)Germany#TTU01.911_0

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2016-08-10
    Changes: Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description