3O9K

Influenza NA in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase.

Rudrawar, S.Dyason, J.C.Rameix-Welti, M.A.Rose, F.J.Kerry, P.S.Russell, R.J.van der Werf, S.Thomson, R.J.Naffakh, N.von Itzstein, M.

(2010) Nat Commun 1: 113-113

  • DOI: 10.1038/ncomms1114
  • Primary Citation of Related Structures:  
    3O9J, 3O9K

  • PubMed Abstract: 
  • Influenza virus sialidase has an essential role in the virus' life cycle. Two distinct groups of influenza A virus sialidases have been established, that differ in the flexibility of the '150-loop', providing a more open active site in the apo form o ...

    Influenza virus sialidase has an essential role in the virus' life cycle. Two distinct groups of influenza A virus sialidases have been established, that differ in the flexibility of the '150-loop', providing a more open active site in the apo form of the group-1 compared to group-2 enzymes. In this study we show, through a multidisciplinary approach, that novel sialic acid-based derivatives can exploit this structural difference and selectively inhibit the activity of group-1 sialidases. We also demonstrate that group-1 sialidases from drug-resistant mutant influenza viruses are sensitive to these designed compounds. Moreover, we have determined, by protein X-ray crystallography, that these inhibitors lock open the group-1 sialidase flexible 150-loop, in agreement with our molecular modelling prediction. This is the first direct proof that compounds may be developed to selectively target the pandemic A/H1N1, avian A/H5N1 and other group-1 sialidase-containing viruses, based on an open 150-loop conformation of the enzyme.


    Organizational Affiliation

    Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland 4222, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuraminidaseA387Influenza A virus (A/duck/Ukraine/1/1963(H3N8))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Explore Q07599 
Go to UniProtKB:  Q07599
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETT
Query on ETT

Download Ideal Coordinates CCD File 
A
5-acetamido-2,6-anhydro-3,5-dideoxy-3-[(2E)-3-(4-methylphenyl)prop-2-en-1-yl]-D-glycero-D-galacto-non-2-enonic acid
C21 H27 N O8
CCPSTGRFUHTVNN-ZSEVYCOTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.491α = 90
b = 90.491β = 90
c = 107.778γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-04-22
    Changes: Advisory, Atomic model, Data collection, Database references, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary