3O9K | pdb_00003o9k

Influenza NA in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.296 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1038/ncomms1114
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 43.26 kDa 
  • Atom Count: 3,032 
  • Modeled Residue Count: 387 
  • Deposited Residue Count: 387 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuraminidase387Influenza A virus (A/duck/Ukraine/1/1963(H3N8))Mutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for Q07599 (Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8))
Explore Q07599 
Go to UniProtKB:  Q07599
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07599
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ETT

Query on ETT



Download:Ideal Coordinates CCD File
B [auth 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.296 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary