3K39

Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Peramivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses.

Oakley, A.J.Barrett, S.Peat, T.S.Newman, J.Streltsov, V.A.Waddington, L.Saito, T.Tashiro, M.McKimm-Breschkin, J.L.

(2010) J Med Chem 

  • DOI: 10.1021/jm100621s
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase (NA), which confers cross-resistance to all NA inhibitors. We analyzed enzyme properties of the D197 and E197 NAs and compared these to a D197N NA, ...

    We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase (NA), which confers cross-resistance to all NA inhibitors. We analyzed enzyme properties of the D197 and E197 NAs and compared these to a D197N NA, known to arise after oseltamivir treatment. Zanamivir and peramivir bound slowly to the wild type NA, but binding of oseltamivir was more rapid. The D197E/N mutations resulted in faster binding of all three inhibitors. Analysis of the crystal structures of D197 and E197 NAs with and without inhibitors showed that the D197E mutation compromised the interaction of neighboring R150 with the N-acetyl group, common to the substrate sialic acid and all NA inhibitors. Although rotation of the E275 in the NA active site occurs upon binding peramivir in both the D197 and E197 NAs, this does not occur upon binding oseltamivir in the E197 NA. Lack of the E275 rotation would also account for the loss of slow binding and the partial resistance of influenza B wild type NAs to oseltamivir.


    Organizational Affiliation

    CSIRO Materials Science and Engineering, Parkville, 343 Royal Parade, Parkville, Victoria, 3052, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuraminidase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
397Influenza B virus (B/Perth/211/2001)Mutation(s): 1 
Gene Names: NA
EC: 3.2.1.18
Find proteins for Q3S340 (Influenza B virus)
Go to UniProtKB:  Q3S340
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCZ
Query on BCZ

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID
C15 H28 N4 O4
XRQDFNLINLXZLB-CKIKVBCHSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
YT3
Query on YT3

Download CCD File 
A, E, I, M
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCZKi :  8.300000190734863   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.964α = 90.03
b = 124.874β = 92.11
c = 125.245γ = 91.27
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance