Crystal structure of influenza neuraminidase N3-H274Y complexed with oseltamivir

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

Starting Model: experimental
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Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance.

Li, Q.Qi, J.Wu, Y.Kiyota, H.Tanaka, K.Suhara, Y.Ohrui, H.Suzuki, Y.Vavricka, C.J.Gao, G.F.

(2013) J Virol 87: 10016-10024

  • DOI: https://doi.org/10.1128/JVI.01129-13
  • Primary Citation of Related Structures:  
    4HZV, 4HZW, 4HZX, 4HZY, 4HZZ, 4I00

  • PubMed Abstract: 

    The influenza virus neuraminidase H274Y substitution is a highly prevalent amino acid substitution associated with resistance to the most heavily used influenza drug, oseltamivir. Previous structural studies suggest that the group specific 252 residue (Y252 in group 1 and T252 in group 2) might be a key factor underlying H274Y resistance. However, H274Y has only been reported in N1 subtypes, which indicates that there must be additional key residues that determine H274Y resistance. Furthermore, we found that members of NA serotype N3 also possess Y252, raising the key question as to whether or not H274Y resistance may also be possible for some group 2 NAs. Here, we demonstrate that the H274Y substitution results in mild oseltamivir resistance for N3. Comparative structural analysis of N3, N1, and their 274Y variants indicates that the interaction of residue 296 (H in N1 and nonaromatic for other serotypes) with conserved W295 is another important determinant of oseltamivir resistance.

  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase387Influenza A virus (A/swine/Missouri/2124514/2006(H2N3))Mutation(s): 1 
Gene Names: NA
Find proteins for A9YN63 (Influenza A virus)
Explore A9YN63 
Go to UniProtKB:  A9YN63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9YN63
Glycosylation Sites: 2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
B, C
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G39

Download Ideal Coordinates CCD File 
F [auth A](3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C14 H24 N2 O4
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
G39 PDBBind:  4HZZ IC50: 8.31 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.113α = 90
b = 108.113β = 90
c = 62.226γ = 90
Software Package:
Software NamePurpose
GUGIdata collection
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: 2013-11-06
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary