5L15

The crystal structure of neuraminidase in complex with oseltamivir from A/Shanghai/2/2013 (H7N9) influenza virus

• PDB DOI: https://doi.org/10.2210/pdb5L15/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus (A/Shanghai/02/2013(H7N9))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-07-28 Released: 2017-08-09 
• Deposition Author(s): Yang, H., Stevens, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.195 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Drug Susceptibility Evaluation of an Influenza A(H7N9) Virus by Analyzing Recombinant Neuraminidase Proteins.

Gubareva, L.V., Sleeman, K., Guo, Z., Yang, H., Hodges, E., Davis, C.T., Baranovich, T., Stevens, J.

(2017) J Infect Dis 216: S566-S574

• PubMed: 28934455 
• DOI: https://doi.org/10.1093/infdis/jiw625
• Primary Citation of Related Structures:  
  5L14, 5L15, 5L17, 5L18


• PubMed Abstract: 
  

  Neuraminidase (NA) inhibitors are the recommended antiviral medications for influenza treatment. However, their therapeutic efficacy can be compromised by NA changes that emerge naturally and/or following antiviral treatment. Knowledge of which molecular changes confer drug resistance of influenza A(H7N9) viruses (group 2NA) remains sparse.

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Organizational Affiliation: 

Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.36 kDa 
• Atom Count: 3,389 
• Modelled Residue Count: 388 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	397	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for R4NFR6 (Influenza A virus) Explore R4NFR6  Go to UniProtKB:  R4NFR6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB GlyCosmos:  G68668TB GlyGen:  G68668TB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G39	E [auth A]	(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid C14 H24 N2 O4 NENPYTRHICXVCS-YNEHKIRRSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.195 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.436	α = 90
b = 182.436	β = 90
c = 182.436	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Yang, H., Stevens, J.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary