4D8S | pdb_00004d8s

Influenza NA in complex with antiviral compound

• PDB DOI: https://doi.org/10.2210/pdb4D8S/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus (A/duck/Ukraine/1/1963(H3N8))
• Mutation(s): Yes 


• Deposited: 2012-01-11 Released: 2013-02-13 
• Deposition Author(s): Kerry, P.S., Russell, R.J.M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Exploring the interactions of unsaturated glucuronides with influenza virus sialidase.

Bhatt, B., Bohm, R., Kerry, P.S., Dyason, J.C., Russell, R.J., Thomson, R.J., von Itzstein, M.

(2012) J Med Chem 55: 8963-8968

• PubMed: 23017008 
• DOI: https://doi.org/10.1021/jm301145k
• Primary Citation Related Structures: 
  4D8S


• PubMed Abstract: 
  

  A series of C3 O-functionalized 2-acetamido-2-deoxy-Δ⁴-β-D-glucuronides were synthesized to explore noncharge interactions in subsite 2 of the influenza virus sialidase active site. In complex with A/N8 sialidase, the parent compound (C3 OH) inverts its solution conformation to bind with all substituents well positioned in the active site. The parent compound inhibits influenza virus sialidase at a sub-μM level; the introduction of small alkyl substituents or an acetyl group at C3 is also tolerated.

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Organizational Affiliation: 
• Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland 4222, Australia.

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: 43.54 kDa 
• Atom Count: 3,120 
• Modeled Residue Count: 388 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	390	Influenza A virus (A/duck/Ukraine/1/1963(H3N8))	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0HX	C [auth A]	pentan-3-yl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid C13 H21 N O6 UUULUCUBSUJBNQ-UFGOTCBOSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.388	α = 90
b = 89.388	β = 90
c = 94.754	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Kerry, P.S., Russell, R.J.M.R.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 2.0: 2020-04-22
  Changes: 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: 2024-11-20
  Changes: Data collection, Database references, Structure summary