5KV8

Crystal structure of a hPIV haemagglutinin-neuraminidase-inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb5KV8/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Human respirovirus 3
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-07-13 Released: 2017-07-12 
• Deposition Author(s): Dirr, L., El-Deeb, I.M., Chavas, L.M.G., Guillon, P., von Itzstein, M.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.200 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

The impact of the butterfly effect on human parainfluenza virus haemagglutinin-neuraminidase inhibitor design.

Dirr, L., El-Deeb, I.M., Chavas, L.M.G., Guillon, P., Itzstein, M.V.

(2017) Sci Rep 7: 4507-4507

• PubMed: 28674426 
• DOI: https://doi.org/10.1038/s41598-017-04656-y
• Primary Citation of Related Structures:  
  5KV8, 5KV9


• PubMed Abstract: 
  

  Human parainfluenza viruses represent a leading cause of lower respiratory tract disease in children, with currently no available approved drug or vaccine. The viral surface glycoprotein haemagglutinin-neuraminidase (HN) represents an ideal antiviral target. Herein, we describe the first structure-based study on the rearrangement of key active site amino acid residues by an induced opening of the 216-loop, through the accommodation of appropriately functionalised neuraminic acid-based inhibitors. We discovered that the rearrangement is influenced by the degree of loop opening and is controlled by the neuraminic acid's C-4 substituent's size (large or small). In this study, we found that these rearrangements induce a butterfly effect of paramount importance in HN inhibitor design and define criteria for the ideal substituent size in two different categories of HN inhibitors and provide novel structural insight into the druggable viral HN protein.

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Organizational Affiliation: 

Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland, 4222, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 101.79 kDa 
• Atom Count: 7,608 
• Modelled Residue Count: 854 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin-neuraminidase	A, B	437	Human respirovirus 3	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for G8G134 (Human respirovirus 3) Explore G8G134  Go to UniProtKB:  G8G134

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6Y6	H [auth A], S [auth B]	2,6-anhydro-3,4,5-trideoxy-4-[4-(methoxymethyl)-1H-1,2,3-triazol-1-yl]-5-[(2-methylpropanoyl)amino]-D-glycero-D-galacto -non-2-enonic acid C17 H26 N4 O8 UFINLBROSUXELC-PWRGDLIESA-N
NDG	C [auth A], D [auth A], E [auth A], L [auth A], N [auth B], O [auth B], P [auth B], X [auth B]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
CIT	M [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MAN	Y [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	F [auth A], Q [auth B]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
SO4	W [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A], J [auth A], K [auth A], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	G [auth A], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6Y6	Binding MOAD:  5KV8	IC50: 1.45e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.200 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.57	α = 90
b = 98.612	β = 90
c = 103.386	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
HKL-2000	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Dirr, L., El-Deeb, I.M., Chavas, L.M.G., Guillon, P., von Itzstein, M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP1094549
National Health and Medical Research Council (NHMRC, Australia)	Australia	ID1047824
National Health and Medical Research Council (NHMRC, Australia)	Australia	ID1071659

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 2.0: 2020-04-22
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary