5KV8 | pdb_00005kv8

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.200 (Depositor), 0.199 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-017-04656-y
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8G134
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6Y6 Query on 6Y6 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain H [auth A]	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		Interactions Focus chain H [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B]
NDG Query on NDG Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain X [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain X [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] L [auth A] N [auth B] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain F [auth A]	F [auth A], Q [auth B]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] T [auth B] U [auth B] 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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A]	G [auth A], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.200 (Depositor), 0.199 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.163 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

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 (Full details and data files)

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
Version 3.2: 2024-10-30
Changes: Structure summary