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)

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

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

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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 C [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain X [auth B]	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]	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]	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 F [auth A] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B]	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]	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]	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 I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain K [auth A] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain V [auth B]	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 G [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth B]	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]

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

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Ligand Structure Quality Assessment

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

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Help and Resources

5KV8

Crystal structure of a hPIV haemagglutinin-neuraminidase-inhibitor complex

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)