9Z47 | pdb_00009z47

Crystal structure of H3N2 in complex with a m-carboxy-phenyl-substituted glucuronyl triazole ligand

PDB DOI: https://doi.org/10.2210/pdb9Z47/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Perth/16/2009(H3N2))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-11-09 Released: 2026-11-11
Deposition Author(s): Li, L.H., Ve, T., Carroux, C., Pascolutti, M., Thomson, R.J., von Itzstein, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of H3N2 in complex with a m-carboxy-phenyl-substituted glucuronyl triazole ligand.

Li, L.H., Ve, T., Carroux, C., Pascolutti, M., Thomson, R.J., von Itzstein, M.

To be published.

Macromolecule Content

Total Structure Weight: 45 kDa
Atom Count: 3,363
Modeled Residue Count: 387
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	387	Influenza A virus (A/Perth/16/2009(H3N2))	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for C6KNH8 (Influenza A virus) Explore C6KNH8 Go to UniProtKB: C6KNH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6KNH8
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	7		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C0N (Subject of Investigation/LOI) Query on A1C0N Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(4P)-1-(2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranuronosyl)-4-(3-carboxyphenyl)-1H-1,2,3-triazole C₁₇ H₁₆ N₄ O₇ HCBOVMLJHJUONH-NWANDNLSSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]