6TWI

Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue 3'-SLN

PDB DOI: https://doi.org/10.2210/pdb6TWI/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/harbour seal/Germany/1/2014(H10N7))
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2020-01-13 Released: 2020-10-21
Deposition Author(s): Zhang, J., Xiong, X., Purkiss, A., Walker, P., Gamblin, S., Skehel, J.J.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.273
R-Value Work: 0.245
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 171.41 kDa
Atom Count: 12,267
Modelled Residue Count: 1,479
Deposited Residue Count: 1,506
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E	325	Influenza A virus (A/harbour seal/Germany/1/2014(H10N7))	Mutation(s): 1 Gene Names: HA
UniProt
Find proteins for A0A0A7HR51 (Influenza A virus) Explore A0A0A7HR51 Go to UniProtKB: A0A0A7HR51
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A7HR51
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	177	Influenza A virus (A/harbour seal/Germany/1/2014(H10N7))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A0A7HR51 (Influenza A virus) Explore A0A0A7HR51 Go to UniProtKB: A0A0A7HR51
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A7HR51
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, J	3		N/A	Interactions Focus chain G Focus chain H Focus chain J Interactions & Density Focus chain G Focus chain H Focus chain J
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	2		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth E] SDF format, chain V [auth F] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F]	K [auth A], O [auth B], Q [auth C], T [auth E], V [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain T [auth E] Focus chain V [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C]	L [auth A], M [auth A], P [auth B], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain R [auth C] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain R [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth C] SDF format, chain U [auth E] MOL2 format, chain N [auth A] MOL2 format, chain S [auth C] MOL2 format, chain U [auth E]	N [auth A], S [auth C], U [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain S [auth C] Focus chain U [auth E] Interactions & Density Focus chain N [auth A] Focus chain S [auth C] Focus chain U [auth E]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	G, H, J	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain G Focus chain H Focus chain J Interactions & Density Focus chain G Focus chain H Focus chain J