6TVS

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

PDB DOI: https://doi.org/10.2210/pdb6TVS/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/harbour seal/Germany/1/2014(H10N7))
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2020-01-10 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: 1.90 Å
R-Value Free: 0.250
R-Value Work: 0.230
R-Value Observed: 0.231

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: 170.74 kDa
Atom Count: 12,883
Modelled Residue Count: 1,477
Deposited Residue Count: 1,506
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A [auth C], C [auth E], E [auth K]	325	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B [auth D], D [auth F], F [auth L]	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

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	G [auth A], I [auth G]	2		N/A	Interactions Focus chain G [auth A] Focus chain I [auth G] Interactions & Density Focus chain G [auth A] Focus chain I [auth G]
Glycosylation Resources
GlyTouCan: G30207PZ GlyCosmos: G30207PZ GlyGen: G30207PZ

Entity ID: 4
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	H [auth B]	3		N/A	Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

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 M [auth D] SDF format, chain Q [auth E] SDF format, chain U [auth F] SDF format, chain Z [auth L] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain U [auth F] MOL2 format, chain Z [auth L]	M [auth D], Q [auth E], U [auth F], Z [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth D] Focus chain Q [auth E] Focus chain U [auth F] Focus chain Z [auth L] Interactions & Density Focus chain M [auth D] Focus chain Q [auth E] Focus chain U [auth F] Focus chain Z [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain V [auth K] SDF format, chain W [auth K] SDF format, chain X [auth K] MOL2 format, chain AA [auth L] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain V [auth K] MOL2 format, chain W [auth K] MOL2 format, chain X [auth K]	AA [auth L] J [auth C] K [auth C] L [auth C] N [auth D] AA [auth L], J [auth C], K [auth C], L [auth C], N [auth D], O [auth D], P [auth E], R [auth E], S [auth F], T [auth F], V [auth K], W [auth K], X [auth K]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth K] Focus chain W [auth K] Focus chain X [auth K] Interactions & Density Focus chain AA [auth L] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth K] Focus chain W [auth K] Focus chain X [auth K]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain Y [auth K] MOL2 format, chain Y [auth K]	Y [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain Y [auth K] Interactions & Density Focus chain Y [auth K]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	H [auth B]	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]