6TVB

Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with human receptor analogue 6'-SLN

PDB DOI: https://doi.org/10.2210/pdb6TVB/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2020-01-09 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: 1.65 Å
R-Value Free: 0.215
R-Value Work: 0.201
R-Value Observed: 0.201

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: 171.09 kDa
Atom Count: 12,834
Modelled Residue Count: 1,484
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 HA1	A, C, E	325	Influenza A virus	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

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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	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-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	3		N/A	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	G, H, I	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I