5HUF

The crystal structure of hemagglutinin from A/gyrfalcon/Washington/41088-6/2014 influenza virus

PDB DOI: https://doi.org/10.2210/pdb5HUF/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2016-01-27 Released: 2016-04-13
Deposition Author(s): Yang, H., Carney, P.J., Guo, Z., Chang, J.C., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.256
R-Value Work: 0.228
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 180.24 kDa
Atom Count: 12,219
Modelled Residue Count: 1,500
Deposited Residue Count: 1,545
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	334	Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A0C4X0C0 (Influenza A virus) Explore A0A0C4X0C0 Go to UniProtKB: A0A0C4X0C0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0C4X0C0
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	181	Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A0C4X0C0 (Influenza A virus) Explore A0A0C4X0C0 Go to UniProtKB: A0A0C4X0C0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0C4X0C0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K	3		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain G Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

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	H, J, L	2		N-Glycosylation	Interactions Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 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 A] SDF format, chain N [auth A] SDF format, chain O [auth C] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain P [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain P [auth C]	M [auth A] N [auth A] O [auth C] P [auth C] Q [auth E] M [auth A], N [auth A], O [auth C], P [auth C], Q [auth E], R [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.256
R-Value Work: 0.228
R-Value Observed: 0.229
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.328	α = 90
b = 252.385	β = 90
c = 70.623	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2016-04-20
Changes: Database references
Version 1.2: 2016-06-08
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

5HUF

The crystal structure of hemagglutinin from A/gyrfalcon/Washington/41088-6/2014 influenza virus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2