2YP7

Haemagglutinin of 2005 Human H3N2 Virus

PDB DOI: https://doi.org/10.2210/pdb2YP7/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2012-10-29 Released: 2012-11-07
Deposition Author(s): Xiong, X., Lin, Y.P., Wharton, S.A., Martin, S.R., Coombs, P.J., Vachieri, S.G., Christodoulou, E., Walker, P.A., Liu, J., Skehel, J.J., Gamblin, S.J., Hay, A.J., Daniels, R.S., McCauley, J.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.216
R-Value Work: 0.183
R-Value Observed: 0.185

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: 59.47 kDa
Atom Count: 4,531
Modelled Residue Count: 490
Deposited Residue Count: 503
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	A	503	Influenza A virus	Mutation(s): 1
UniProt
Find proteins for I2D7A8 (Influenza A virus) Explore I2D7A8 Go to UniProtKB: I2D7A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I2D7A8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	J [auth A], K [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.216
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.89	α = 90
b = 100.89	β = 90
c = 386.26	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2012-12-26
Changes: Database references, Refinement description, Structure summary
Version 1.2: 2013-01-16
Changes: Database references
Version 1.3: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary

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Help and Resources

2YP7

Haemagglutinin of 2005 Human H3N2 Virus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources