4UNZ

Structure of the A_Equine_Newmarket_2_93 H3 haemagglutinin in complex with 6SO4-Sialyl Lewis X

PDB DOI: https://doi.org/10.2210/pdb4UNZ/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/eq/Newmarket/93/(H3N8))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-05-31 Released: 2014-07-23
Deposition Author(s): Vachieri, S.G., Collins, P.J., Haire, L.F., Ogrodowicz, R.W., Martin, S.R., Walker, P.A., Xiong, X., Gamblin, S.J., Skehel, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 180.22 kDa
Atom Count: 12,397
Modelled Residue Count: 1,482
Deposited Residue Count: 1,509
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAY SUBUNIT OF HAEMAGGLUTININ	A, C, E	330	Influenza A virus (A/eq/Newmarket/93/(H3N8))	Mutation(s): 0
UniProt
Find proteins for Q82847 (Influenza A virus) Explore Q82847 Go to UniProtKB: Q82847
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82847
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 HAEMAGGLUTININ HA2 CHAIN	B, D, F	173	Influenza A virus (A/eq/Newmarket/93/(H3N8))	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose	H, P, U	4		N/A	Interactions Focus chain H Focus chain P Focus chain U Interactions & Density Focus chain H Focus chain P Focus chain U
Glycosylation Resources
GlyTouCan: G80722US GlyCosmos: G80722US GlyGen: G80722US

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K, L, O, S J, K, L, O, S, T	2		N-Glycosylation	Interactions Focus chain J Focus chain K Focus chain L Focus chain O Focus chain S Focus chain T Interactions & Density Focus chain J Focus chain K Focus chain L Focus chain O Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, R	3		N-Glycosylation	Interactions Focus chain M Focus chain R Interactions & Density Focus chain M Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	N	6		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q	2		N-Glycosylation	Interactions Focus chain Q Interactions & Density Focus chain Q
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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 AA [auth F] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth C] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth E]	AA [auth F] V [auth A] W [auth A] X [auth A] Y [auth C] AA [auth F], V [auth A], W [auth A], X [auth A], Y [auth C], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth C] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth C] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.551	α = 90
b = 125.751	β = 90
c = 165.107	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-23
Type: Initial release
Version 1.1: 2014-08-13
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary