4UO2

Structure of the A_Equine_Richmond_07 H3 haemagglutinin in complex with Sialyl Lewis X

PDB DOI: https://doi.org/10.2210/pdb4UO2/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/equine/Richmond/1/2007(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: 2.70 Å
R-Value Free: 0.256
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: 184.34 kDa
Atom Count: 12,916
Modelled Residue Count: 1,485
Deposited Residue Count: 1,503
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 HAEMAGGLUTININ HA1 CHAIN	A, C, E	329	Influenza A virus (A/equine/Richmond/1/2007(H3N8))	Mutation(s): 0
UniProt
Find proteins for C3TUR9 (Influenza A virus) Explore C3TUR9 Go to UniProtKB: C3TUR9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3TUR9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 HAEMAGGLUTININ HA2 CHAIN	B, D, F	172	Influenza A virus (A/equine/Richmond/1/2007(H3N8))	Mutation(s): 0
UniProt
Find proteins for C3TUR9 (Influenza A virus) Explore C3TUR9 Go to UniProtKB: C3TUR9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3TUR9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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, O, W	5		N-Glycosylation	Interactions Focus chain G Focus chain O Focus chain W Interactions & Density Focus chain G Focus chain O Focus chain W
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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, P, U, V, X H, P, U, V, X, Y	2		N-Glycosylation	Interactions Focus chain H Focus chain P Focus chain U Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain H Focus chain P Focus chain U Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	I	4		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 6
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	J, M, Q, R, Z	3		N-Glycosylation	Interactions Focus chain J Focus chain M Focus chain Q Focus chain R Focus chain Z Interactions & Density Focus chain J Focus chain M Focus chain Q Focus chain R Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
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-beta-D-glucopyranose	AA [auth a], K, S	4		N/A	Interactions Focus chain AA [auth a] Focus chain K Focus chain S Interactions & Density Focus chain AA [auth a] Focus chain K Focus chain S
Glycosylation Resources
GlyTouCan: G00054MO GlyCosmos: G00054MO GlyGen: G00054MO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	4		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
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	BA [auth b], T	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain T Interactions & Density Focus chain BA [auth b] Focus chain T
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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 CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth E] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth E]	CA [auth A], DA [auth A], EA [auth A], FA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth E] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth E]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900121 Query on PRD_900121	AA [auth K], K [auth S], S [auth a]	Sialyl-Lewis X antigen, beta anomer	Oligosaccharide / Antigen		Interactions Focus chain AA [auth a] Focus chain K Focus chain S Interactions & Density Focus chain AA [auth a] Focus chain K Focus chain S

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.296	α = 90
b = 129.794	β = 90
c = 193.634	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 1.2: 2014-11-19
Changes: Data collection
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