4CQR

H5 (VN1194) Ser227Asn/Gln196Arg Mutant Haemagglutinin in Complex with Human Receptor Analogue 6'SLN

PDB DOI: https://doi.org/10.2210/pdb4CQR/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Vietnam/1194/2004(H5N1))
Expression System: Gallus gallus
Mutation(s): Yes

Deposited: 2014-02-21 Released: 2014-05-28
Deposition Author(s): Xiong, X., Xiao, H., Martin, S.R., Coombs, P.J., Liu, J., Collins, P.J., Vachieri, S.G., Walker, P.A., Lin, Y.P., McCauley, J.W., Gamblin, S.J., Skehel, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.235
R-Value Work: 0.200
R-Value Observed: 0.202

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: 59.15 kDa
Atom Count: 4,139
Modelled Residue Count: 483
Deposited Residue Count: 492
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	326	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 2 Gene Names: HA
UniProt
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34 Go to UniProtKB: Q6DQ34
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DQ34
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	166	Influenza A virus (A/Vietnam/1194/2004(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q6DQ34 (Influenza A virus) Explore Q6DQ34 Go to UniProtKB: Q6DQ34
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DQ34
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-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	D	5		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42769XG GlyCosmos: G42769XG GlyGen: G42769XG

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	E	2		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G63069TR GlyCosmos: G63069TR GlyGen: G63069TR

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	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MPO Query on MPO Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.235
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.077	α = 90
b = 101.077	β = 90
c = 451.337	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2014-06-11
Changes: Database references
Version 1.2: 2018-11-07
Changes: Data collection, Database references, Source and taxonomy, Structure summary
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: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary