4BH3

Haemagglutinin from a Transmissible Mutant H5 Influenza Virus in Complex with Human Receptor Analogue 6'-SLN

PDB DOI: https://doi.org/10.2210/pdb4BH3/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2013-03-29 Released: 2013-04-24
Deposition Author(s): Xiong, X., Coombs, P.J., Martin, S.R., Liu, J., Xiao, H., McCauley, J.W., Locher, K., Walker, P.A., Collins, P.J., Kawaoka, Y., Skehel, J.J., Gamblin, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.221
R-Value Work: 0.190
R-Value Observed: 0.192

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: 58.87 kDa
Atom Count: 4,499
Modelled Residue Count: 491
Deposited Residue Count: 495
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	A	328	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q5EP31 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q5EP31 Go to UniProtKB: Q5EP31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5EP31
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	B	167	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q5EP31 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q5EP31 Go to UniProtKB: Q5EP31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5EP31
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05686QK GlyCosmos: G05686QK GlyGen: G05686QK

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	D	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.221
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.015	α = 90
b = 102.015	β = 90
c = 331.15	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: 2013-04-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-24
Type: Initial release
Version 1.1: 2013-05-15
Changes: Database references, Refinement description
Version 1.2: 2013-05-22
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