4D00

Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in Complex with Human Receptor Analogue 6'SLN

PDB DOI: https://doi.org/10.2210/pdb4D00/pdb

Classification: VIRAL PROTEIN
Organism(s): unidentified influenza virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-04-23 Released: 2014-06-11
Deposition Author(s): Xiong, X., Haire, L.F., Vachieri, S.G., Collins, P.J., Walker, P.A., Martin, S.R., Zhang, Y., McCauley, J.W., Gamblin, S.J., Skehel, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.209
R-Value Observed: 0.210

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: 174.61 kDa
Atom Count: 12,576
Modelled Residue Count: 1,483
Deposited Residue Count: 1,527
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ HA1	A, C, E	326	unidentified influenza virus	Mutation(s): 0
UniProt
Find proteins for Q0A448 (Influenza A virus (strain A/Duck/Germany/1949 H10N7)) Explore Q0A448 Go to UniProtKB: Q0A448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0A448
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HAEMAGGLUTININ HA1	B, D, F	183	unidentified influenza virus	Mutation(s): 0
UniProt
Find proteins for P12581 (Influenza A virus (strain A/Chicken/Germany/n/1949 H10N7)) Explore P12581 Go to UniProtKB: P12581
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12581
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Reference Sequence

Oligosaccharides

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Entity ID: 3
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	G, I, K	3		N/A	Interactions Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain G Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

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, J, L	2		N-Glycosylation	Interactions Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 N [auth A] SDF format, chain U [auth E] SDF format, chain M [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth E] MOL2 format, chain N [auth A] MOL2 format, chain U [auth E] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth E]	M [auth A] N [auth A] Q [auth C] R [auth C] T [auth E] M [auth A], N [auth A], Q [auth C], R [auth C], T [auth E], U [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth E] Focus chain U [auth E]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth A] SDF format, chain S [auth D] MOL2 format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain S [auth D]	O [auth A], P [auth B], S [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth B] Focus chain S [auth D] Interactions & Density Focus chain O [auth A] Focus chain P [auth B] Focus chain S [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.209
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.601	α = 90
b = 183.169	β = 90
c = 192.145	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-06-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-11
Type: Initial release
Version 1.1: 2014-07-30
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

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Help and Resources

4D00

Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in Complex with Human Receptor Analogue 6'SLN

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2