4KOM

The structure of hemagglutinin from avian-origin H7N9 influenza virus in complex with avian receptor analog 3'SLNLN (NeuAcα2-3Galβ1-4GlcNAcβ1-3Galβ1-4Glc)

PDB DOI: https://doi.org/10.2210/pdb4KOM/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-05-12 Released: 2013-11-06
Deposition Author(s): Shi, Y., Zhang, W., Wang, F., Qi, J., Song, H., Wu, Y., Gao, F., Zhang, Y., Fan, Z., Gong, W., Wang, D., Shu, Y., Wang, Y., Yan, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.272
R-Value Work: 0.223
R-Value Observed: 0.225

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: 55.19 kDa
Atom Count: 3,923
Modelled Residue Count: 480
Deposited Residue Count: 483
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	314	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for V5IRU4 (Influenza A virus) Explore V5IRU4 Go to UniProtKB: V5IRU4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5IRU4
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	169	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for V5IRU3 (Influenza A virus) Explore V5IRU3 Go to UniProtKB: V5IRU3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5IRU3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	C	4		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G69440RD GlyCosmos: G69440RD GlyGen: G69440RD

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.272
R-Value Work: 0.223
R-Value Observed: 0.225
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.06	α = 90
b = 117.06	β = 90
c = 296.429	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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4KOM

The structure of hemagglutinin from avian-origin H7N9 influenza virus in complex with avian receptor analog 3'SLNLN (NeuAcα2-3Galβ1-4GlcNAcβ1-3Galβ1-4Glc)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2