4LKJ

The structure of hemagglutinin L226Q mutant (H3 numbering) from a avian-origin H7N9 influenza virus (A/Anhui/1/2013) in complex with avian receptor analog 3'SLNLN

• PDB DOI: https://doi.org/10.2210/pdb4LKJ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-07-07 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.98 kDa 
• Atom Count: 3,880 
• Modelled Residue Count: 482 
• Deposited Residue Count: 482 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin	A	314	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for V5IRV5 (Influenza A virus) Explore V5IRV5  Go to UniProtKB:  V5IRV5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin	B	168	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for V5IRV2 (Influenza A virus) Explore V5IRV2  Go to UniProtKB:  V5IRV2

Oligosaccharides

Help

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	C	3		N/A
Glycosylation Resources
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067	C	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.285 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.909	α = 90
b = 116.909	β = 90
c = 297.076	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary