4KDQ

Crystal structure of the hemagglutinin of A/Xinjiang/1/2006 virus

• PDB DOI: https://doi.org/10.2210/pdb4KDQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Xinjiang/1/2006(H5N1)), Influenza A virus (A/chicken/Guangdong/174/04(H5N1))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-04-25 Released: 2013-07-24 
• Deposition Author(s): Lu, X., Shi, Y., Zhang, W., Zhang, Y., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

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: 167.22 kDa 
• Atom Count: 11,805 
• Modelled Residue Count: 1,455 
• Deposited Residue Count: 1,455 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth C], C [auth E]	321	Influenza A virus (A/Xinjiang/1/2006(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for C5HMM2 (Influenza A virus) Explore C5HMM2  Go to UniProtKB:  C5HMM2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	D [auth B], E [auth D], F	164	Influenza A virus (A/chicken/Guangdong/174/04(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q6J0Q2 (Influenza A virus) Explore Q6J0Q2  Go to UniProtKB:  Q6J0Q2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], I [auth C], J [auth C], K [auth E], L [auth E], M [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.049	α = 90
b = 72.049	β = 90
c = 365.862	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: 2013-07-24 
Deposition Author(s): Lu, X., Shi, Y., Zhang, W., Zhang, Y., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Source and taxonomy, Structure summary