4K62

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/Indonesia/5/2005

• PDB DOI: https://doi.org/10.2210/pdb4K62/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Indonesia/5/2005(H5N1))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-04-15 Released: 2013-05-22 
• Deposition Author(s): Zhang, W., Shi, Y., Lu, X., Shu, Y., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 220.86 kDa 
• Atom Count: 15,877 
• Modelled Residue Count: 1,940 
• Deposited Residue Count: 1,940 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E, G	321	Influenza A virus (A/Indonesia/5/2005(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus) Explore A8HWY8  Go to UniProtKB:  A8HWY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F, H	164	Influenza A virus (A/Indonesia/5/2005(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A8HWY8 (Influenza A virus) Explore A8HWY8  Go to UniProtKB:  A8HWY8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 
• Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.507	α = 90
b = 70.507	β = 90
c = 489.563	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: 2013-05-22 
Deposition Author(s): Zhang, W., Shi, Y., Lu, X., Shu, Y., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2022-08-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description