5E34

Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133a deletion) from the influenza virus A/chicken/Vietnam/NCVD-093/2008 (H5N1) with LSTa

• PDB DOI: https://doi.org/10.2210/pdb5E34/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1))
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2015-10-01 Released: 2015-12-02 
• Deposition Author(s): Zhu, X., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 

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: 59.57 kDa 
• Atom Count: 4,137 
• Modelled Residue Count: 498 
• Deposited Residue Count: 513 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	333	Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1))	Mutation(s): 3  Gene Names: HA
UniProt
Find proteins for C4P282 (Influenza A virus) Explore C4P282  Go to UniProtKB:  C4P282

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	180	Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for C4P282 (Influenza A virus) Explore C4P282  Go to UniProtKB:  C4P282

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G46776WR GlyCosmos:  G46776WR GlyGen:  G46776WR

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.824	α = 90
b = 130.824	β = 90
c = 133.368	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary