5YKC | pdb_00005ykc

crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012

• PDB DOI: https://doi.org/10.2210/pdb5YKC/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2017-10-13 Released: 2018-10-17 
• Deposition Author(s): Lin, T.H., Lee, M.S., Wu, W.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012

Lin, T.H., Lee, M.S., Wu, W.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 202.07 kDa 
• Atom Count: 12,092 
• Modeled Residue Count: 1,488 
• Deposited Residue Count: 1,758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	586	Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))	Mutation(s): 0
UniProt
Find proteins for A0A059VBQ9 (Influenza A virus) Explore A0A059VBQ9  Go to UniProtKB:  A0A059VBQ9
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [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: 2.82 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.424	α = 90
b = 220.103	β = 90
c = 186.508	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Lin, T.H., Lee, M.S., Wu, W.G.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary