5BNY

Crystal structure of hemagglutinin of A/Chicken/Guangdong/S1311/2010 (H6N6)

• PDB DOI: https://doi.org/10.2210/pdb5BNY/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/chicken/Guangdong/S1311/2010(H6N6))
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2015-05-26 Released: 2015-08-12 
• Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.245 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

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: 179.04 kDa 
• Atom Count: 12,460 
• Modelled Residue Count: 1,492 
• Deposited Residue Count: 1,545 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E	324	Influenza A virus (A/chicken/Guangdong/S1311/2010(H6N6))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A067YZV9 (Influenza A virus) Explore A0A067YZV9  Go to UniProtKB:  A0A067YZV9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F	191	Influenza A virus (A/chicken/Guangdong/S1311/2010(H6N6))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A067YZV9 (Influenza A virus) Explore A0A067YZV9  Go to UniProtKB:  A0A067YZV9

Oligosaccharides

Help

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], M [auth A], N [auth A], O [auth C], P [auth C], Q [auth C], R [auth E], S [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	K	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.245 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.26	α = 90
b = 137.37	β = 90
c = 198.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01- AI067839

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• 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, Refinement description, Structure summary