6CF7

Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in complex with small molecule JNJ4796

• PDB DOI: https://doi.org/10.2210/pdb6CF7/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Solomon Islands/3/2006(H1N1))
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2018-02-13 Released: 2019-02-13 
• Deposition Author(s): Kadam, R.U., Wilson, I.A.
• 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: 2.72 Å
• R-Value Free: 0.249 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 

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: 59.32 kDa 
• Atom Count: 4,157 
• Modelled Residue Count: 493 
• Deposited Residue Count: 500 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	326	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 1  Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus) Explore A7Y8I1  Go to UniProtKB:  A7Y8I1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	174	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for F2NZB4 (Influenza A virus) Explore F2NZB4  Go to UniProtKB:  F2NZB4

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EZ7	H [auth B]	N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl)methyl]piperazine-1-carbonyl}pyridin-4-yl)-1,3-benzoxazol-5-yl]acetamide C28 H27 N9 O3 VMAAUIZLAZYALS-RUZDIDTESA-N
NAG	G [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: 2.72 Å
• R-Value Free: 0.249 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.445	α = 90
b = 161.445	β = 90
c = 161.445	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-13 
Deposition Author(s): Kadam, R.U., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2019-03-20
  Changes: Data collection, Database references
• Version 1.3: 2019-03-27
  Changes: Data collection, Database references
• Version 1.4: 2019-04-10
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2019-12-18
  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: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary