Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 346.44 kDa 
• Atom Count: 24445 
• Modelled Residue Count: 2922 
• Deposited Residue Count: 3024 
• Unique protein chains: 2

5T6S

Crystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral drug arbidol

• PDB DOI: 10.2210/pdb5T6S/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Shanghai/02/2013(H7N9))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-09-01 Released: 2017-01-04 
• Deposition Author(s): Kadam, R.U., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.250 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol.

Kadam, R.U., Wilson, I.A.

(2017) Proc Natl Acad Sci U S A 114: 206-214

• PubMed: 28003465 
• DOI: 10.1073/pnas.1617020114
• Primary Citation of Related Structures:  
  5T6N, 5T6S


• PubMed Abstract: 
  

The broad-spectrum antiviral drug Arbidol shows efficacy against influenza viruses by targeting the hemagglutinin (HA) fusion machinery. However, the structural basis of the mechanism underlying fusion inhibition by Arbidol has remained obscure, thereby hindering its further development as a specific and optimized influenza therapeutic. We determined crystal structures of Arbidol in complex with influenza virus HA from pandemic 1968 H3N2 and recent 2013 H7N9 viruses. Arbidol binds in a hydrophobic cavity in the HA trimer stem at the interface between two protomers. This cavity is distal to the conserved epitope targeted by broadly neutralizing stem antibodies and is ∼16 Å from the fusion peptide. Arbidol primarily makes hydrophobic interactions with the binding site but also induces some conformational rearrangements to form a network of inter- and intraprotomer salt bridges. By functioning as molecular glue, Arbidol stabilizes the prefusion conformation of HA that inhibits the large conformational rearrangements associated with membrane fusion in the low pH of the endosome. This unique binding mode compared with the small-molecule inhibitors of other class I fusion proteins enhances our understanding of how small molecules can function as fusion inhibitors and guides the development of broad-spectrum therapeutics against influenza virus.

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Organizational Affiliation: 

The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E, G, I, K	321	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21  Go to UniProtKB:  R4NN21

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F, H, J, L	183	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21  Go to UniProtKB:  R4NN21

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N, Q, R, S	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
75U	DA [auth F], FA [auth H], IA [auth J], NA [auth L], V [auth B], W [auth B]	ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-[(phenylsulfanyl)methyl]-1H-indole-3-carboxylate C22 H25 Br N2 O3 S KCFYEAOKVJSACF-UHFFFAOYSA-N
NAG	AA [auth D], BA [auth D], CA [auth E], EA [auth F], GA [auth H], HA [auth I], JA [auth J], KA [auth J], MA [auth K], OA [auth L], T [auth A], U [auth A], X [auth B], Y [auth B], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	LA [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.250 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.419	α = 90
b = 231.49	β = 96.88
c = 127.85	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-01 
• Released Date: 2017-01-04 
Deposition Author(s): Kadam, R.U., Wilson, I.A.

Revision History  

• Version 1.0: 2017-01-04
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary