5IF2

Crystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-576 (5,6-dichloro-1H-1,3-benzodiazol-2-yl)methanol

• PDB DOI: https://doi.org/10.2210/pdb5IF2/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Wilson-Smith/1933(H1N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-25 Released: 2017-02-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA

Pierce, P., Muruthi, M.M., Abendroth, J., Moen, S.O., Begley, D.W., Davies, D.R., Marathias, V.M., Staker, B.L., Myler, P.J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.43 kDa 
• Atom Count: 3,339 
• Modelled Residue Count: 409 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	464	Influenza A virus (A/Wilson-Smith/1933(H1N1))	Mutation(s): 0  Gene Names: PA
UniProt
Find proteins for P15659 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1)) Explore P15659  Go to UniProtKB:  P15659

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6B1	B [auth A]	(5,6-dichloro-1H-benzimidazol-2-yl)methanol C8 H6 Cl2 N2 O GOUGSJWBRLTBDO-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.89	α = 90
b = 68.89	β = 90
c = 396.92	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references