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

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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group P15659
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
ID Chains  Name / Formula / InChI Key 2D Diagram 3D Interactions
6B1
Query on 6B1
Download Ideal Coordinates CCD File 
 B [auth A] (5,6-dichloro-1H-benzimidazol-2-yl)methanol
C8 H6 Cl2 N2 O
GOUGSJWBRLTBDO-UHFFFAOYSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
 C [auth A] DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
 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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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