7XME

Structure of Influenza A virus polymerase basic protein 2 (PB2) with an azazindole derivative

• PDB DOI: https://doi.org/10.2210/pdb7XME/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Influenza A virus (A/Victoria/3/1975(H3N2))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-04-25 Released: 2023-05-03 
• Deposition Author(s): Zhang, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.330 
• R-Value Work: 0.250 
• R-Value Observed: 0.254 

Literature

Discovery of a novel azaindole derivatives targeting the influenza PB2 cap binding region

Zhang, Z., Liu, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.97 kDa 
• Atom Count: 5,011 
• Modelled Residue Count: 618 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	A, B, C, D	166	Influenza A virus (A/Victoria/3/1975(H3N2))	Mutation(s): 0  Gene Names: PB2
UniProt
Find proteins for P31345 (Influenza A virus (strain A/Victoria/3/1975 H3N2)) Explore P31345  Go to UniProtKB:  P31345

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GIH (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	(2~{S},3~{S})-3-[[5-dimethoxyphosphoryl-4-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid C22 H25 F N5 O5 P HZZFRSXJRJLLCP-CMKMFDCUSA-N
IOD	E [auth A], G [auth B], I [auth C], K [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.330 
• R-Value Work: 0.250 
• R-Value Observed: 0.254 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.791	α = 90
b = 31.306	β = 95.31
c = 114.552	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Zhang, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description