9FXX | pdb_00009fxx

Influenza polymerase A C-terminal domain of PA subunit with stapled peptide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9FXX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/California/07/2009(H1N1))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-02 Released: 2025-07-16 
• Deposition Author(s): Radilova, K., Brynda, J.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.277 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Influenza polymerase A C-terminal domain of PA subunit

Radilova, K., Zima, V., Brynda, J., Konvalinka, J., Machara, A., Kozisek, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.55 kDa 
• Atom Count: 3,426 
• Modeled Residue Count: 432 
• Deposited Residue Count: 471 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	461	Influenza A virus (A/California/07/2009(H1N1))	Mutation(s): 0  Gene Names: PA EC: 3.1
UniProt
Find proteins for D4HI62 (Influenza A virus) Explore D4HI62  Go to UniProtKB:  D4HI62

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Stapled peptide inhibitor	B	10	Influenza A virus (A/California/07/2009(H1N1))	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
A1IG4 (Subject of Investigation/LOI)	F [auth B]	(E)-but-2-ene C4 H8 IAQRGUVFOMOMEM-ONEGZZNKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.277 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.019	α = 90
b = 118.797	β = 90
c = 123.848	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Radilova, K., Brynda, J.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	LX22NPO5103

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release