9FXV | pdb_00009fxv

Influenza polymerase A C-terminal domain of PA subunit with peptide inhibitor containing two norleucines

PDB DOI: https://doi.org/10.2210/pdb9FXV/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/California/07/2009(H1N1)), synthetic construct
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.279 (Depositor), 0.241 (DCC)
R-Value Work:
0.242 (Depositor)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FXV

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 54.5 kDa
Atom Count: 3,564
Modeled Residue Count: 430
Deposited Residue Count: 471
Unique protein chains: 2

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4HI62
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide inhibitor	B	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.279 (Depositor), 0.241 (DCC)
R-Value Work: 0.242 (Depositor)
R-Value Observed: 0.243 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.857	α = 90
b = 119.561	β = 90
c = 123.281	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.