7K0W | pdb_00007k0w

The crystal structure of the 2009/H1N1/California PA endonuclease (construct with truncated loop 51-72) in complex with Baloxavir acid

• PDB DOI: https://doi.org/10.2210/pdb7K0W/pdb

• Classification: VIRAL PROTEIN, HYDROLASE
• Organism(s): Influenza A virus (A/California/04/2009(H1N1))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-06 Released: 2020-12-16 
• Deposition Author(s): Kumar, G., White, S.W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the influenza virus PA endonuclease in complex with Baloxavir Acid

Kumar, G., White, S.W.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.93 kDa 
• Atom Count: 1,530 
• Modeled Residue Count: 179 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	197	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0  Gene Names: PA EC: 3.1
UniProt
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S0  Go to UniProtKB:  C3W5S0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E4Z (Subject of Investigation/LOI)	B [auth A]	Baloxavir acid C24 H19 F2 N3 O4 S FIDLLEYNNRGVFR-CTNGQTDRSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E4Z	BindingDB:  7K0W	Kd: 208 (nM) from 1 assay(s)
		IC50: min: 1, max: 8160 (nM) from 6 assay(s)
		EC50: min: 0.68, max: 1.22 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.718	α = 90
b = 89.718	β = 90
c = 133.763	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Kumar, G., White, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI098757

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description