8DQS | pdb_00008dqs

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023032

• PDB DOI: https://doi.org/10.2210/pdb8DQS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-19 Released: 2022-09-14 
• Deposition Author(s): Cuypers, M.G., Slavish, J.P., Rankovic, Z., White, S.W.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023032

Cuypers, M.G., Slavish, J.P., Rankovic, Z., White, S.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.36 kDa 
• Atom Count: 1,531 
• Modeled Residue Count: 180 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PA-X	A	197	Influenza A virus	Mutation(s): 0  Gene Names: PA
UniProt
Find proteins for C6H0Y9 (Influenza A virus) Explore C6H0Y9  Go to UniProtKB:  C6H0Y9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QQ4	E [auth A]	Hexa Vinylpyrrolidone K15 C36 H56 N6 O6 OFPQNVWJHZVWCZ-CMPUJJQDSA-N
T8I (Subject of Investigation/LOI)	D [auth A]	5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[4-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide C20 H17 F3 N4 O4 YIRAQEAGUHKGLT-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.782	α = 90
b = 88.782	β = 90
c = 135.117	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Cuypers, M.G., Slavish, J.P., Rankovic, Z., White, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references
• Version 1.2: 2023-10-18
  Changes: Refinement description