6VLL | pdb_00006vll

The crystal structure of the 2009/H1N1/California PA endonuclease mutant I38T in complex with SJ000986213

• PDB DOI: https://doi.org/10.2210/pdb6VLL/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Luxembourg/43/2009(H1N1))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-01-24 Released: 2021-02-24 
• Deposition Author(s): Cuypers, M.G., Slavish, P.J., Rankovic, Z., White, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.284 (Depositor) 
• R-Value Work: 
  0.235 (Depositor) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000986213

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 23.82 kDa 
• Atom Count: 1,503 
• Modeled Residue Count: 182 
• 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/Luxembourg/43/2009(H1N1))	Mutation(s): 1  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
R3J (Subject of Investigation/LOI)	B [auth A]	benzyl [2-(5-hydroxy-4-{[2-(2-methoxypyridin-4-yl)ethyl]carbamoyl}-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate C24 H27 N5 O6 FTJIBWRYBXLDQU-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.284 (Depositor) 
• R-Value Work:  0.235 (Depositor) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.693	α = 90
b = 90.693	β = 90
c = 132.456	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Currently 6VLL does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Cuypers, M.G., Slavish, P.J., Rankovic, Z., White, S.W.

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description