6V56 | pdb_00006v56

The crystal structure of the 2009 H1N1 PA endonuclease wild type in complex with SJ000985494

• PDB DOI: https://doi.org/10.2210/pdb6V56/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Luxembourg/43/2009(H1N1))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-03 Released: 2021-02-10 
• Deposition Author(s): Cuypers, M.G., Slavish, P.J., Rankovic, Z., White, S.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.262 (Depositor) 
• R-Value Work: 
  0.244 (Depositor) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000985494

Cuypers, M.G., Slavish, P.J., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.54 kDa 
• Atom Count: 1,521 
• Modeled Residue Count: 178 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein,Polymerase acidic protein	A	197	Influenza A virus (A/Luxembourg/43/2009(H1N1))	Mutation(s): 0  Gene Names: PA
UniProt
Find proteins for C6H0Y9 (Influenza A virus) Explore C6H0Y9  Go to UniProtKB:  C6H0Y9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QQ4	C [auth A]	Hexa Vinylpyrrolidone K15 C36 H56 N6 O6 OFPQNVWJHZVWCZ-CMPUJJQDSA-N
QPY (Subject of Investigation/LOI)	B [auth A]	benzyl (2S)-2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)pyrrolidine-1-carboxylate C24 H25 N9 O5 GEKIERMMQOYZBF-HNNXBMFYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.244 (Depositor) 
• R-Value Observed: 0.245 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36v56

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.546	α = 90
b = 89.546	β = 90
c = 132.78	γ = 90

Software Package:

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

Structure Validation

Currently 6V56 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Cuypers, M.G., Slavish, P.J., Rankovic, Z., White, S.W.

Revision History  

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