8E21

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023034

PDB DOI: https://doi.org/10.2210/pdb8E21/pdb

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

Deposited: 2022-08-12 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.276
R-Value Work: 0.221
R-Value Observed: 0.223

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023034

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

To be published.

Macromolecule Content

Total Structure Weight: 24.44 kDa
Atom Count: 1,514
Modelled Residue Count: 180
Deposited Residue Count: 197
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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): 0 Gene Names: PA
UniProt
Find proteins for C6H0Y9 (Influenza A virus) Explore C6H0Y9 Go to UniProtKB: C6H0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6H0Y9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QQ4 Query on QQ4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	Hexa Vinylpyrrolidone K15 C₃₆ H₅₆ N₆ O₆ OFPQNVWJHZVWCZ-CMPUJJQDSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
U9U (Subject of Investigation/LOI) Query on U9U 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]	5-hydroxy-6-oxo-N-[2-(pyridin-4-yl)ethyl]-2-{[2-(trifluoromethyl)phenyl]methyl}-3,6-dihydropyrimidine-4-carboxamide C₂₀ H₁₇ F₃ N₄ O₃ FACMTIGIIYGQOE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]