7MY5

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503

PDB DOI: https://doi.org/10.2210/pdb7MY5/pdb

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

Deposited: 2021-05-20 Released: 2022-05-25
Deposition Author(s): Cuypers, M.G., Slavish, J.P., Rankovic, Z., White, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.215

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 SJ000988503

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

To be published.

Macromolecule Content

Total Structure Weight: 24.61 kDa
Atom Count: 1,539
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/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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3W5S0
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]	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]
Y5V (Subject of Investigation/LOI) Query on Y5V Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide C₂₁ H₂₁ N₃ O₅ KEGVYPYJMJWBAI-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] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [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]	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]