7MY5 | pdb_00007my5

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.213 (Depositor), 0.210 (DCC)
R-Value Observed:
0.215 (Depositor)

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 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
Modeled 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] 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]
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] mmCIF 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] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF 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] 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]