8EDZ | pdb_00008edz

The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ000986319

PDB DOI: https://doi.org/10.2210/pdb8EDZ/pdb

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

Deposited: 2022-09-06 Released: 2022-10-05
Deposition Author(s): Cuypers, M.G., Slavish, J.P., Jayaraman, S., 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: 2.65 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.212 (Depositor), 0.212 (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 1.1 of the entry. See complete history.

Literature

The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ000986319

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

To be published.

Macromolecule Content

Total Structure Weight: 24.52 kDa
Atom Count: 1,507
Modeled Residue Count: 178
Deposited Residue Count: 197
Unique protein chains: 1

Macromolecules

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| 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): 1 Gene Names: PA
UniProt
Find proteins for C6H0Y9 (Influenza A virus) Explore C6H0Y9 Go to UniProtKB: C6H0Y9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Hexa Vinylpyrrolidone K15 C₃₆ H₅₆ N₆ O₆ OFPQNVWJHZVWCZ-CMPUJJQDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
WFW (Subject of Investigation/LOI) Query on WFW Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	benzyl [2-(6-{[2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ethyl]carbamoyl}-5-hydroxy-4-oxo-1,4-dihydropyrimidin-2-yl)propan-2-yl]carbamate C₂₄ H₂₆ N₈ O₅ NCRFYYQIIFPHLD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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 E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]