7LP7 | pdb_00007lp7

The crystal structure of the wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000983476

PDB DOI: https://doi.org/10.2210/pdb7LP7/pdb

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

Deposited: 2021-02-11 Released: 2022-02-16
Deposition Author(s): Cuypers, M.G., Slavish, P.J., Rankovic, Z., White, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.216 (Depositor), 0.214 (DCC)
R-Value Observed:
0.218 (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 the wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000983476

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

To be published.

Macromolecule Content

Total Structure Weight: 24.49 kDa
Atom Count: 1,535
Modeled Residue Count: 180
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): 0 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]
YAD (Subject of Investigation/LOI) Query on YAD 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]	(phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate C₂₄ H₂₅ N₅ O₅ PLCSROHBVUGSBJ-SFHVURJKSA-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 D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [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]