7XME | pdb_00007xme

Structure of Influenza A virus polymerase basic protein 2 (PB2) with an azazindole derivative

PDB DOI: https://doi.org/10.2210/pdb7XME/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Influenza A virus (A/Victoria/3/1975(H3N2))
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-25 Released: 2023-05-03
Deposition Author(s): Zhang, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.330 (Depositor), 0.319 (DCC)
R-Value Work:
0.250 (Depositor), 0.253 (DCC)
R-Value Observed:
0.254 (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

Discovery of a novel azaindole derivatives targeting the influenza PB2 cap binding region

Zhang, Z., Liu, X.

To be published.

Macromolecule Content

Total Structure Weight: 77.97 kDa
Atom Count: 5,011
Modeled Residue Count: 618
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	A, B, C, D	166	Influenza A virus (A/Victoria/3/1975(H3N2))	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for P31345 (Influenza A virus (strain A/Victoria/3/1975 H3N2)) Explore P31345 Go to UniProtKB: P31345
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31345
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GIH (Subject of Investigation/LOI) Query on GIH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	(2~{S},3~{S})-3-[[5-dimethoxyphosphoryl-4-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid C₂₂ H₂₅ F N₅ O₅ P HZZFRSXJRJLLCP-CMKMFDCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]