8T8X

Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb8T8X/pdb

Classification: VIRAL PROTEIN
Organism(s): Terrestrivirus sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-23 Released: 2023-11-15
Deposition Author(s): Zong, G., Wang, H., Shears, S.B.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.229
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Biochemical and Structural Characterization of a Giant Virus Inositol Pyrophosphate Kinase

Zong, G., Wang, H., Shears, S.B.

(2023) EMBO J

Macromolecule Content

Total Structure Weight: 29.95 kDa
Atom Count: 1,891
Modelled Residue Count: 216
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinase	A	249	Terrestrivirus sp.	Mutation(s): 0 Gene Names: Terrestrivirus9_15
UniProt
Find proteins for A0A3G4ZNY6 (Terrestrivirus sp) Explore A0A3G4ZNY6 Go to UniProtKB: A0A3G4ZNY6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3G4ZNY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CD (Subject of Investigation/LOI) Query on CD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]