8T93

Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-L-(1,2,3,4)-IP4

• PDB DOI:  https://doi.org/10.2210/pdb8T93/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Biochemical and Structural Characterization of a Giant Virus Inositol Pyrophosphate Kinase

Zong, G., Wang, H., Shears, S.B.

(2023) EMBO J 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.64 kDa 
• Atom Count: 2,054 
• Modelled Residue Count: 216 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZNQ (Subject of Investigation/LOI)	D [auth A]	(1R,2S,3S,4R,5S,6S)-5,6-dihydroxycyclohexane-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)] C6 H16 O18 P4 MRVYFOANPDTYBY-VTJCEZEHSA-N
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.671	α = 90
b = 103.415	β = 90
c = 103.674	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Zong, G., Wang, H., Shears, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZI AES080046-31

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release