8ZWQ | pdb_00008zwq

pseudorabies virus dUTPase structure

• PDB DOI: https://doi.org/10.2210/pdb8ZWQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Suid alphaherpesvirus 1
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2024-06-13 Released: 2025-06-18 
• Deposition Author(s): Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.339 (Depositor), 0.337 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.280 (Depositor) 

Starting Model: in silico

Literature

Structural definition of pseudorabies virus dUTPase reveals a novel folding dimer in the herpesviruses family

Wang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 119.22 kDa 
• Atom Count: 7,214 
• Modeled Residue Count: 896 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dUTPase	A, B [auth C], C [auth B], D	276	Suid alphaherpesvirus 1	Mutation(s): 0  Gene Names: UL50 EC: 3.6.1.23
UniProt
Find proteins for Q90030 (Suid herpesvirus 1 (strain Kaplan)) Explore Q90030  Go to UniProtKB:  Q90030

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP (Subject of Investigation/LOI)	F [auth A]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.339 (Depositor), 0.337 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.280 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.249	α = 90
b = 103.264	β = 99.472
c = 98.733	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81801998

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release