8C8I

Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)

• PDB DOI: https://doi.org/10.2210/pdb8C8I/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-20 Released: 2024-05-01 
• Deposition Author(s): Kohegyi, B.K., Nyiri, K., Vertessy, B.G.
• Funding Organization(s): Hungarian National Research, Development and Innovation Office

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Starting Models: experimental

Literature

Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)

Kohegyi, B.K., Nyiri, K., Vertessy, B.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 94.19 kDa 
• Atom Count: 6,111 
• Modelled Residue Count: 821 
• Deposited Residue Count: 825 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial	A, B, C	128	Homo sapiens	Mutation(s): 0  Gene Names: DUT EC: 3.6.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P33316 (Homo sapiens) Explore P33316  Go to UniProtKB:  P33316
PHAROS:  P33316 GTEx:  ENSG00000128951

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Orf20	D, E, F	147	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q9F0J8 (Staphylococcus aureus) Explore Q9F0J8  Go to UniProtKB:  Q9F0J8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.45	α = 90
b = 82.66	β = 90
c = 139.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Kohegyi, B.K., Nyiri, K., Vertessy, B.G.

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Funding Organization	Location	Grant Number
Hungarian National Research, Development and Innovation Office	Hungary	PD134324

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release