8I6D

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form VI

• PDB DOI: https://doi.org/10.2210/pdb8I6D/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-27 Released: 2023-07-12 
• Deposition Author(s): Raj, P., Paul, A., Gopal, B.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.270 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment

Kesharwani, S., Raj, P., Paul, A., Roy, K., Bhanot, A., Mehta, A., Gopal, A., Varshney, U., Gopal, B., Sundriyal, S.

(2023) Eur J Med Chem 258: 115604

• DOI: https://doi.org/10.1016/j.ejmech.2023.115604

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.18 kDa 
• Atom Count: 3,542 
• Modelled Residue Count: 444 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B	238	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ung, Rv2976c, MTCY349.11 EC: 3.2.2.27
UniProt
Find proteins for P9WFQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFQ9  Go to UniProtKB:  P9WFQ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ODF	C [auth A], D [auth A], F [auth B]	5-oxidanyl-1~{H}-pyrimidine-2,4-dione C4 H4 N2 O3 OFJNVANOCZHTMW-UHFFFAOYSA-N
PEG	G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.270 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.98	α = 90
b = 77.99	β = 102.02
c = 59.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Raj, P., Paul, A., Gopal, B.

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Funding Organization	Location	Grant Number
Other government	India	--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release