5NGZ | pdb_00005ngz

Ube2T in complex with fragment EM04

• PDB DOI: https://doi.org/10.2210/pdb5NGZ/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-21 Released: 2017-05-03 
• Deposition Author(s): Morreale, F.E., Bortoluzzi, A., Chaugule, V.K., Arkinson, C., Walden, H., Ciulli, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Allosteric Targeting of the Fanconi Anemia Ubiquitin-Conjugating Enzyme Ube2T by Fragment Screening.

Morreale, F.E., Bortoluzzi, A., Chaugule, V.K., Arkinson, C., Walden, H., Ciulli, A.

(2017) J Med Chem 60: 4093-4098

• PubMed: 28437106 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00147
• Primary Citation Related Structures: 
  5NGZ


• PubMed Abstract: 
  

  Ube2T is the E2 ubiquitin-conjugating enzyme of the Fanconi anemia DNA repair pathway and it is overexpressed in several cancers, representing an attractive target for the development of inhibitors. Despite the extensive efforts in targeting the ubiquitin system, very few E2 binders have currently been discovered. Herein we report the identification of a new allosteric pocket on Ube2T through a fragment screening using biophysical methods. Several fragments binding to this site inhibit ubiquitin conjugation in vitro.

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Organizational Affiliation: 
• MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom.
Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee DD1 5EH, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.72 kDa 
• Atom Count: 1,276 
• Modeled Residue Count: 152 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 T	A	197	Homo sapiens	Mutation(s): 0  Gene Names: UBE2T, HSPC150, PIG50 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPD8 (Homo sapiens) Explore Q9NPD8  Go to UniProtKB:  Q9NPD8
PHAROS:  Q9NPD8 GTEx:  ENSG00000077152

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BG	B [auth A]	1-(1,3-benzothiazol-2-yl)methanamine C8 H8 N2 S VLBUERZRFSORRZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2BG	BindingDB:  5NGZ	Kd: 1.30e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.817	α = 90
b = 55.817	β = 90
c = 185.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Morreale, F.E., Bortoluzzi, A., Chaugule, V.K., Arkinson, C., Walden, H., Ciulli, A.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description