7U8Y

TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics

• PDB DOI: https://doi.org/10.2210/pdb7U8Y/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-09 Released: 2023-03-15 
• Deposition Author(s): Hemphill, W.O., Harvey, S.E., Simpson, S.R., Smalley, T.L., Salsbury, F.R., Perrino, F.W., Hollis, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics

Hemphill, W.O., Harvey, S.E., Simpson, S.R., Smalley, T.L., Salsbury, F.R., Perrino, F.W., Hollis, T.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 51.68 kDa 
• Atom Count: 3,664 
• Modelled Residue Count: 445 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Three-prime repair exonuclease 1	A, B	229	Mus musculus	Mutation(s): 0  Gene Names: Trex1 EC: 3.1.11.2
UniProt
Find proteins for Q91XB0 (Mus musculus) Explore Q91XB0  Go to UniProtKB:  Q91XB0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZN (Subject of Investigation/LOI)	C [auth A], D [auth A], G [auth B], H [auth B]	ALIZARIN RED C14 H8 O7 S JKYKXTRKURYNGW-UHFFFAOYSA-N
MN	E [auth A], F [auth A], I [auth B], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.555	α = 90
b = 127.555	β = 90
c = 80.01	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Coot	model building
CrysalisPro	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Hemphill, W.O., Harvey, S.E., Simpson, S.R., Smalley, T.L., Salsbury, F.R., Perrino, F.W., Hollis, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI116725
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM110734
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA012197
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32-AI007401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM095440

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description