7U8Y | pdb_00007u8y

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 & NIH Common Fund Data Resources
Find proteins for Q91XB0 (Mus musculus) Explore Q91XB0 Go to UniProtKB: Q91XB0
IMPC: MGI:1328317
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91XB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZN (Subject of Investigation/LOI) Query on AZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	ALIZARIN RED C₁₄ H₈ O₇ S JKYKXTRKURYNGW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.222 (Depositor), 0.223 (DCC)
R-Value Work: 0.181 (Depositor), 0.190 (DCC)
R-Value Observed: 0.183 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary