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Structure of TREX1 in complex with a nucleotide

Analyse Structure of TREX1 in complex with a nucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O4G
Type: protein
Length: 868 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Three prime repair exonuclease 1
EC: 3.1.11.2
UniProt: Q91XB0
Ligands: TMP, MG
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Three prime repair exonuclease 1 (EC 3.1.11.2)	protein	217	40% helix, 17% strand	Q91XB0

Ligands and binding sites

TMP · Thymidine-5'-phosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.74	0.77	101	empty
2	462	0.65	0.78	50	empty
3	203	0.54	0.78	28	MG, TMP
4	194	0.53	0.78	27	MG, TMP
5	218	0.52	0.76	25	MG, TMP

Interfaces

5 interfaces between chains.

A–C · 1778 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 1771 Å² buried · 37 hydrogen bonds · protein-protein
A–D · 324 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 122 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 26 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2O4G · Structure of TREX1 in complex with a nucleotide · the same entry in another collection · chain A against A, TM-score 1.00
Q91XB0 · AlphaFold monomer V2.0 prediction for three-prime repair exonuclease 1 (Q91XB0) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q91XB0
Elsewhere: RCSB PDB 2O4G · PDBe 2O4G · UniProt Q91XB0

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