MolNFT v1 · #111331 · protein + DNA

TREX1-dsdna complex

4YNQ · Three-prime repair exonuclease 1: “TREX1-dsdna complex”. X-ray diffraction, 2 ligands (DT, MG), 13 pockets (best druggability 0.63). MolNFT v1 #111331 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YNQ
Type: protein + DNA
Length: 985 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Three-prime repair exonuclease 1; DNA (24-mer); DNA (5'…
EC: 3.1.11.2
UniProt: Q91XB0
Ligands: DT, MG
Pockets: 13 · best druggability 0.63

Structure

x-ray diffraction · 6 distinct chains · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Three-prime repair exonuclease 1 (EC 3.1.11.2)	protein	227	39% helix, 16% strand	Q91XB0
B	Three-prime repair exonuclease 1 (EC 3.1.11.2)	protein	225	38% helix, 16% strand	Q91XB0
C	Three-prime repair exonuclease 1 (EC 3.1.11.2)	protein	227	38% helix, 16% strand	Q91XB0
D	Three-prime repair exonuclease 1 (EC 3.1.11.2)	protein	224	38% helix, 16% strand	Q91XB0
E, G	DNA (24-mer)	dna	21	—	—
F, H	DNA (5'- D(PGPTPGPCPTPGPAPCPGPTPCPAPGPCPAPCPGPAPCPG)-3')	dna	20	—	—

Ligands and binding sites

DT · Thymidine-5'-monophosphate · ligand · chains B, H
MG · Magnesium ion · metal · 4 copies · chains A, E, B, C, D, G

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	473	0.63	0.76	47	empty
2	472	0.62	0.76	35	empty
3	426	0.61	0.76	47	empty
4	332	0.58	0.77	31	empty
5	272	0.57	0.78	35	MG

Interfaces

14 interfaces between chains.

C–D · 1789 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 1774 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 819 Å² buried · 69 hydrogen bonds · nucleic-nucleic
G–H · 818 Å² buried · 76 hydrogen bonds · nucleic-nucleic
A–E · 582 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

4YNQ · TREX1-dsDNA complex · the same entry in another collection · chain H against H, 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 B 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 4YNQ · PDBe 4YNQ · UniProt Q91XB0

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