MolNFT v1 · #80750 · protein + DNA

Mouse TREX1 D200N mutant

3U6F · Three prime repair exonuclease 1: “Mouse TREX1 D200N mutant”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.65). MolNFT v1 #80750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3U6F
Type: protein + DNA
Length: 443 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Three prime repair exonuclease 1; 5'-D(*GP*AP*CP*G)-3'
EC: 3.1.11.2
UniProt: Q91XB0
Ligands: MG
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Three prime repair exonuclease 1 (EC 3.1.11.2)	protein	218	37% helix, 17% strand	Q91XB0
A	Three prime repair exonuclease 1 (EC 3.1.11.2)	protein	217	38% helix, 17% strand	Q91XB0
C, D	5'-D(GPAPCPG)-3'	dna	4	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, C, A, D
BU1 · 1,4-butanediol · additive · 2 copies · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.65	0.78	48	BU1
2	63	0.35	0.78	13	empty
3	64	0.34	0.77	16	empty

Interfaces

3 interfaces between chains.

B–A · 1781 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 575 Å² buried · 13 hydrogen bonds · protein-nucleic
B–C · 564 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

3U6F · Mouse TREX1 D200N mutant · the same entry in another collection · chain B against B, 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 3U6F · PDBe 3U6F · UniProt Q91XB0

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