MolNFT v1 · #103356 · protein + DNA

Crystal structure of tatd in complex with trinucleotide DNA

4PE8 · Tat-linked quality control protein tatd: “Crystal structure of tatd in complex with trinucleotide DNA”. X-ray diffraction, 2 pockets (best druggability 0.60). MolNFT v1 #103356 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4PE8
Type: protein + DNA
Length: 263 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tat-linked quality control protein tatd; DNA (5'-D(*GP*CP*T)-3')
EC: 3.1.15.-
UniProt: P27859
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tat-linked quality control protein tatd (EC 3.1.15.-)	protein	260	44% helix, 15% strand	P27859
B	DNA (5'-D(GPCP*T)-3')	dna	3	—	—

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.60	0.86	33	empty
2	152	0.51	0.79	18	empty

Interfaces

1 interface between chains.

A–B · 426 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

4PE8 · Crystal structure of TatD in complex with trinucleotide DNA · the same entry in another collection · chain A against A, TM-score 1.00
P27859 · AlphaFold monomer V2.0 prediction for 3'-5' SSDNA/RNA exonuclease tatd (P27859) · 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 P27859
Elsewhere: RCSB PDB 4PE8 · PDBe 4PE8 · UniProt P27859

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