MolNFT v1 · #92649 · protein

Crystal structure of TDP2 from C. elegans

4GEW · 5'-tyrosyl-DNA phosphodiesterase: “Crystal structure of TDP2 from C. elegans”. X-ray diffraction, 1 pocket (best druggability 0.31). MolNFT v1 #92649 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GEW
Type: protein
Length: 324 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-tyrosyl-DNA phosphodiesterase
EC: 3.1.4.-
UniProt: Q9XWG3
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-tyrosyl-DNA phosphodiesterase (EC 3.1.4.-)	protein	324	30% helix, 27% strand	Q9XWG3

Ligands and binding sites

GOL · Glycerol · additive · 9 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.31	0.75	16	GOL

Compared structures

4GEW · Crystal structure of TDP2 from C. elegans · the same entry in another collection · chain A against A, TM-score 1.00
Q9XWG3 · AlphaFold monomer V2.0 prediction for 5'-tyrosyl-DNA phosphodiesterase (Q9XWG3) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 Q9XWG3
Elsewhere: RCSB PDB 4GEW · PDBe 4GEW · UniProt Q9XWG3

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