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Zinc-dependent bifunctional nuclease

Analyse Zinc-dependent bifunctional nuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3W52
Type
protein
Length
256 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
1.76
Source
Arabidopsis thaliana
Molecule
Endonuclease 2
EC
3.1.30.1
UniProt
Q9C9G4
Ligands
ADE, NAG, BMA, ZN, SO4
Pockets
1 · best druggability 0.33

Structure

x-ray diffraction · resolution 1.76 · 1 distinct chain · 63% helix, 7% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndonuclease 2 (EC 3.1.30.1)protein25663% helix, 7% strandQ9C9G4

Ligands and binding sites

  • ADE · Adenine · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
  • BMA · beta-D-mannopyranose · sugar · chains A
  • ZN · Zinc ion · metal · 3 copies · chains A
  • SO4 · Sulfate ion · ion · 3 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1630.330.7724ADE, ZN, SO4

Modifications

Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

  • 3W52 · Zinc-dependent bifunctional nuclease · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9C9G4 · AlphaFold monomer V2.0 prediction for endonuclease 2 (Q9C9G4) · a predicted model of the same protein · chain A against A, TM-score 1.00

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