Crystal structure of mus musculus (mm) endonuclease V in complex with a 23MER RNA oligo containing an inosine after a 15 min soak in 10 mm MG2+

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).

Ligands and binding sites

• MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
• K · Potassium ion · metal · 2 copies · chains A, C, B, D
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
• TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A
• PGE · Triethylene glycol · additive · 2 copies · chains A, B

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.

Interfaces

6 interfaces between chains.

• A–C · 819 Ų buried · 25 hydrogen bonds · protein-nucleic
• B–D · 785 Ų buried · 23 hydrogen bonds · protein-nucleic
• C–D · 599 Ų buried · 46 hydrogen bonds · nucleic-nucleic
• B–C · 424 Ų buried · 9 hydrogen bonds · protein-nucleic
• A–D · 399 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

• 6OZR · Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8C9A2 · AlphaFold monomer V2.0 prediction for endonuclease V (Q8C9A2) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q8C9A2
• Elsewhere: RCSB PDB 6OZR · PDBe 6OZR · UniProt Q8C9A2