Structure of the SMURF2 hect domain with a high affinity ubiquitin variant (ubv)

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).

Ligands and binding sites

• NA · Sodium ion · metal · 2 copies · chains A
• CL · Chloride ion · ion · 6 copies · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
• EDO · 1,2-ethanediol · additive · chains 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, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 780 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

• 7M3Q · Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV) · the same entry in another collection · chain A against A, TM-score 1.00
• P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain B against A, TM-score 0.92
• Q9HAU4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase SMURF2 (Q9HAU4) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q9HAU4
• Every structure of UniProt P62987
• Elsewhere: RCSB PDB 7M3Q · PDBe 7M3Q · UniProt Q9HAU4 · UniProt P62987