Crystal structure of deubiquitinase mindy-1 in complex with ubiquitin

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).

Ligands and binding sites

• AYE · prop-2-en-1-amine · ligand · chains A, D
• SO4 · Sulfate ion · ion · 3 copies · chains A, D
• CL · Chloride ion · ion · chains A
• DIO · 1,4-diethylene dioxide · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–D · 718 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 5JQS · Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
• Q8N5J2 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase mindy-1… · a predicted model of the same protein · chain A against A, TM-score 0.98
• P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 Q8N5J2
• Every structure of UniProt P62992
• Elsewhere: RCSB PDB 5JQS · PDBe 5JQS · UniProt Q8N5J2 · UniProt P62992