Crystal structure of human USP2 in complex with ubiquitin and 6- thioguanine

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).

Ligands and binding sites

• DX4 · 2-amino-1,9-dihydro-6H-purine-6-thione · ligand · chains A
• NA · Sodium ion · metal · 5 copies · chains A, B
• ZN · Zinc ion · metal · chains A
• CL · Chloride ion · ion · 5 copies · chains A, B

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–B · 2133 Ų buried · 47 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 5XU8 · Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine · the same entry in another collection · chain A against A, TM-score 1.00
• O75604 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 2 (O75604) · a predicted model of the same protein · chain A against A, TM-score 0.99
• P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 O75604
• Every structure of UniProt P62992
• Elsewhere: RCSB PDB 5XU8 · PDBe 5XU8 · UniProt O75604 · UniProt P62992