Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-(4-(3,4-difluoro-phenyl)-piperidin-1-ylsulfonyl)-phenyl)-4- oxo-butanoic acid

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 20% strand (DSSP).

Ligands and binding sites

• ZOG · 4-{4-[4-(3,4-difluorophenyl)piperidine-1-sulfonyl]phenyl}-4-oxobutanoic acid · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• CA · Calcium ion · metal · chains B
• EDO · 1,2-ethanediol · additive · chains 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 97 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 7MS5 · Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with… · the same entry in another collection · chain A against A, TM-score 1.00
• P45974 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 5 (P45974) · a predicted model of the same protein · chain A 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 P45974
• Elsewhere: RCSB PDB 7MS5 · PDBe 7MS5 · UniProt P45974