Crystal structure of zebrafish sirtuin 5 in complex with 3- methyl-succinylated CPS1-peptide

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).

Ligands and binding sites

• BEZ · Benzoic acid · ligand · 2 copies · chains A, D
• JO3 · (2R)-2-methylbutanedioic acid · ligand · chains A, D
• SUH · (2S)-2-methylbutanedioic acid · ligand · chains A, D
• ZN · Zinc ion · metal · 2 copies · chains A, B
• NA · Sodium ion · metal · chains B
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · chains A, B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–B · 674 Ų buried · 11 hydrogen bonds · protein-protein
• A–D · 512 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent (covalent ligand).

Compared structures

• 4UU7 · Crystal structure of zebrafish Sirtuin 5 in complex with 3-methyl- succinylated… · the same entry in another collection · chain A against A, TM-score 1.00
• Q6DHI5 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q6DHI5
• Every structure of UniProt Q5R209
• Elsewhere: RCSB PDB 4UU7 · PDBe 4UU7 · UniProt Q6DHI5 · UniProt Q5R209