Structure of hdac like protein from bordetella alcaligenes in complex with the photoswitchable inhibitor CEW65

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).

Ligands and binding sites

• C65 · (2E)-N-hydroxy-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-enamide · ligand · 4 copies · chains A, B, C, D
• K · Potassium ion · metal · 8 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, C, D
• 1PE · Pentaethylene glycol · additive · 2 copies · chains B, C

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 1772 Ų buried · 30 hydrogen bonds · protein-protein
• C–D · 1766 Ų buried · 28 hydrogen bonds · protein-protein
• A–C · 958 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 943 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 409 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 5G3W · Structure of HDAC like protein from Bordetella Alcaligenes in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
• Q70I53 · AlphaFold monomer V2.0 prediction for histone deacetylase-like amidohydrolase (Q70I53) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q70I53
• Elsewhere: RCSB PDB 5G3W · PDBe 5G3W · UniProt Q70I53