› 6wi3

X-ray diffraction
2.35Å resolution

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167711 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone deacetylase 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 385 amino acids
Theoretical weight: 43.9 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92769 (Residues: 2-385; Coverage: 79%)
Gene name: HDAC2
Sequence domains: Histone deacetylase domain
(SHA)W(DTH)DN(DSN)(DME)(DAS)K peptide macrocycle Chains: F, G, H
Molecule details ›
Chains: F, G, H
Length: 9 amino acids
Theoretical weight: 1.16 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ZN 3 x ZN
Ligand NA 6 x NA
Ligand NHE 1 x NHE
Ligand PGE 4 x PGE
Ligand PG4 4 x PG4
4 modified residues:
Ligand DTH 3 x DTH
Ligand DSN 3 x DSN
Ligand MED 3 x MED
Ligand DAS 3 x DAS

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 92.162Å b: 97.593Å c: 139.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.254
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

5 review citations

Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives.
Du et al. (2022)
4 more

1 mention without citation

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.
Hosseinzadeh et al. (2021)