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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with oxamflatin

Source organism: Danio rerio
Biochemical function: not assigned
Biological process: not assigned
Cellular component: not assigned

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EC 3.5.1.98: Histone deacetylase

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Systematic name:
Histone amidohydrolase
Alternative Name(s):
  • HDAC

GO terms

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence family

Pfam Protein family (Pfam)
PF00850
Domain description: Histone deacetylase domain
Occurring in:
  1. UBP-type domain-containing protein
The deposited structure of PDB entry 5efb contains 1 copy of Pfam domain PF00850 (Histone deacetylase domain) in UBP-type domain-containing protein. Showing 1 copy in chain A [auth D].

InterPro InterPro annotations
IPR000286
Domain description: Histone deacetylase family
Occurring in:
  1. UBP-type domain-containing protein
IPR023801
Domain description: Histone deacetylase domain
Occurring in:
  1. UBP-type domain-containing protein
IPR023696
Domain description: Ureohydrolase domain superfamily
Occurring in:
  1. UBP-type domain-containing protein
IPR017320
Domain description: Histone deacetylase class II, eukaryotic-type
Occurring in:
  1. UBP-type domain-containing protein
IPR037138
Domain description: Histone deacetylase domain superfamily
Occurring in:
  1. UBP-type domain-containing protein

Structure domain

CATH CATH domain
3.40.800.20
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Arginase; Chain A
Homology: Histone deacetylase domain
Occurring in:
  1. UBP-type domain-containing protein
The deposited structure of PDB entry 5efb contains 1 copy of CATH domain 3.40.800.20 (Arginase; Chain A) in UBP-type domain-containing protein. Showing 1 copy in chain A [auth D].

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