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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 169)

Source organism: Homo sapiens
Biochemical function: not assigned
Biological process: not assigned
Cellular component: not assigned

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EC 1.14.11.66: [Histone H3]-trimethyl-L-lysine(9) demethylase

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Systematic name:
[Histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9),2-oxoglutarate:oxygen oxidoreductase

GO terms

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

Sequence families

Pfam Protein families (Pfam)
PF02373
Domain description: JmjC domain, hydroxylase
Occurring in:
  1. Lysine-specific demethylase 4D
The deposited structure of PDB entry 5pmb contains 1 copy of Pfam domain PF02373 (JmjC domain, hydroxylase) in Lysine-specific demethylase 4D. Showing 1 copy in chain A.

PF02375
Domain description: jmjN domain
Occurring in:
  1. Lysine-specific demethylase 4D
The deposited structure of PDB entry 5pmb contains 1 copy of Pfam domain PF02375 (jmjN domain) in Lysine-specific demethylase 4D. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR003349
Domain description: JmjN domain
Occurring in:
  1. Lysine-specific demethylase 4D
IPR003347
Domain description: JmjC domain
Occurring in:
  1. Lysine-specific demethylase 4D

Structure domain

CATH CATH domain
2.60.120.650
Class: Mainly Beta
Architecture: Sandwich
Topology: Jelly Rolls
Homology: Cupin
Occurring in:
  1. Lysine-specific demethylase 4D
The deposited structure of PDB entry 5pmb contains 1 copy of CATH domain 2.60.120.650 (Jelly Rolls) in Lysine-specific demethylase 4D. Showing 1 copy in chain A.

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