PDBsum entry 6f5r

Oxidoreductase

PDB id: 6f5r

Contents

Protein chain

327 a.a.

Ligands

EDO ×9

SO4 ×2

CQZ

Metals

_ZN

_CL

_NI

Waters ×342

PDB id:

6f5r

Name:

Oxidoreductase

Title:

Crystal structure of kdm4d with gf028 ligand

Structure:

Lysine-specific demethylase 4d. Chain: a. Fragment: jmjd2d. Synonym: jmjc domain-containing histone demethylation protein 3d, jumonji domain-containing protein 2d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: kdm4d, jhdm3d, jmjd2d. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.61Å R-factor: 0.168 R-free: 0.192

Authors:

P.H.Malecki,A.Link,M.S.Weiss,U.Heinemann

Key ref:

P.H.Malecki et al. Crystal structure of kdm4d with gf028 ligand. To be published, .

Date:

02-Dec-17 Release date: 12-Dec-18

Protein chain

Q6B0I6  (KDM4D_HUMAN) -  Lysine-specific demethylase 4D from Homo sapiens

Seq: 523 a.a.

Struc: 327 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.11.66 - [histone H3]-trimethyl-L-lysine(9) demethylase.
• Reaction: N₆,N₆,N₆-trimethyl-L-lysyl₉-[histone H3] + 2 2-oxoglutarate + 2 O2 = N₆-methyl-L-lysyl₉-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2

N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 2 × 2-oxoglutarate + 2 × O2 = N(6)-methyl-L-lysyl(9)-[histone H3] + 2 × formaldehyde (Bound ligand (Het Group name = EDO) matches with 50.00% similarity) + 2 × succinate + 2 × CO2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site