Brand  (β version)

PDB ID: 6F5R

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Ligands
Code Name Style Show Link
CL Chloride ion PoSSuM
CQZ 2-(3-oxidanylpropylamino)pyridine-4-carboxylic acid PoSSuM
EDO 1,2-ethanediol PoSSuM
NI Nickel (II) ion PoSSuM
SO4 Sulfate ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
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Structure summary

Code : 6F5R   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE
Title : Crystal Structure of KDM4D with GF028 ligand
Release Data : 2018-12-12
Compound :
mol_id molecule chains synonym
1 Lysine-specific demethylase 4D A JmjC domain-containing histone demethylation protein 3D,Jumonji domain-containing protein 2D
ec: 1.14.11.-
fragment: JMJD2D
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: KDM4D, JHDM3D, JMJD2D
expression_system_vector_type: plasmid
Authors : Malecki, P.H., Link, A., Weiss, M.S., Heinemann, U.
Keywords : KDM4D, KDM4 ligand binding, ligand optimization, drug development, inhibitor design, cancer, epigenetics, OXIDOREDUCTASE
Exp. method : X-RAY DIFFRACTION ( 1.6070 Å )
Citation :

Crystal Structure of KDM4D with GF028 ligand

Malecki, P.H.,Link, A.,Weiss, M.S.  et al.
To be published 

Reaction

Chain : A
UniProt : Q6B0I6 (KDM4D_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
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 + 2 succinate + 2 CO2 1.14.11.66 PubMed:16603238
-
Cofactor: Evidence: Note:
Fe(2+) ECO:0000250
Binds 1 Fe(2+) ion per subunit.