5TVR image
Deposition Date 2016-11-09
Release Date 2017-02-01
Last Version Date 2024-10-30
Entry Detail
PDB ID:
5TVR
Keywords:
OXIDOREDUCTASE
Title:
JMJD2A in complex with Ni(II) and alpha-Ketoglutarate
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.09 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 2 21 21
5TVR validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Lysine-specific demethylase 4A
Gene (Uniprot):KDM4A
Chain IDs:A, B
Chain Length:359
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:O75164 Pfam ID:PF02375, PF02373 EC:1.14.11.27
Ligand Molecules
AKG
NI
ZN
Primary Citation
The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A.
Chem. Commun. (Camb.) 53 2174 2177 (2017)
PMID: 28144654 DOI: 10.1039/c6cc09882g

Abstact

JIB-04, a specific inhibitor of the O2-activating, Fe-dependent histone lysine demethylases, is revealed to disrupt the binding of O2 in KDM4A/JMJD2A through a continuous O2-consumption assay, X-ray crystal structure data, and molecular docking.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5TVS