5TVS

JMJD2A in complex with Ni(II)

• PDB DOI: https://doi.org/10.2210/pdb5TVS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-09 Released: 2017-02-01 
• Deposition Author(s): Cascella, B., Lee, S.G., Jez, J.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.267 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A.

Cascella, B., Lee, S.G., Singh, S., Jez, J.M., Mirica, L.M.

(2017) Chem Commun (Camb) 53: 2174-2177

• PubMed: 28144654 
• DOI: https://doi.org/10.1039/c6cc09882g
• Primary Citation of Related Structures:  
  5TVR, 5TVS


• PubMed Abstract: 
  

  JIB-04, a specific inhibitor of the O ₂ -activating, Fe-dependent histone lysine demethylases, is revealed to disrupt the binding of O ₂ in KDM4A/JMJD2A through a continuous O ₂ -consumption assay, X-ray crystal structure data, and molecular docking.

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Organizational Affiliation: 

Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA. [e-mail] and Department of Biology, Washington University, St. Louis, Missouri 63130, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.78 kDa 
• Atom Count: 5,766 
• Modelled Residue Count: 696 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B	359	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164  Go to UniProtKB:  O75164
PHAROS:  O75164 GTEx:  ENSG00000066135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.267 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.689	α = 90
b = 101.14	β = 90
c = 148.894	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PHASER	phasing
Coot	model building
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Cascella, B., Lee, S.G., Jez, J.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI-097119
Department of Defense (DOD, United States)	United States	W81XWH-10-1-0442

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-02-15
  Changes: Database references
• Version 1.2: 2017-02-22
  Changes: Data collection, Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 1.4: 2019-04-10
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2019-11-27
  Changes: Author supporting evidence
• Version 1.6: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-11-06
  Changes: Structure summary