5TVS

JMJD2A in complex with Ni(II)

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • 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)

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 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


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

  • DOI: 10.1039/c6cc09882g
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • JIB-04, a specific inhibitor of the O <sub>2 </sub>-activating, Fe-dependent histone lysine demethylases, is revealed to disrupt the binding of O <sub>2 </sub> in KDM4A/JMJD2A through a continuous O <sub>2 </sub>-consumption assay, X-ray crystal stru ...

    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.


    Organizational Affiliation

    Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA. mirica@wustl.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B
359Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11
Find proteins for O75164 (Homo sapiens)
Go to UniProtKB:  O75164
NIH Common Fund Data Resources
PHAROS  O75164
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
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 = 56.689α = 90
b = 101.14β = 90
c = 148.894γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHASERphasing
Cootmodel building
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI-097119
Department of Defense (DOD, United States)United StatesW81XWH-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