4GD4

Crystal Structure of JMJD2A Complexed with Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystal Structure of JMJD2A Complexed with Inhibitor

King, O.N.F.Krojer, T.Arrowsmith, C.H.Edwards, A.Bountra, C.McDonough, M.A.Schofield, C.J.Structural Genomics Consortium (SGC)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B
381Homo sapiensMutation(s): 0 
Gene Names: KDM4A (JHDM3A, JMJD2, JMJD2A, KIAA0677)
EC: 1.14.11.-
Find proteins for O75164 (Homo sapiens)
Go to Gene View: KDM4A
Go to UniProtKB:  O75164
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0WS
Query on 0WS

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Download CCD File 
A, B
2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid
C9 H7 N3 O2
NTNYOLXCVCDWFY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.750α = 90.00
b = 150.030β = 90.00
c = 57.490γ = 90.00
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
XDSdata reduction
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Other
  • Version 1.2: 2014-10-08
    Type: Database references
  • Version 1.3: 2014-12-03
    Type: Structure summary
  • Version 1.4: 2018-01-24
    Type: Database references
  • Version 1.5: 2018-01-31
    Type: Database references