4D6Q

crystal structure of human JMJD2D in complex with 2,4-PDCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Human Jmjd2D in Complex with 2,4-Pdca

Krojer, T.Vollmar, M.Bradley, A.Crawley, L.Szykowska, A.Burgess-Brown, N.Gileadi, C.Johansson, C.Oppermann, U.Bountra, C.Arrowsmith, C.H.Edwards, A.von Delft, F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 4D
A
343Homo sapiensMutation(s): 0 
Gene Names: KDM4DJHDM3DJMJD2D
EC: 1.14.11.66
Find proteins for Q6B0I6 (Homo sapiens)
Go to UniProtKB:  Q6B0I6
NIH Common Fund Data Resources
PHAROS  Q6B0I6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PD2
Query on PD2

Download CCD File 
A
PYRIDINE-2,4-DICARBOXYLIC ACID
C7 H5 N O4
MJIVRKPEXXHNJT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.91α = 90
b = 71.91β = 90
c = 151.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references