4D6S

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound 5,6-Dimethylbenzimidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of Human Jmjd2D in Complex with N-Oxalylglycine and Bound 5,6- Dimethylbenzimidazole

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 sapiensGene Names: KDM4D (JHDM3D, JMJD2D)
EC: 1.14.11.-
Find proteins for Q6B0I6 (Homo sapiens)
Go to Gene View: KDM4D
Go to UniProtKB:  Q6B0I6
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMD
Query on DMD

Download SDF File 
Download CCD File 
A
5,6-DIMETHYLBENZIMIDAZOLE
C9 H10 N2
LJUQGASMPRMWIW-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.139 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.225α = 90.00
b = 71.225β = 90.00
c = 150.208γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release