4D6R

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound o-toluenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Human Jmjd2D in Complex with N-Oxalylglycine and Bound O-Toluenesulfonamide

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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSINE-SPECIFIC DEMETHYLASE 4D343Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens)
Explore Q6B0I6 
Go to UniProtKB:  Q6B0I6
PHAROS:  Q6B0I6
GTEx:  ENSG00000186280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B0I6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IEJ
Query on IEJ

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
O-TOLUENESULFONAMIDE
C7 H9 N O2 S
YCMLQMDWSXFTIF-UHFFFAOYSA-N
OGA
Query on OGA

Download Ideal Coordinates CCD File 
H [auth A]N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.514α = 90
b = 71.514β = 90
c = 150.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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