4D6R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.172
  • R-Value Work: 0.145

Literature

Macromolecules
Sequence Display for 4D6R

Classification: TRANSCRIPTION

Total Structure Weight: 40611.98

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 4D A 343 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JUMONJI DOMAIN, RESIDUES 1-342
Gene Name(s): KDM4D Gene View JHDM3D JMJD2D
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IEJ
Query on IEJ

A O-TOLUENESULFONAMIDE
C7 H9 N O2 S
YCMLQMDWSXFTIF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OGA
Query on OGA

A N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.172
  • R-Value Work: 0.145
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 71.51 α = 90.00
b = 71.51 β = 90.00
c = 150.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-11-14
  • Released Date: 2014-12-24
  • Deposition author(s): 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.

Revision History

  • Version 1_0: 2014-12-24

    Type: Initial release