4AAP

Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Jmjd5 Domain of Human Lysine- Specific Demethylase 8 (Kdm8) in Complex with N- Oxalylglycine (Nog)

Vollmar, M.Johansson, C.Krojer, T.Canning, P.Allerston, C.Gadhave, A.von Delft, F.Bountra, C.Arrowsmith, C.H.Weigelt, J.Edwards, A.Oppermann, U.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSINE-SPECIFIC DEMETHYLASE 8A, B239Homo sapiensMutation(s): 0 
Gene Names: KDM8JMJD5
EC: 1.14.11.27 (PDB Primary Data), 1.14.11 (UniProt), 3.4 (UniProt)
Find proteins for Q8N371 (Homo sapiens)
Explore Q8N371 
Go to UniProtKB:  Q8N371
NIH Common Fund Data Resources
PHAROS  Q8N371
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA

Download CCD File 
A, B
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.575α = 90
b = 68.575β = 90
c = 269.003γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references