4QU1

Crystal structure of human JMJD5 jmj-c domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Histone Arginine Demethylase JMJD5

Liu, H.L.Wang, C.Dege, C.Ning, F.K.Weisz, J.Hansen, K.Zang, J.Y.Pan, C.H.Marrack, P.Kappler, J.Hagmen, J.Zhang, G.Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 8
A
236Homo sapiensMutation(s): 0 
Gene Names: KDM8 (JMJD5)
EC: 1.14.11.27, 3.4.-.-
Find proteins for Q8N371 (Homo sapiens)
Go to Gene View: KDM8
Go to UniProtKB:  Q8N371
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download SDF File 
Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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: 1.57 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.627α = 90.00
b = 65.030β = 90.00
c = 77.782γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-3000data scaling
ADSCdata collection
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release