3UYJ

Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.351 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG

Su, X.Li, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 8
A, B
248Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.351 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.393α = 90.00
b = 68.393β = 90.00
c = 266.686γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-12-06 
  • Released Date: 2011-12-21 
  • Deposition Author(s): Su, X., Li, H.

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release