3UYJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report



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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 8AB248Homo sapiensMutation(s): 0 
Gene Names: JMJD5KDM8
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
AKG
Query on AKG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.393α = 90
b = 68.393β = 90
c = 266.686γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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