4GAZ

Crystal Structure of a Jumonji Domain-containing Protein JMJD5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of a Jumonji Domain-containing Protein JMJD5

Wang, H.Zhou, X.Zhang, X.Tao, Y.Chen, N.Zang, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 8AB252Homo 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
OGA
Query on OGA

Download CCD File 
A, B
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-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: 2.81 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.431α = 90
b = 69.431β = 90
c = 270.052γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release