2YU1

Crystal structure of hJHDM1A complexed with a-ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for histone demethylation by JHDM1

Han, Z.Liu, P.Gu, L.Zhang, Y.Li, H.Chen, S.Chai, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
JmjC domain-containing histone demethylation protein 1A
A
451Homo sapiensMutation(s): 1 
Gene Names: KDM2A (CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KIAA1004)
EC: 1.14.11.27
Find proteins for Q9Y2K7 (Homo sapiens)
Go to Gene View: KDM2A
Go to UniProtKB:  Q9Y2K7
Small Molecules
Ligands 2 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
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.238 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.255α = 90.00
b = 81.255β = 90.00
c = 124.010γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CrystalCleardata collection
DENZOdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-05 
  • Released Date: 2007-04-24 
  • Deposition Author(s): Han, Z.

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-08-09
    Type: Refinement description, Source and taxonomy