2YU2

Crystal structure of hJHDM1A without a-ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.5 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JmjC domain-containing histone demethylation protein 1A451Homo sapiensMutation(s): 1 
Gene Names: hJHDM1A
EC: 1.14.11.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2K7 (Homo sapiens)
Explore Q9Y2K7 
Go to UniProtKB:  Q9Y2K7
PHAROS:  Q9Y2K7
GTEx:  ENSG00000173120 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2K7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.15α = 90
b = 81.15β = 90
c = 124.47γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-05-29
    Changes: Data collection