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JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE
2YBK
Primary Citation
 
 
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  •   Molecular Description Hide
    Classification: Oxidoreductase
    Structure Weight: 89233.24
    Molecule: LYSINE-SPECIFIC DEMETHYLASE 4A
    Polymer: 1 Type: protein Length: 381
    Chains: A, B
    EC#: 1.14.11   
    Fragment: CATALYTIC DOMAIN, RESIDUES 1-359
    Organism Homo sapiens
    Gene Names KDM4A JHDM3A JMJD2 JMJD2A KIAA0677
    UniProtKB:   Protein Feature View | Search PDB | O75164  
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
     
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    Identifier Details
    2GF7  DOUBLE TUDOR DOMAIN STRUCTURE 
    2GFA  DOUBLE TUDOR DOMAIN COMPLEX STRUCTURE 
    2GP3  CRYSTAL STRUCTURE OF THE CATALYTIC CORE COMAIN OF JMJD2A 
    2GP5  CRYSTAL STRUCTURE OF CATALYTIC CORE DOMAIN OF JMJD2ACOMPLEXED WITH ALPHA-KETOGLUTARATE 
    2VD7  CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR PYRIDINE-2,4-DICARBOXYLIC ACID 
    2WWJ  STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A 
    2YBP  JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36ME3 PEPTIDE (30-41) 
    2YBS  JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36ME3 PEPTIDE (30-41) 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    2HG
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    Download      		2HG C5 H8 O5
    (2R)-2-hydroxypentanedioic acid
    		2HG:2YBK
    CL
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    Download      		CL Cl
    CHLORIDE ION
    NI
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    Download      		NI Ni
    NICKEL (II) ION
    ZN
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    Download      		ZN Zn
    ZINC ION
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    2HG
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    Download      		2HG
    IC50: 24000 nM (100) - data from BindingDB  
    IC50: 24000 nM - data from BindingMOAD  
    IC50: 24000 nM - data from PDBbind  
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
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  Biological Assembly 1       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Chowdhury, R.,  Mcdonough, M.A.,  Schofield, C.J.

    Deposition:   2011-03-08
    Release:   2011-04-06
    Last Modified (REVDAT):   2011-05-11
     
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.40
    R-Value: 0.203 (obs.)
    R-Free: 0.236
    Space Group: P 21 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 101.13 α = 90.00 
    b = 149.33 β = 90.00 
    c = 56.53 γ = 90.00