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ceKDM7A from C.elegans, complex with H3K4me3 peptide and NOG
3N9L
Primary Citation
 
 
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  •   Molecular Description Hide
    Classification: Oxidoreductase
    Structure Weight: 63887.69
    Molecule: Putative uncharacterized protein
    Polymer: 1 Type: protein Length: 528
    Chains: A
    Fragment: PHD domain, UNP residues 201-724
    Organism Caenorhabditis elegans
    Gene Name F29B9.2
    UniProtKB:   Protein Feature View | Search PDB | Q9GYI0  
    Molecule: Histone H3 peptide
    Polymer: 2 Type: protein Length: 15
    Chains: B
    Fragment: JMJC domain, UNP residues 2-16
    Details: H3K4me3
    Organism Caenorhabditis elegans
    Gene Names his-2 T10C6.13 his-6 F45F2.13 his-9 ZK131.3 his-13 ZK131.7 his-17 K06C4.5 his-25 ZK131.2 his-27 K06C4.13 his-32 F17E9.10 his-42 F08G2.3 his-45 B0035.10 his-49 F07B7.5 his-55 F54E12.1 his-59 F55G1.2 his-63 F22B3.2
    UniProtKB:   Protein Feature View | Search PDB | P08898  
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Caenorhabditis elegans   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct (Caenorhabditis elegans)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3N9M  apo lysine demethylase 
    3N9N  lysine demethylase with Histone H3(K4me3K9me2) and NOG 
    3N9O  lysine demethylase with Histone H3(K4me3) and Histone H3(K9me2) and NOG 
    3N9P  lysine demethylase with Histone H3(K4me3K27me2) and NOG 
    3N9Q  lysine demethylase with Histone H3(K4me3) and Histone H3(K27me2) and NOG 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    FE2
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    Download      		FE2 Fe
    FE (II) ION
    OGA
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    Download      		OGA C4 H5 N O5
    N-OXALYLGLYCINE
    		OGA:3N9L
    ZN
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    Download      		ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    M3L
    Search      		M3L C9 H21 N2 O2 LYS lPeptideLinking
     
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  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
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  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Yang, Y.,  Hu, L.,  Wang, P.,  Hou, H.,  Chen, C.D.,  Xu, Y.

    Deposition:   2010-05-31
    Release:   2010-06-30
    Last Modified (REVDAT):   2010-08-11
     
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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]:   2.80
    R-Value: 0.200 (obs.)
    R-Free: 0.255
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 68.91 α = 90.00 
    b = 87.26 β = 90.00 
    c = 102.49 γ = 90.00