Brand  (β version)

PDB ID: 5PHE

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Ligands
Code Name Style Show Link
231 4-phenyl-1h-imidazole PoSSuM
EDO 1,2-ethanediol PoSSuM
NI Nickel (II) ion PoSSuM
OGA N-oxalylglycine PoSSuM
SO4 Sulfate ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
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Structure summary

Code : 5PHE   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE
Title : PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09453a
Release Data : 2017-03-15
Compound :
mol_id molecule chains synonym
1 Lysine-specific demethylase 4D A JmjC domain-containing histone demethylation protein 3D,Jumonji domain-containing protein 2D
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: KDM4D, JHDM3D, JMJD2D
Authors : Pearce, N.M., Krojer, T., Talon, R., Bradley, A.R., Fairhead, M., Sethi, R., Wright, N., MacLean, E., Collins, P., Brandao-Neto, J., Douangamath, A., Renjie, Z., Dias, A., Vollmar, M., Ng, J., Szykowska, A., Burgess-Brown, N., Brennan, P.E., Cox, O., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.
Keywords : PanDDA, SGC - Diamond I04-1 fragment screening, Jmj domain, epigenetics, OXIDOREDUCTASE
Exp. method : X-RAY DIFFRACTION ( 1.3510 Å )
Citation :

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce, N.M.,Krojer, T.,Bradley, A.R.  et al.
(2017)  Nat Commun  8 : 15123 - 15123

PubMed: 28436492
DOI: 10.1038/ncomms15123

Reaction

Chain : A
UniProt : Q6B0I6 (KDM4D_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 2 2- oxoglutarate + 2 O2 = N(6)-methyl-L-lysyl(9)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 1.14.11.66 PubMed:16603238
-
Cofactor: Evidence: Note:
Fe(2+) ECO:0000250
Binds 1 Fe(2+) ion per subunit.