SMTL ID : 2ybk.1 (1 other biounit)

JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: 2HG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.256, H.262, C.328, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: Y.81, R.120, F.224 Ligand excluded by PLIP

1 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)

2HG.4: 11 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, H.298 Ligands: NI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230 Hydrogen bonds: A:S.218, A:N.220, A:K.228 Water bridges: A:K.263, A:K.263 Salt bridges: A:H.210, A:K.228, A:K.263, A:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. (2011)

Release Date

2011-04-06

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4A

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