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

JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-1-1-mer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: S2G.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.9

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 GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.81, R.120, F.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120, A:R.120

1 x S2G: (2S)-2-HYDROXYPENTANEDIOIC ACID(Non-covalent)

S2G.4: 14 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, T.292, H.298, S.310 Chain B: K.7 Ligands: NI.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.207 Hydrogen bonds: A:S.218, A:N.220, A:S.310 Water bridges: A:E.212, A:K.263 Salt bridges: A:K.228, 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

2011-03-30

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A
HISTONE H3.1T: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

LYSINE-SPECIFIC DEMETHYLASE 4A

HISTONE H3.1T

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