SMTL ID : 4qx7.2 (1 other biounit)

Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-oligomer

Ligands

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 12 residues within 4Å: Chain A: N.107, I.109, L.166, T.174, H.177, D.179, Y.187, K.194, H.249, V.251 Chain C: K.8 Ligands: NI.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.109, A:Y.187, A:V.251 Hydrogen bonds: A:T.174, A:Y.187 Water bridges: A:T.174 Salt bridges: A:H.177, A:K.194

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

NI.2: 5 residues within 4Å: Chain A: H.177, D.179, Y.187, H.249 Ligands: AKG.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.177, A:D.179, A:H.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, Z. et al., A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36. Genes Dev. (2014)

Release Date

2014-11-05

Peptides

Lysine-specific demethylase 2A: A
Lysine-specific demethylase 2A: B
Histone H3.2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

Lysine-specific demethylase 2A

Lysine-specific demethylase 2A

Histone H3.2

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