SMTL ID : 4qxb.1 (1 other biounit)

crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.174, A:Y.187, A:Y.187 Water bridges: A:T.174 Salt bridges: A:K.194, A:H.249

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

NI.2: 4 residues within 4Å: Chain A: H.177, D.179, H.249 Ligands: OGA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.177, A:D.179, A:H.249, H2O.6

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
A

B
B

C
E

Lysine-specific demethylase 2A

Lysine-specific demethylase 2A

Histone H3.2

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