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

the crystal structure of KDM6B bound with H3K27me3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-oligomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.233, E.235, H.313 Ligands: OGA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.233, A:E.235, A:H.313, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.418, C.421, C.445, C.448 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.418, A:C.421, A:C.445, A:C.448

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

OGA.3: 13 residues within 4Å: Chain A: Y.222, K.224, T.230, H.233, E.235, S.241, N.243, W.253, H.313, V.315, A.325 Chain B: K.4 Ligands: NI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.241, A:N.243 Water bridges: A:T.230 Salt bridges: A:K.224, A:H.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kruidenier, L. et al., A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature (2012)

Release Date

2012-08-08

Peptides

Lysine-specific demethylase 6B: A
SYNTHESIZED methylation peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Lysine-specific demethylase 6B

SYNTHESIZED methylation peptide

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