SMTL ID : 7uva.1 (1 other biounit)

Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.178, D.180, H.250 Ligands: OH0.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.178, A:D.180, A:H.250, OH0.2

1 x OH0: N-heptanoyl-N-hydroxy-beta-alanine(Covalent)

OH0.2: 15 residues within 4Å: Chain A: N.108, I.110, Y.165, L.167, T.175, H.178, D.180, V.186, Y.188, K.195, H.250, V.252, N.264 Chain C: C.8 Ligands: FE.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.165, A:L.167, A:V.186, A:V.252 Hydrogen bonds: A:N.108, A:T.175, A:Y.188, A:Y.188 Water bridges: A:T.175 Salt bridges: A:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spangler, C.J. et al., Structural basis of paralog-specific KDM2A/B nucleosome recognition. Nat.Chem.Biol. (2023)

Release Date

2023-02-22

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
C

Lysine-specific demethylase 2A

Lysine-specific demethylase 2A

Histone H3.2

Related Entries With Identical Sequence