SMTL ID : 7jvw.2 (1 other biounit)

Crystal structure of human histone deacetylase 8 (HDAC8) G320R mutation complexed with M344

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x B3N: 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide(Non-covalent)

B3N.1: 12 residues within 4Å: Chain A: K.33, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, G.304, Y.306 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.208, A:F.208 Hydrogen bonds: A:H.143

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: B3N.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.267

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: D.176, L.177, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.4: 4 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.189, A:T.192, A:V.195, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osko, J.D. et al., Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders. J.Struct.Biol. (2020)

Release Date

2020-12-16

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 8

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