SMTL ID : 5dc7.1 (1 other biounit)

Crystal structure of D176A-Y306F HDAC8 in complex with a tetrapeptide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ACE- ARG- HIS- ALY- ALY- MCM: Fluor-de-Lys tetrapeptide assay substrate(Non-covalent)

ACE-ARG-HIS-ALY-ALY-MCM.1: 22 residues within 4Å: Chain A: K.33, I.94, E.95, G.97, Y.100, D.101, W.141, H.143, E.148, G.151, F.152, D.178, H.180, F.208, P.209, G.210, D.267, M.274, G.304, F.306 Ligands: ZN.2, GOL.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.100, A:Y.100, A:W.141, A:F.152, A:F.152, A:F.208, A:F.208, A:F.208, A:F.208 Hydrogen bonds: A:I.94, A:E.95, A:Y.100, A:D.101, A:D.101, A:D.101, A:G.151 Water bridges: A:G.206 Salt bridges: A:K.33, A:E.148

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: ACE-ARG-HIS-ALY-ALY-MCM.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:H.180, A:D.267

1 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.192, A:V.195, A:Y.225, H2O.1, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: K.145, E.148, S.150, F.208, P.209 Ligands: ACE-ARG-HIS-ALY-ALY-MCM.1, ACE-ARG-HIS-ALY-ALY-MCM.1, ACE-ARG-HIS-ALY-ALY-MCM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.148 Water bridges: A:S.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gantt, S.M. et al., General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry (2016)

Release Date

2016-02-03

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8

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