SMTL ID : 4qa7.1

Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

1 x ACE- ARG- HIS- ALY- ALY: tetrapeptide substrate(Non-covalent)

ACE-ARG-HIS-ALY-ALY.1: 22 residues within 4Å: Chain A: I.94, E.95, Y.100, D.101, W.141, H.143, E.148, G.151, F.152, D.178, H.180, G.206, F.208, P.209, G.210, D.267, M.274, G.304, F.306 Ligands: ZN.2, MCM.5, GOL.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.100, A:W.141, A:F.152, A:F.208, A:F.208, A:F.208 Hydrogen bonds: A:I.94, A:E.95, A:D.101, A:G.151 Salt bridges: 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.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.267, H2O.1

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:L.200 K.4: 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.2

1 x MCM: 7-AMINO-4-METHYL-CHROMEN-2-ONE(Non-covalent)

MCM.5: 6 residues within 4Å: Chain A: K.33, Y.100, D.101, F.152 Ligands: ACE-ARG-HIS-ALY-ALY.1, ACE-ARG-HIS-ALY-ALY.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.100, A:F.152 Hydrogen bonds: A:D.101 Salt bridges: A:K.33

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: K.145, E.148, F.208, P.209 Ligands: ACE-ARG-HIS-ALY-ALY.1, ACE-ARG-HIS-ALY-ALY.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.145, A:K.145, A:E.148 Water bridges: A:D.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decroos, C. et al., Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders. Acs Chem.Biol. (2014)

Release Date

2014-08-06

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8