SMTL ID : 5d1c.2 (1 other biounit)

Crystal structure of D233G-Y306F HDAC8 in complex with a tetrapeptide substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x ACE- ARG- HIS- ALY- ALY- MCM: HDAC8 Fluor de Lys tetrapeptide substrate(Non-covalent)

ACE-ARG-HIS-ALY-ALY-MCM.1: 21 residues within 4Å: Chain A: K.33, I.94, 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.4, GOL.5 20 PLIP interactions: 20 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:I.94, A:Y.100, A:D.101, A:D.101, A:D.101, A:G.151 Water bridges: A:K.33, A:G.206 Salt bridges: A:K.33, A:E.148

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.176, 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.3: 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:T.192, A:V.195, A:Y.225, H2O.3, H2O.9

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: ACE-ARG-HIS-ALY-ALY-MCM.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:H.180, A:D.267, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.148 Water bridges: A:S.150, A:P.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decroos, C. et al., Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders. Biochemistry (2015)

Release Date

2015-10-21

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 8

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