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

Crystal structure of human histone deacetylase 8 (HDAC8) E66D/Y306F double mutation complexed with a tetrapeptide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x ACE- ARG- HIS- ALY- ALY- MCM: ACE-ARG-HIS-ALY-ALY-MCM(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.5, EDO.9 22 PLIP interactions: 22 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:G.97, A:Y.100, A:D.101, A:D.101, A:D.101, A:G.151 Water bridges: A:K.33, A:K.33, A:G.206 Salt bridges: A:K.33, A:E.148

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: P.281, V.282, Y.317, L.346, E.347, I.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.346, A:I.348 EDO.3: 5 residues within 4Å: Chain A: K.132, V.133, L.292, Q.295, L.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.132, A:L.296 EDO.4: 5 residues within 4Å: Chain A: A.270, G.271, N.310, I.348, T.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.270, A:N.310, A:T.349 Water bridges: A:N.307 EDO.9: 7 residues within 4Å: Chain A: S.150, D.183, 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 Water bridges: A:K.145, A:S.150, A:D.183

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.1

2 x K: POTASSIUM ION(Non-covalent)

K.6: 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.178, A:H.180, A:S.199, A:L.200 K.7: 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.6

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: D.66, T.69, I.120, L.160, L.163, R.164, R.167 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.66, A:D.66, A:T.69, A:L.160, A:R.164, A:R.167, A:R.167

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
A

Histone deacetylase 8

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