SMTL ID : 2v5w.2 (1 other biounit)

Crystal structure of HDAC8-substrate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GLY- GLY- GLY: GLYCYL-GLYCYL-GLYCINE(Non-covalent)

GLY-GLY-GLY.1: 8 residues within 4Å: Chain A: K.145, D.147, E.148, F.208, P.209 Ligands: ACE-ARG-HIS-ALY-ALY-MCM.2, ACE-ARG-HIS-ALY-ALY-MCM.2, ACE-ARG-HIS-ALY-ALY-MCM.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.145, A:S.150, A:S.150 Water bridges: A:E.148, A:E.148

1 x ACE- ARG- HIS- ALY- ALY- MCM: PEPTIDIC SUBSTRATE(Non-covalent)

ACE-ARG-HIS-ALY-ALY-MCM.2: 22 residues within 4Å: Chain A: K.33, I.94, G.97, 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: GLY-GLY-GLY.1, ZN.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: 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:G.97, A:D.101, A:D.101, A:G.151, A:H.180 Water bridges: A:K.33, A:E.148, A:G.206 Salt bridges: A:K.33, A:E.148

2 x K: POTASSIUM ION(Non-covalent)

K.3: 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.4: 5 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:T.192, A:V.195, A:Y.225, H2O.9

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.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:H.180, A:D.267, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vannini, A. et al., Substrate Binding to Histone Deacetylases as Revealed by Crystal Structure of Hdac8-Substrate Complex. Embo Rep. (2007)

Release Date

2007-09-04

Peptides

HISTONE DEACETYLASE 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HISTONE DEACETYLASE 8

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