SMTL ID : 3rqd.2 (2 other biounits)

Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x 02G- GLY- BB9- 03Y- VAL: Largazole(Non-covalent)

02G-GLY-BB9-03Y-VAL.1: 14 residues within 4Å: Chain A: Y.100, D.101, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, M.274, G.304, Y.306 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.152, A:F.208, A:F.208 Hydrogen bonds: A:D.101 Water bridges: A:G.151

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: 02G-GLY-BB9-03Y-VAL.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:H.180, A:D.267

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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.176, A:D.178, A:H.180, A:L.200 K.4: 4 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:V.195, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cole, K.E. et al., Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases. J.Am.Chem.Soc. (2011)

Release Date

2011-08-24

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 8

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