SMTL ID : 3ew8.1

Crystal Structure Analysis of human HDAC8 D101L variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 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: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:F.189, A:T.192, A:V.195, H2O.1, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: B3N.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.178, A:H.180, A:D.267, H2O.1, H2O.1

1 x B3N: 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide(Non-covalent)

B3N.4: 15 residues within 4Å: Chain A: Y.100, L.101, H.142, H.143, F.152, D.178, H.180, F.208, D.267, G.304, Y.306 Ligands: ZN.2, GOL.6, GOL.7, GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.100, A:F.152, A:F.208 Hydrogen bonds: A:Y.306 Water bridges: A:F.208, A:F.208

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 2 residues within 4Å: Chain A: Q.236, D.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.236

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: G.140, H.143, G.151, C.153, G.303, G.304, Y.306 Ligands: B3N.4, GOL.7, GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.140, A:H.143, A:Y.306, A:Y.306 GOL.7: 12 residues within 4Å: Chain A: G.140, W.141, H.143, G.151, F.152, C.153, G.303, G.304, Y.306 Ligands: B3N.4, GOL.6, GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.140, A:Y.306 Water bridges: A:Y.306 GOL.8: 12 residues within 4Å: Chain A: G.140, W.141, H.143, G.151, F.152, C.153, G.303, G.304, Y.306 Ligands: B3N.4, GOL.6, GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.140, A:W.141, A:Y.306 Water bridges: A:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowling, D.P. et al., Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry (2008)

Release Date

2008-12-30

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8