SMTL ID : 3mz4.1 (1 other biounit)

Crystal structure of D101L Mn2+ HDAC8 complexed with M344

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

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

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.1, H2O.1

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

B3N.4: 12 residues within 4Å: Chain A: Y.100, L.101, H.142, H.143, F.152, D.178, H.180, F.208, D.267, Y.306 Ligands: MN.1, GOL.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.100, A:L.101, A:F.152, A:F.152, A:F.208 Hydrogen bonds: A:H.143, A:H.180, A:Y.306 Water bridges: A:F.208

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: G.140, W.141, H.143, G.151, F.152, G.303, G.304, Y.306 Ligands: MN.1, B3N.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.140, A:Y.306, A:Y.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowling, D.P. et al., Structures of metal-substituted human histone deacetylase 8 provide mechanistic inferences on biological function. Biochemistry (2010)

Release Date

2010-06-23

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8

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