SMTL ID : 3mz7.1

Crystal structure of D101L Co2+ HDAC8 complexed with M344

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x CO: COBALT (II) ION(Non-covalent)

CO.1: 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.6, H2O.6

2 x K: POTASSIUM ION(Non-covalent)

K.2: 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.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: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, G.151, D.178, H.180, F.208, D.267, Y.306 Ligands: CO.1, GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.100, A:L.101, A:F.208, A:F.208 Hydrogen bonds: A:H.143, A:D.178, A:Y.306

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.141, H.143, G.151, F.152, G.303, G.304, Y.306 Ligands: B3N.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.140, 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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