SMTL ID : 5edu.2 (1 other biounit)

Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 13 residues within 4Å: Chain A: D.32, K.33, W.80, A.81, D.83, R.84, E.129, E.171, P.172, Y.173, F.174, W.248, W.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.33, A:K.33, A:E.129

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.559, H.561, D.652 Ligands: TSN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.559, A:D.559, A:H.561, A:D.652

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: D.557, D.559, H.561, S.580, L.581, H.582 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.557, A:D.557, A:D.559, A:H.561, A:S.580 K.4: 5 residues within 4Å: Chain A: F.570, D.573, V.576, F.609, T.610 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.570, A:V.576, A:F.609

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.5: 13 residues within 4Å: Chain A: H.410, P.411, S.478, H.520, H.521, G.529, F.530, D.559, H.561, F.590, D.652, Y.692 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.530, A:F.530, A:F.590, A:F.590, A:F.590 Hydrogen bonds: A:H.521

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hai, Y. et al., Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat.Chem.Biol. (2016)

Release Date

2016-07-27

Peptides

Maltose-binding periplasmic protein, Histone deacetylase 6 chimera: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltose-binding periplasmic protein, Histone deacetylase 6 chimera

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