SMTL ID : 5edu.1 (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: 15 residues within 4Å: Chain A: N.30, D.32, K.33, W.80, A.81, D.83, R.84, E.129, E.171, P.172, Y.173, F.174, W.248, M.348, W.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.80, A:R.84, A:R.84, A:E.171, A:Y.173

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.2: 14 residues within 4Å: Chain A: H.409, H.410, P.411, H.520, H.521, G.529, F.530, D.559, H.561, F.590, D.652, L.659, Y.692 Ligands: ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.530, A:F.590, A:F.590, A:F.590, A:L.659, A:L.659 Hydrogen bonds: A:H.521, A:Y.692

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.559, H.561, D.652 Ligands: TSN.2 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.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 K.5: 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

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
B

Maltose-binding periplasmic protein, Histone deacetylase 6 chimera

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