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

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 in complex with trichostatin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.177, H.179, D.270, G.308 Ligands: TSN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.270

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.2: 14 residues within 4Å: Chain A: W.25, S.97, H.139, H.140, G.148, F.149, D.177, H.179, W.208, D.270, K.277, G.308, Y.310 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:W.208 Hydrogen bonds: A:H.140, A:K.277, A:G.308, A:Y.310

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, V.199, H.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.175 NH4.4: 4 residues within 4Å: Chain A: F.188, D.191, V.194, Y.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.191

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: P.260, Q.261, A.298, Q.299, R.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.299, A:R.301 Water bridges: A:A.298

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

HDAC6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HDAC6

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