SMTL ID : 6uo2.2 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed with Trichostatin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.270

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: F.188, D.191, V.194, Y.227 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:V.194, A:Y.227, H2O.2, H2O.3 K.3: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, V.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.177, A:H.179, A:S.198, A:V.199

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.4: 15 residues within 4Å: Chain A: W.25, H.29, P.30, S.97, H.139, H.140, G.148, F.149, D.177, H.179, W.208, D.270, G.308, Y.310 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:W.208, A:W.208 Hydrogen bonds: A:H.139, A:H.140, A:G.308 pi-Stacking: A:F.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osko, J.D. et al., Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry (2019)

Release Date

2019-12-04

Peptides

HDAC6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HDAC6

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