SMTL ID : 6uo5.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) Y363F mutant complexed with AR-42

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

1 x QCP: AR-42(Non-covalent)

QCP.1: 15 residues within 4Å: Chain A: H.29, P.30, S.97, H.140, G.148, F.149, D.177, H.179, W.208, D.270, K.277, G.308, G.309, F.310 Ligands: ZN.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:W.208, A:F.310 Hydrogen bonds: A:S.97, A:S.97, A:K.277, A:G.309 pi-Stacking: A:F.149 pi-Cation interactions: A:H.179

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

EDO.2: 5 residues within 4Å: Chain A: H.292, K.295, S.325, G.328, D.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.295, A:S.325

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.177, H.179, D.270 Ligands: QCP.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:D.177, A:H.179, A:D.270, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.4: 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.175, A:H.179, A:S.198, A:V.199 K.5: 4 residues within 4Å: Chain A: F.188, D.191, V.194, Y.227 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.188, A:D.191, A:V.194, A:Y.227, H2O.3

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

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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