SMTL ID : 6wyp.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with SAHA-BPyne

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.191, H.193, D.284 Ligands: UFS.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.191, A:D.191, A:H.193, A:D.284

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.189, D.191, H.193, S.212, V.213, H.214 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.189, A:D.189, A:H.193, A:S.212, A:V.213 K.3: 4 residues within 4Å: Chain A: F.202, D.205, V.208, Y.241 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.202, A:D.205, A:V.208, A:Y.241

1 x UFS: N~1~-(4-{4-[(hex-5-ynoyl)amino]benzene-1-carbonyl}phenyl)-N~8~-hydroxyoctanediamide(Non-covalent)

UFS.4: 16 residues within 4Å: Chain A: S.42, P.44, S.111, H.153, H.154, G.162, F.163, D.191, H.193, W.222, D.284, P.290, L.291, G.322, Y.324 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.44, A:F.163, A:F.163, A:F.163, A:W.222, A:W.222, A:W.222, A:L.291 Hydrogen bonds: A:H.154 Water bridges: A:S.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osko, J.D. et al., Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-09-02

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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