SMTL ID : 6uii.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 5-[(3-aminopropyl)amino]pentane-1-thiol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x SS9: 5-[(3-aminopropyl)amino]pentane-1-thiol(Non-covalent)

SS9.1: 14 residues within 4Å: Chain A: A.24, D.94, H.136, H.137, G.145, F.146, D.174, H.176, W.205, D.267, E.274, G.305, F.307 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.146, A:W.205 Hydrogen bonds: A:E.274

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.174, H.176, D.267 Ligands: SS9.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.174, A:D.174, A:H.176, A:D.267

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.172, D.174, H.176, S.195, W.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.172, A:D.174, A:H.176, A:S.195, A:W.196 K.4: 4 residues within 4Å: Chain A: F.185, D.188, V.191, F.224 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.185, A:D.188, A:V.191, A:F.224, H2O.1

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: Y.199, H.201, D.212, Y.213, P.229, N.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.213, A:N.231, A:N.231, A:N.231 Salt bridges: A:H.201 PO4.6: 5 residues within 4Å: Chain A: H.201, N.231, K.232, S.340, E.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.343 Water bridges: A:N.231 Salt bridges: A:H.201, A:K.232 PO4.7: 2 residues within 4Å: Chain A: H.43, H.321 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.43, A:H.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herbst-Gervasoni, C.J. et al., Binding ofN8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation. Biochemistry (2019)

Release Date

2019-12-04

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10