SMTL ID : 7kuv.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Acetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 10 residues within 4Å: Chain A: P.136, H.138, H.139, G.147, D.176, H.178, D.269, G.307, Y.309 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.136 Hydrogen bonds: A:Y.309 Salt bridges: A:H.138, A:H.139, A:H.178

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

EDO.2: 5 residues within 4Å: Chain A: H.291, M.294, S.324, G.327, D.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.291, A:D.328 Water bridges: A:T.330, A:R.416 EDO.3: 7 residues within 4Å: Chain A: S.5, G.6, S.7, R.127, N.128, L.325, L.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.6, A:S.7, A:R.127

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.176, H.178, D.269 Ligands: ACT.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.176, A:D.176, A:H.178, A:D.269, ACT.1

2 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: D.174, D.176, H.178, S.197, W.198 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.174, A:D.174, A:D.176, A:H.178, A:W.198 K.6: 4 residues within 4Å: Chain A: F.187, D.190, V.193, F.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.187, A:V.193, A:F.226, H2O.3, H2O.5

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

PO4.7: 6 residues within 4Å: Chain A: Y.201, H.203, D.214, Y.215, P.231, N.233 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.215, A:Y.215, A:N.233, A:N.233, A:N.233 Water bridges: A:N.349 Salt bridges: A:H.203 PO4.8: 5 residues within 4Å: Chain A: H.203, N.233, K.234, S.342, E.345 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.345, A:E.345 Water bridges: A:N.233, A:K.234, A:K.234 Salt bridges: A:H.203, A:K.234 PO4.9: 4 residues within 4Å: Chain A: H.45, H.323, K.409, R.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.45, A:R.410 Salt bridges: A:H.45, A:H.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herbst-Gervasoni, C.J. et al., X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. Biochemistry (2021)

Release Date

2021-02-03

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10