SMTL ID : 5td7.1

Crystal structure of histone deacetylase 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.176, H.178, D.269 Ligands: FKS.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.176, A:D.176, A:H.178, A:D.269

2 x K: POTASSIUM ION(Non-covalent)

K.2: 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:H.178, A:S.197, A:W.198 K.3: 4 residues within 4Å: Chain A: F.187, D.190, V.193, F.226 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.187, A:D.190, A:V.193, A:F.226, H2O.1

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

PO4.4: 5 residues within 4Å: Chain A: H.203, D.214, Y.215, P.231, N.233 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.215, A:Y.215, A:N.233, A:N.233, A:N.233 Salt bridges: A:H.203 PO4.5: 4 residues within 4Å: Chain A: L.336, E.577, R.666 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.577 Salt bridges: A:R.666 PO4.6: 4 residues within 4Å: Chain A: L.282, R.332, I.333, S.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.334, A:S.334 PO4.7: 3 residues within 4Å: Chain A: Q.348, N.349, V.674 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.349 PO4.8: 5 residues within 4Å: Chain A: H.203, N.233, K.234, S.342, E.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.233, A:E.345, A:E.345 Salt bridges: A:H.203 PO4.9: 4 residues within 4Å: Chain A: Q.78, G.81, M.82, E.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.78, A:G.81 PO4.10: 5 residues within 4Å: Chain A: S.334, G.335, R.511, N.579 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.335, A:N.579 Water bridges: A:L.336 Salt bridges: A:R.511

1 x FKS: 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol(Non-covalent)

FKS.11: 16 residues within 4Å: Chain A: D.96, P.136, H.138, H.139, G.147, F.148, C.149, D.176, H.178, W.207, D.269, E.276, E.306, G.307, F.309 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.148, A:F.148, A:W.207, A:W.207 Hydrogen bonds: A:H.139

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.12: 3 residues within 4Å: Chain A: V.531, N.547, R.666 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.531, A:N.547, A:R.666

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hai, Y. et al., Histone deacetylase 10 structure and molecular function as a polyamine deacetylase. Nat Commun (2017)

Release Date

2017-05-24

Peptides

Zgc:55652: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Zgc:55652