SMTL ID : 6uhu.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x Q7V: 5-(3-azanylpropylamino)pentyl-$l^{3}-oxidanyl-bis(oxidanyl)boron(Non-covalent)

Q7V.1: 18 residues within 4Å: Chain A: P.23, A.24, I.27, D.94, P.134, H.136, H.137, G.145, F.146, D.174, H.176, W.205, D.267, E.274, E.304, G.305, Y.307 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.27, A:F.146, A:F.146, A:W.205 Hydrogen bonds: A:A.24, A:H.136, A:Y.307, A:Y.307

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.174, H.176, D.267 Ligands: Q7V.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.174, A:D.174, A:H.176, A:D.267

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

PO4.3: 6 residues within 4Å: Chain A: Y.199, H.201, D.212, Y.213, P.229, N.231 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.213, A:Y.213, A:N.231, A:N.231, A:N.231 Water bridges: A:E.343 Salt bridges: A:H.201 PO4.4: 5 residues within 4Å: Chain A: H.201, N.231, K.232, S.340, E.343 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.231, A:S.340, A:E.343, A:E.343 Salt bridges: A:H.201 PO4.5: 4 residues within 4Å: Chain A: H.43, H.321, K.407, R.408 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.408, A:R.408, A:R.408 Salt bridges: A:H.43, A:H.321

2 x K: POTASSIUM ION(Non-covalent)

K.6: 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.172, A:D.174, A:H.176, A:W.196 K.7: 4 residues within 4Å: Chain A: F.185, D.188, V.191, F.224 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.185, A:D.188, A:V.191, A:F.224

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

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