SMTL ID : 7kuq.1

Crystal Structure of Danio rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x Q9C: N-{4-[(3-aminopropyl)amino]butyl}acetamide(Non-covalent)

Q9C.1: 14 residues within 4Å: Chain A: E.26, A.96, P.136, H.139, G.147, F.148, D.176, H.178, W.207, D.269, E.276, G.307, F.309 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.136, A:F.148, A:F.148, A:W.207 Hydrogen bonds: A:E.26, A:G.147, A:E.276

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.176, H.178, D.269 Ligands: Q9C.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.176, A:H.178, A:D.269, H2O.1, Q9C.1

2 x K: POTASSIUM ION(Non-covalent)

K.3: 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.4: 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:D.190, A:V.193, H2O.3, H2O.5

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

PO4.5: 3 residues within 4Å: Chain A: Q.58, H.105, K.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.58 Water bridges: A:K.108, A:K.108 Salt bridges: A:K.108 PO4.6: 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:S.342 Water bridges: A:N.233 Salt bridges: A:H.203, A:K.234 PO4.7: 4 residues within 4Å: Chain A: H.45, H.323, K.409, R.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.410 Salt bridges: A:H.45, A:H.323

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain A: Y.94 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.24, A:D.24, A:E.26, A:A.96, A:V.97, A:V.97

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

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