SMTL ID : 7kus.1

Crystal Structure of Danio rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: A.4, V.121, R.124, V.126, R.127, A.298, K.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.121, A:R.124 Water bridges: A:S.638 PEG.2: 6 residues within 4Å: Chain A: S.5, G.6, S.7, R.127, L.325, L.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.6, A:S.7 Water bridges: A:N.128

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

EDO.3: 6 residues within 4Å: Chain A: H.291, M.294, S.324, G.327, D.328, T.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.291, A:S.324 Water bridges: A:T.330, A:R.416, A:Q.608, A:Q.608

1 x X54: 1-({4-[(3-aminopropyl)amino]butyl}amino)ethane-1,1-diol(Non-covalent)

X54.4: 14 residues within 4Å: Chain A: E.26, A.96, P.136, H.138, G.147, F.148, D.176, H.178, W.207, D.269, E.276, G.307, Y.309 Ligands: ZN.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.26, A:P.136, A:F.148, A:F.148, A:W.207 Hydrogen bonds: A:E.26, A:G.147, A:Y.309 Water bridges: A:E.276, A:E.276 Salt bridges: A:H.138, A:H.178

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: D.176, H.178, D.269 Ligands: X54.4 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.6: 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:S.197 K.7: 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.7

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

PO4.8: 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 PO4.9: 5 residues within 4Å: Chain A: H.203, N.233, K.234, S.342, E.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.342 Water bridges: A:N.233, A:K.234 Salt bridges: A:H.203, A:K.234 PO4.10: 6 residues within 4Å: Chain A: V.54, Q.116, D.119, S.120, K.123, E.125 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.116, A:S.120, A:E.125, A:E.125 Water bridges: A:Q.116, A:D.119 PO4.11: 5 residues within 4Å: Chain A: H.45, H.323, K.409, R.410, M.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.410 Water bridges: A:H.45 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

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