SMTL ID : 6csr.1 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with phenylhydroxamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: BHO.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.3: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.3, H2O.8

1 x BHO: BENZHYDROXAMIC ACID(Non-covalent)

BHO.4: 11 residues within 4Å: Chain A: H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, Y.311 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.278 Hydrogen bonds: A:H.140, A:Y.311 pi-Stacking: A:F.149, A:F.209

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

EDO.5: 5 residues within 4Å: Chain A: L.123, T.124, G.125, R.302 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.302, A:R.302 EDO.6: 5 residues within 4Å: Chain A: L.123, T.166, L.170, R.302 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.123, A:R.302, A:R.302 EDO.7: 4 residues within 4Å: Chain A: P.30, L.32, Y.311, L.313 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.28 EDO.8: 5 residues within 4Å: Chain A: A.66, L.67, C.68, H.69, K.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.66 Water bridges: A:R.160 EDO.9: 3 residues within 4Å: Chain A: R.17, R.58, L.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:L.59 Water bridges: A:L.59 EDO.10: 4 residues within 4Å: Chain A: M.19, L.20, H.22, P.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.19, A:E.103 EDO.11: 5 residues within 4Å: Chain A: L.59, E.81, Y.105, T.106, L.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.81 EDO.12: 2 residues within 4Å: Chain A: G.223, K.224 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6. Biochemistry (2018)

Release Date

2018-05-30

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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