SMTL ID : 5efj.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x 5OM- DPR- ALA- DAL: HC toxin(Non-covalent)

5OM-DPR-ALA-DAL.1: 18 residues within 4Å: Chain A: H.29, N.96, S.97, P.137, H.139, H.140, G.148, F.149, C.150, D.178, H.180, F.209, D.271, L.278, E.308, G.309, Y.311 Ligands: ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:F.209, A:F.209, A:F.209 Hydrogen bonds: A:S.97, A:S.97, A:S.97, A:H.140, A:Y.311

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: 5OM-DPR-ALA-DAL.1 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.3: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 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.4: 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.4, H2O.5

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.226, G.227, Y.228, F.359, W.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.226

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 3 residues within 4Å: Chain A: W.25, P.85, R.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.25 NO3.7: 5 residues within 4Å: Chain A: H.293, G.329, D.330, S.331, P.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.331

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

EDO.8: 4 residues within 4Å: Chain A: L.46, R.51, S.325, D.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.51 Water bridges: A:S.325 EDO.9: 4 residues within 4Å: Chain A: Q.120, A.121, T.124, Q.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.124 Water bridges: A:N.117, A:Q.120, A:Q.126 EDO.10: 4 residues within 4Å: Chain A: H.293, Q.294, M.296, S.297 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hai, Y. et al., Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat.Chem.Biol. (2016)

Release Date

2016-07-27

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Hdac6 protein

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