SMTL ID : 5efk.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant) in complex with alpha tubulin K40 tripeptide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x SER- ASP- ALY: alpha tubulin K40 tripeptide(Non-covalent)

SER-ASP-ALY.1: 16 residues within 4Å: Chain A: N.96, S.97, P.137, H.140, G.148, F.149, D.178, H.180, F.209, N.211, D.271, L.278, G.309, F.311 Ligands: ZN.2, MCM.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.137, A:F.149, A:F.149, A:F.209, A:F.209, A:F.209 Hydrogen bonds: A:N.96, A:S.97, A:S.97, A:G.148 Water bridges: A:N.96, A:S.97

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: SER-ASP-ALY.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271, H2O.1

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.1, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.226, A:Y.228 Water bridges: A:Y.228

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

PEG.6: 5 residues within 4Å: Chain A: Q.163, S.164, T.166, R.167, E.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.163 Water bridges: A:E.168

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

NO3.7: 3 residues within 4Å: Chain A: W.25, P.85, N.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.85, A:N.89

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

EDO.8: 3 residues within 4Å: Chain A: H.293, M.296, S.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.293 Water bridges: A:S.297

1 x MCM: 7-AMINO-4-METHYL-CHROMEN-2-ONE(Non-covalent)

MCM.9: 5 residues within 4Å: Chain A: P.30, P.277, L.278 Ligands: SER-ASP-ALY.1, SER-ASP-ALY.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.30, A:L.278 Water bridges: A:S.97

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
B

Hdac6 protein