SMTL ID : 5efn.1 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4 Lys6 tripeptide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ARG- GLY- 5OL: histone H4 tripeptide(Non-covalent)

ARG-GLY-5OL.1: 16 residues within 4Å: Chain A: N.96, S.97, P.137, H.139, G.148, F.149, C.150, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.2, MCM.7 14 PLIP interactions: 14 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:Y.311, A:Y.311, A:Y.311 Salt bridges: A:H.139, A:H.180

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: ARG-GLY-5OL.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.178, A:H.180, A:S.199, A:L.200 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

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

EDO.5: 3 residues within 4Å: Chain A: R.47, S.50, R.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.50 EDO.6: 3 residues within 4Å: Chain A: E.142, D.144, T.145 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.144, A:H.187

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

MCM.7: 4 residues within 4Å: Chain A: P.30, L.278 Ligands: ARG-GLY-5OL.1, ARG-GLY-5OL.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

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