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

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trifluoroketone transition state analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 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: FKS.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: 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.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.1, H2O.4

1 x FKS: 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol(Non-covalent)

FKS.4: 17 residues within 4Å: Chain A: S.97, P.137, H.139, H.140, G.148, F.149, C.150, D.178, H.180, F.209, D.271, E.308, G.309, Y.311 Ligands: ZN.1, BR.5, BR.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:F.149, A:F.209, A:F.209 Hydrogen bonds: A:H.140, A:Y.311

3 x BR: BROMIDE ION(Non-covalent)

BR.5: 3 residues within 4Å: Chain A: H.180, L.278 Ligands: FKS.4 Ligand excluded by PLIP BR.6: 4 residues within 4Å: Chain A: E.44, R.47, L.49, S.50 Ligand excluded by PLIP BR.7: 2 residues within 4Å: Chain A: F.149 Ligands: FKS.4 Ligand excluded by PLIP

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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