SMTL ID : 5eei.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

1 x SHH: OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE(Non-covalent)

SHH.1: 15 residues within 4Å: Chain A: H.29, P.30, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.149, A:F.209, A:F.209, A:F.209, A:L.278, A:L.278 Hydrogen bonds: A:H.139, A:H.140, A:H.140

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: D.178, V.179, H.180, D.271, G.309, Y.311 Ligands: SHH.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: 10 residues within 4Å: Chain A: H.139, D.176, W.177, D.178, H.180, H.181, G.182, 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: 6 residues within 4Å: Chain A: F.189, D.192, V.195, L.196, Y.197, 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.5

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.167, R.171, E.262 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.167, A:R.167, A:R.171, A:R.171 Water bridges: A:R.167 GOL.6: 3 residues within 4Å: Chain A: R.42, E.45, L.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:E.45

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 1 residues within 4Å: Ligands: CL.8 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: T.166, R.167, L.170 Ligands: CL.7 Ligand excluded by PLIP

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

EDO.9: 4 residues within 4Å: Chain A: G.275, N.312, T.314, S.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.312, A:S.315

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

Related Entries With Identical Sequence