SMTL ID : 5g0g.1

Crystal structure of Danio rerio HDAC6 CD1 in complex with trichostatin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.192, H.194, D.285, G.323 Ligands: TSN.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.192, A:D.192, A:H.194, A:D.285

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: F.203, D.206, V.209, Y.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.206, A:D.206 NA.3: 6 residues within 4Å: Chain A: D.190, D.192, H.194, S.213, V.214, H.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.190, A:V.214

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

CL.4: 5 residues within 4Å: Chain A: W.40, K.104, A.107, Y.114, L.115 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.143 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: S.255, S.298, L.349, P.350, S.351, S.352 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.136, Q.141 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: C.356, E.357 Ligand excluded by PLIP

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.9: 14 residues within 4Å: Chain A: W.40, S.112, H.154, H.155, G.163, F.164, D.192, H.194, W.223, D.285, K.292, G.323, Y.325 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.164, A:W.223, A:W.223 Hydrogen bonds: A:H.155, A:K.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyake, Y. et al., Structural Insights Into Hdac6 Tubulin Deacetylation and its Selective Inhibition. Nat.Chem.Biol. (2016)

Release Date

2016-07-27

Peptides

HDAC6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HDAC6