SMTL ID : 5g0j.1

Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker intact) in complex with Nexturastat A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

monomer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: D.220 Ligand excluded by PLIP CL.2: 6 residues within 4Å: Chain A: Q.379, T.380, F.381, E.382, T.743, L.768 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.536, D.575, H.577, D.668 Ligands: N4R.9 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.575, A:H.577, A:D.668, H2O.6, N4R.9

5 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: H.155, D.193, H.195, D.286, G.324, Y.326 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.193, A:D.193, A:D.286, A:Y.326, H2O.3 K.5: 4 residues within 4Å: Chain A: F.586, D.589, V.592, Y.625 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.586, A:D.589, A:V.592, A:Y.625 K.6: 6 residues within 4Å: Chain A: D.191, D.193, H.195, S.214, V.215, H.216 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.191, A:D.193, A:H.195, A:S.214, A:V.215 K.7: 4 residues within 4Å: Chain A: F.204, D.207, V.210, Y.243 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.204, A:D.207, A:V.210, A:Y.243 K.8: 6 residues within 4Å: Chain A: D.573, D.575, H.577, S.596, L.597, H.598 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.573, A:D.575, A:H.577, A:S.596, A:L.597

1 x N4R: NEXTURASTAT A(Non-covalent)

N4R.9: 15 residues within 4Å: Chain A: H.426, P.427, S.494, H.536, H.537, G.545, F.546, D.575, H.577, F.606, D.668, L.675, G.706, Y.708 Ligands: ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.606, A:F.606, A:L.675 Hydrogen bonds: A:G.545, A:D.575 Water bridges: A:H.577 pi-Stacking: A:H.426, A:F.546, A:H.577

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

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