SMTL ID : 5g0i.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.590, H.592, D.683 Ligands: N4R.7 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.590, A:H.592, A:D.683, N4R.7, H2O.13 ZN.2: 4 residues within 4Å: Chain A: D.208, H.210, D.301 Ligands: N4R.8 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.208, A:H.210, A:D.301, H2O.5, N4R.8

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.588, D.590, H.592, S.611, L.612 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.588, A:D.590, A:H.592, A:S.611, A:L.612 K.4: 4 residues within 4Å: Chain A: F.601, D.604, V.607, Y.640 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.601, A:D.604, A:V.607, A:Y.640, H2O.14 K.5: 6 residues within 4Å: Chain A: D.206, D.208, H.210, S.229, V.230, H.231 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.206, A:D.206, A:D.208, A:H.210, A:S.229 K.6: 4 residues within 4Å: Chain A: F.219, D.222, V.225, Y.258 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.219, A:V.225, A:Y.258, H2O.6, H2O.6

2 x N4R: NEXTURASTAT A(Non-covalent)

N4R.7: 13 residues within 4Å: Chain A: H.441, P.442, S.509, P.549, H.552, G.560, F.561, H.592, F.621, D.683, L.690, Y.723 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.442, A:F.621, A:L.690, A:L.690 Hydrogen bonds: A:G.560, A:Y.723 Water bridges: A:S.509 pi-Stacking: A:F.561 N4R.8: 13 residues within 4Å: Chain A: H.60, P.61, S.128, P.168, H.171, G.179, F.180, H.210, W.239, D.301, K.308, Y.341 Ligands: ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.61, A:F.180, A:W.239, A:W.239, A:K.308 Hydrogen bonds: A:S.128, A:S.128, A:G.179, A:Y.341 pi-Stacking: A:F.180

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

CL.9: 3 residues within 4Å: Chain A: N.501, D.505, I.510 Ligand excluded by PLIP

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

EDO.10: 6 residues within 4Å: Chain A: T.39, G.40, T.41, R.159, L.357, L.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.40, A:T.41 Water bridges: A:T.41

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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