SMTL ID : 5g0h.1

Crystal structure of Danio rerio HDAC6 CD2 in complex with (S)- trichostatin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x E1Z: S-Trichostatin A(Non-covalent)

E1Z.1: 15 residues within 4Å: Chain A: N.493, S.494, H.536, H.537, G.545, F.546, D.575, H.577, F.606, N.608, D.668, L.675, Y.708 Ligands: ZN.4, EDO.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.546, A:F.546, A:F.606, A:F.606, A:L.675 Hydrogen bonds: A:H.537

2 x K: POTASSIUM ION(Non-covalent)

K.2: 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 K.3: 4 residues within 4Å: Chain A: F.586, D.589, V.592, Y.625 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.586, A:D.589, A:V.592, A:Y.625, H2O.8

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.575, H.577, D.668 Ligands: E1Z.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.575, A:D.575, A:H.577, A:D.668

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

EDO.5: 3 residues within 4Å: Chain A: L.520, T.563, L.567 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.520, A:L.520 EDO.6: 2 residues within 4Å: Chain A: S.468, K.469 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.468 Water bridges: A:S.468, A:K.469 EDO.7: 3 residues within 4Å: Chain A: T.743, N.747, N.763 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.747, A:N.747 EDO.8: 5 residues within 4Å: Chain A: H.419, N.420, D.423, S.424, P.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.420 EDO.9: 7 residues within 4Å: Chain A: K.635, M.636, G.637, P.639, E.640, Q.679, K.739 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.640, A:Q.679 Water bridges: A:K.739 EDO.10: 5 residues within 4Å: Chain A: R.623, G.624, Y.625, F.756, W.757 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.623 Water bridges: A:R.623, A:F.756 EDO.11: 4 residues within 4Å: Chain A: W.422, D.423, S.424, H.425 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.424, A:H.425 EDO.12: 5 residues within 4Å: Chain A: P.405, M.693, L.724, L.725, G.726 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.724 EDO.13: 4 residues within 4Å: Chain A: Y.492, N.493, S.494 Ligands: E1Z.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.494 Water bridges: A:I.495 EDO.14: 2 residues within 4Å: Chain A: R.623, F.756 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.623

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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