SMTL ID : 5eek.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: TSN.4 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.2: 6 residues within 4Å: Chain A: D.176, D.178, H.180, 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.3: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.189, A:V.195, A:Y.228, H2O.2, H2O.5

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.4: 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, Y.311 Ligands: ZN.1, GOL.38 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:F.149, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:H.140

26 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 4 residues within 4Å: Chain A: K.219, G.221, L.222 Ligands: NH4.31 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: K.84, P.85, R.86 Ligands: NH4.30 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: W.25 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: L.278 Ligands: IOD.9 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: L.278 Ligands: IOD.8 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: G.223 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: M.245, H.290, Q.294 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: A.260, P.261, L.298, A.299 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: R.274, E.318 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: P.277, N.312 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: F.208, F.209 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: M.245, A.246, H.249 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: S.344 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: H.29 Ligands: EDO.39 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: Q.16, R.17 Ligand excluded by PLIP IOD.20: 5 residues within 4Å: Chain A: E.44, R.47, L.49, S.50 Ligands: NH4.33 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: R.54, P.56 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: R.17 Ligands: NH4.28 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: K.72 Ligands: IOD.24 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain A: S.71, K.72 Ligands: IOD.23 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: D.241, L.335 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: P.254, R.257 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: K.342, T.343 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain A: H.250, L.341 Ligands: NH4.34 Ligand excluded by PLIP IOD.36: 2 residues within 4Å: Chain A: P.340, L.341 Ligand excluded by PLIP IOD.37: 2 residues within 4Å: Chain A: H.53, Q.126 Ligand excluded by PLIP

6 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.28: 3 residues within 4Å: Chain A: R.17, L.59 Ligands: IOD.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.17 NH4.30: 2 residues within 4Å: Chain A: K.84 Ligands: IOD.6 No protein-ligand interaction detected (PLIP) NH4.31: 4 residues within 4Å: Chain A: Q.186, H.187, E.190 Ligands: IOD.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.186, A:E.190 NH4.32: 2 residues within 4Å: Chain A: R.257, A.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.257 NH4.33: 3 residues within 4Å: Chain A: R.47, S.50 Ligands: IOD.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.50, A:S.50 NH4.34: 2 residues within 4Å: Chain A: N.350 Ligands: IOD.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.350 Water bridges: A:N.350

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

CL.29: 3 residues within 4Å: Chain A: K.78, E.81, H.82 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.38: 1 residues within 4Å: Ligands: TSN.4 No protein-ligand interaction detected (PLIP)

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

EDO.39: 4 residues within 4Å: Chain A: Y.95, N.96, S.97 Ligands: IOD.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.96, A:S.97 Water bridges: A:I.98 EDO.40: 5 residues within 4Å: Chain A: Y.14, D.15, Q.16, F.40, R.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.15, A:Q.16, A:R.54, A:R.54

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
A

Hdac6 protein

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