SMTL ID : 5wgi.1

Ultrahigh resolution crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with TSA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.139, D.178, V.179, H.180, D.271, G.309, Y.311 Ligands: TSN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

1 x TSN: TRICHOSTATIN A(Non-covalent)

TSN.2: 17 residues within 4Å: Chain A: D.26, H.29, P.30, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.1, PEG.21 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:H.139, A:H.140, A:D.178, A:Y.311

2 x K: POTASSIUM ION(Non-covalent)

K.3: 10 residues within 4Å: Chain A: H.139, D.176, W.177, D.178, H.180, H.181, G.182, 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.4: 7 residues within 4Å: Chain A: F.189, E.190, D.192, V.195, L.196, Y.197, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.6, H2O.7

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

CL.5: 4 residues within 4Å: Chain A: R.17, L.59, T.106, L.110 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: E.44, R.47, L.49, S.50 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.84, P.85, R.86 Ligand excluded by PLIP

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

EDO.8: 4 residues within 4Å: Chain A: Y.95, N.96, S.97 Ligands: PEG.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.96, A:S.97, A:S.97 Water bridges: A:I.98 EDO.9: 6 residues within 4Å: Chain A: M.83, R.86, D.87, R.90, L.91, E.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.86, A:D.87, A:R.90, A:R.90, A:E.94 EDO.10: 8 residues within 4Å: Chain A: H.22, N.23, M.24, D.26, S.27, H.28, L.32, P.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.27 Water bridges: A:N.23 EDO.11: 4 residues within 4Å: Chain A: K.143, H.187, I.188, E.190 No protein-ligand interaction detected (PLIP) EDO.12: 1 residues within 4Å: Chain A: N.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2 EDO.13: 5 residues within 4Å: Chain A: R.160, Q.163, S.164, E.168 Ligands: MG.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.163, A:D.192 EDO.14: 3 residues within 4Å: Chain A: R.58, T.61, E.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.61, A:E.64 Water bridges: A:T.61 EDO.15: 1 residues within 4Å: Chain A: Q.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.120 EDO.16: 3 residues within 4Å: Chain A: T.124, G.125, Q.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.124

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 3 residues within 4Å: Chain A: R.38, L.313, T.314 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.38, A:R.38, A:T.314, A:T.314 Water bridges: A:T.314 GOL.18: 7 residues within 4Å: Chain A: E.258, P.358, F.359, W.360, S.361, R.364 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.361, A:R.364, A:R.364 GOL.19: 7 residues within 4Å: Chain A: R.226, G.227, Y.228, E.258, F.359, W.360 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.226, A:F.359

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 1 residues within 4Å: Chain A: H.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.249 PEG.21: 9 residues within 4Å: Chain A: N.23, W.25, H.29, S.97, I.98, F.99, F.149 Ligands: TSN.2, EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.29 Water bridges: A:N.23

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.22: 4 residues within 4Å: Chain A: R.160, E.168, S.194 Ligands: EDO.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-12-06

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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