SMTL ID : 5h4d.2 (1 other biounit)

Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

monomer

Ligands

1 x ARG- HIS- LYS- ALY: ARG-HIS-LYS(Non-covalent)

ARG-HIS-LYS-ALY.1: 15 residues within 4Å: Chain A: F.60, I.110, H.128, I.171, V.172, F.173, F.174, G.175, E.176, P.177, L.178, P.206 Ligands: MCM.2, BBI.7, NAD.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.60, A:I.110, A:I.171, A:L.178, A:L.178 Hydrogen bonds: A:V.172, A:G.175, A:E.176, A:E.176, A:L.178

1 x MCM: 7-AMINO-4-METHYL-CHROMEN-2-ONE(Non-covalent)

MCM.2: 4 residues within 4Å: Chain A: F.174, G.175 Ligands: ARG-HIS-LYS-ALY.1, ARG-HIS-LYS-ALY.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.174 pi-Stacking: A:F.174

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

PEG.3: 7 residues within 4Å: Chain A: R.104, A.121, S.122, K.123, L.124, V.125, R.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:R.104, A:R.181 PEG.5: 2 residues within 4Å: Chain A: Q.140, R.141 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.136, A:C.139, A:C.160, A:C.163

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: D.147, R.159 No protein-ligand interaction detected (PLIP)

1 x BBI: (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone(Non-covalent)

BBI.7: 6 residues within 4Å: Chain A: R.38, E.57, F.174, V.204 Ligands: ARG-HIS-LYS-ALY.1, NAD.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.38 pi-Cation interactions: A:R.38

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.8: 22 residues within 4Å: Chain A: G.25, A.26, G.27, S.29, T.30, P.31, I.34, D.36, R.38, Q.108, N.109, I.110, D.111, H.128, G.199, T.200, S.201, N.224, D.245, V.246 Ligands: ARG-HIS-LYS-ALY.1, BBI.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.110 Hydrogen bonds: A:A.26, A:S.29, A:T.30, A:T.30, A:Q.108, A:Q.108, A:I.110, A:D.111, A:D.111, A:D.111, A:T.200, A:S.201, A:S.201, A:R.225, A:V.246 Salt bridges: A:R.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride. To Be Published

Release Date

2017-11-08

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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