SMTL ID : 8qt2.1

Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.143, C.148, C.169, C.172 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.143, A:C.148, A:C.169, A:C.172

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

EDO.2: 3 residues within 4Å: Chain A: A.267, W.268, L.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.268, A:L.269

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 8 residues within 4Å: Chain A: K.73, K.74, P.76, E.77, T.166, K.168, L.175 Ligands: BU3.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.77, A:T.166, A:T.166, A:K.168

1 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.4: 3 residues within 4Å: Chain A: K.73, K.74 Ligands: BTB.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.74 Hydrogen bonds: A:K.73 Water bridges: A:K.73

1 x WU8: 3-dodecylsulfanyl-2,2-dimethyl-propanoic acid(Non-covalent)

WU8.5: 14 residues within 4Å: Chain A: F.44, R.45, L.51, F.67, F.79, L.86, P.88, F.91, I.117, D.118, H.135, F.138, V.181 Chain B: K.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.44, A:L.51, A:F.67, A:F.67, A:F.79, A:L.86, A:L.86, A:F.91, A:I.117, A:H.135, A:F.138, A:F.138 Hydrogen bonds: A:R.45 Water bridges: A:H.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., New Super-Slow Substrates as novel Sirtuin-Inhibitors. To Be Published

Release Date

2024-10-23

Peptides

NAD-dependent protein deacetylase sirtuin-2: A
Peptide-based super-slow substrate TNFn-6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-2

Peptide-based super-slow substrate TNFn-6

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