SMTL ID : 8qt0.1

Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: A.267, W.268, L.269 Ligands: EDO.4, EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.267, A:L.269

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

EDO.3: 3 residues within 4Å: Chain A: Q.20, K.106, W.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.20 EDO.4: 3 residues within 4Å: Chain A: W.268 Ligands: PEG.2, EDO.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.13 EDO.5: 8 residues within 4Å: Chain A: T.11, L.12, E.13, V.266, A.267, W.268 Ligands: PEG.2, EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.267

1 x WWE: 3-dodecylsulfanyl-3-methyl-butanoic acid(Non-covalent)

WWE.6: 12 residues within 4Å: Chain A: R.45, F.67, A.83, Y.87, P.88, F.91, I.117, D.118, H.135, F.138, V.181 Chain B: K.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.67, A:A.83, A:Y.87, A:F.91, A:I.117, A:D.118, A:F.138, 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-3: 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-3

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