SMTL ID : 8qt3.1

Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-5 and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x ALA- LEU- PRO- LYS- LYS- NIY- GLY: Peptide-based super-slow substrate TNFn-5(Non-covalent)

ALA-LEU-PRO-LYS-LYS-NIY-GLY.1: 16 residues within 4Å: Chain A: H.135, V.181, F.182, F.183, G.184, E.185, S.186, L.187, A.189, F.192, Q.213, V.214, Q.215, P.216 Ligands: NAD.6, WU3.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.183, A:L.187, A:A.189, A:F.192, A:F.192, A:F.192, A:F.192, A:V.214, A:Q.215 Hydrogen bonds: A:V.181, A:G.184, A:E.185, A:L.187, A:Q.215, A:Q.215

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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

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

EDO.3: 2 residues within 4Å: Chain A: L.226, Y.263 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: T.37, S.38, K.235, E.271 Ligands: NAD.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.235, A:K.235 EDO.5: 3 residues within 4Å: Chain A: A.267, W.268, L.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.267, A:L.269

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

NAD.6: 28 residues within 4Å: Chain A: G.32, A.33, G.34, T.37, I.41, P.42, D.43, F.44, R.45, L.51, Q.115, N.116, I.117, D.118, H.135, G.209, T.210, S.211, V.214, N.234, K.235, E.236, G.270, E.271, C.272 Ligands: ALA-LEU-PRO-LYS-LYS-NIY-GLY.1, EDO.4, WU3.7 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.33, A:L.51 Hydrogen bonds: A:A.33, A:G.34, A:T.37, A:F.44, A:R.45, A:I.117, A:D.118, A:D.118, A:D.118, A:H.135, A:G.209, A:T.210, A:S.211, A:S.211, A:L.212, A:N.234, A:K.235, A:E.236, A:E.236, A:C.272 Water bridges: A:S.38, A:D.273 pi-Stacking: A:F.44

1 x WU3: (2S)-2-dodecylsulfanylpropanoic acid(Non-covalent)

WU3.7: 12 residues within 4Å: Chain A: F.44, L.51, F.67, L.86, Y.87, F.91, I.117, F.138, V.181, F.183 Ligands: ALA-LEU-PRO-LYS-LYS-NIY-GLY.1, NAD.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.67, A:L.86, A:Y.87, A:F.91, A:F.91, A:I.117, A:F.138, A:F.138

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2

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