SMTL ID : 8qt4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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

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

EDO.2: 5 residues within 4Å: Chain A: Y.52, S.211, Q.213, V.214 Ligands: NAD.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.52, A:S.211, A:Q.213 Water bridges: A:S.211, A:Q.213 EDO.3: 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 EDO.7: 2 residues within 4Å: Chain A: L.10, F.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.257 EDO.10: 3 residues within 4Å: Chain A: R.122, Y.139 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.139, A:Y.139

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

BTB.4: 7 residues within 4Å: Chain A: S.211, Q.213, E.236, K.237, A.238, G.239, Q.240 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.236, A:G.239, A:Q.240, A:Q.240, A:Q.240 Water bridges: A:K.237

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 2 residues within 4Å: Chain A: S.46 Ligands: BU3.6 No protein-ligand interaction detected (PLIP)

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

BU3.6: 7 residues within 4Å: Chain A: R.45, S.46, P.47, K.235, E.236 Ligands: DMS.5, NAD.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.45

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 5 residues within 4Å: Chain A: R.122, I.123, G.125, E.127 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.123, A:G.125

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

NAD.9: 30 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, L.212, V.214, N.234, K.235, E.236, G.270, E.271, C.272 Chain B: K.6 Ligands: EDO.2, BU3.6, WU8.11 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:A.33, A:L.51 Hydrogen bonds: A:A.33, A:T.37, 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:T.210, A:S.211, A:S.211, A:L.212, A:N.234, A:K.235, A:E.236, A:E.236, A:E.271, A:C.272 Water bridges: A:S.38, A:S.211, A:Q.213, A:D.273

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

WU8.11: 16 residues within 4Å: Chain A: I.41, F.44, L.51, F.67, A.83, Y.87, F.91, I.117, D.118, H.135, F.138, L.154, V.181, F.183 Chain B: K.6 Ligands: NAD.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.41, A:L.51, A:Y.87, A:F.91, A:F.91, A:I.117, A:I.117, A:H.135, A:F.138, A:L.154

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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