SMTL ID : 9vgz.1

SIRT2-F96A structure in complex with H3K18myr peptide and native NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ARG- LYS- GLN- LEU- ALA: Histone H3.1(Non-covalent)

ALA-PRO-ARG-LYS-GLN-LEU-ALA.1: 13 residues within 4Å: Chain A: H.138, V.184, F.185, F.186, G.187, E.188, S.189, L.190, Q.216, V.217, Q.218, P.219 Ligands: MYR.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.184, A:F.186, A:L.190 Hydrogen bonds: A:G.187, A:G.187, A:E.188, A:Q.216, A:Q.218, A:Q.218

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

NAD.2: 24 residues within 4Å: Chain A: G.35, A.36, G.37, T.40, I.44, P.45, D.46, A.47, R.48, L.54, Q.118, N.119, I.120, D.121, H.138, G.212, T.213, S.214, N.237, K.238, G.273, E.274, C.275 Ligands: MYR.6 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.36, A:L.54 Hydrogen bonds: A:A.36, A:G.37, A:T.40, A:T.40, A:A.47, A:R.48, A:I.120, A:D.121, A:D.121, A:D.121, A:H.138, A:G.212, A:T.213, A:S.214, A:N.237, A:K.238, A:C.275 Water bridges: A:T.40, A:R.48, A:R.48 Salt bridges: A:R.48

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

EDO.3: 2 residues within 4Å: Chain A: W.271, L.272 No protein-ligand interaction detected (PLIP)

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

PEG.4: 5 residues within 4Å: Chain A: Q.277, L.280, A.281, E.284, L.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.277

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.146, C.151, C.172, C.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.146, A:C.151, A:C.172, A:C.175

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.6: 11 residues within 4Å: Chain A: I.44, F.70, L.89, F.94, I.120, H.138, F.141, V.184, F.186 Ligands: ALA-PRO-ARG-LYS-GLN-LEU-ALA.1, NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.44, A:F.70, A:L.89, A:F.94, A:I.120, A:I.120, A:F.141, A:F.141, A:F.186 Hydrogen bonds: A:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, N. et al., Structural basis of SIRT2 pre-catalysis NAD+ binding dynamics and mechanism. Rsc Chem Biol (2025)

Release Date

2025-09-24

Peptides

NAD-dependent protein deacetylase sirtuin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2