SMTL ID : 9vg0.1

SIRT2 structure in complex with H3K18myr peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

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

ALA-PRO-ARG-LYS-GLN-LEU.1: 13 residues within 4Å: Chain A: H.138, V.184, F.186, G.187, E.188, S.189, L.190, F.195, Q.216, V.217, Q.218, P.219 Ligands: MYR.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.186, A:L.190, A:F.195, A:V.217 Hydrogen bonds: A:V.184, A:G.187, A:G.187, A:E.188, A:S.189, A:S.189, A:Q.218, A:Q.218

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

EDO.2: 6 residues within 4Å: Chain A: S.41, P.96, T.97, I.98, D.276, H.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.41, A:S.41, A:I.98 Water bridges: A:D.276 EDO.3: 3 residues within 4Å: Chain A: A.270, W.271, L.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.270, A:L.272 EDO.4: 10 residues within 4Å: Chain A: A.68, I.69, F.70, E.71, Y.74, F.75, H.78, P.79, P.81, F.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.69, A:E.71, A:H.78, A:F.82 EDO.5: 6 residues within 4Å: Chain A: S.39, I.44, F.47, N.119, I.120, D.121 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.39, A:S.39, A:I.120, A:D.121 Water bridges: A:F.47, A:R.48 EDO.6: 5 residues within 4Å: Chain A: F.75, K.76, K.77, P.79, L.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.75

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.8: 12 residues within 4Å: Chain A: F.47, R.48, F.70, L.89, F.94, I.120, H.138, F.141, I.183, V.184, F.186 Ligands: ALA-PRO-ARG-LYS-GLN-LEU.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.47, A:F.47, A:F.47, A:F.70, A:L.89, A:F.94, A:I.120, A:F.141, A:F.141, A:I.183 Hydrogen bonds: A:R.48

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

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