SMTL ID : 9vem.1

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

monomer

Ligands

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

PRO-ARG-LYS-GLN-LEU-ALA.1: 13 residues within 4Å: Chain A: H.136, V.182, F.183, F.184, G.185, E.186, L.188, Q.214, V.215, Q.216, P.217 Ligands: NAD.2, MYR.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.184, A:V.215 Hydrogen bonds: A:V.182, A:G.185, A:E.186, A:Q.214, A:Q.216, A:Q.216

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

NAD.2: 27 residues within 4Å: Chain A: G.33, A.34, G.35, T.38, I.42, P.43, D.44, F.45, R.46, S.47, Q.116, N.117, I.118, D.119, H.136, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.271, E.272, C.273 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, MYR.12 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.34, A:F.45 Hydrogen bonds: A:A.34, A:G.35, A:T.38, A:T.38, A:D.44, A:F.45, A:R.46, A:Q.116, A:I.118, A:D.119, A:H.136, A:G.210, A:T.211, A:S.212, A:S.212, A:L.213, A:N.235, A:K.236, A:K.236, A:E.237, A:C.273 Water bridges: A:S.39, A:Q.214

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

PEG.3: 8 residues within 4Å: Chain A: S.39, A.40, K.93, P.94, T.95, I.96, D.274, H.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.93, A:I.96, A:D.274 PEG.4: 3 residues within 4Å: Chain A: L.11, F.258, S.260 No protein-ligand interaction detected (PLIP)

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

EDO.5: 2 residues within 4Å: Chain A: S.223, K.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.223, A:K.224 EDO.7: 2 residues within 4Å: Chain A: K.238, Q.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.238, A:Q.241 Water bridges: A:K.238 EDO.8: 2 residues within 4Å: Chain A: K.93, H.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.93, A:H.298 EDO.9: 3 residues within 4Å: Chain A: D.292, R.295, R.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.292 EDO.10: 1 residues within 4Å: Chain A: R.295 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: A.268, W.269, L.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.268, A:L.270

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain A: C.144, C.149, C.170, C.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.144, A:C.149, A:C.170, A:C.173

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.12: 10 residues within 4Å: Chain A: F.45, F.68, L.87, F.92, I.118, H.136, V.182, F.184 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.45, A:F.68, A:L.87, A:F.92 Hydrogen bonds: A:H.136

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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