SMTL ID : 9v7w.1

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

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

PRO-ARG-LYS-GLN-LEU-ALA.1: 15 residues within 4Å: Chain A: R.48, E.67, H.138, V.184, F.185, F.186, G.187, E.188, S.189, L.190, Q.216, V.217, Q.218 Ligands: NAD.10, MYR.15 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.67, A:F.186, A:F.186, A:L.190, A:Q.218 Hydrogen bonds: A:V.184, A:G.187, A:E.188, A:L.190, A:Q.216, A:Q.218, A:Q.218

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

PEG.2: 8 residues within 4Å: Chain A: S.41, A.42, K.95, P.96, T.97, I.98, D.276, H.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.41, A:K.95, A:I.98, A:D.276 PEG.4: 4 residues within 4Å: Chain A: L.280, A.281, E.284, L.285 No protein-ligand interaction detected (PLIP)

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

EDO.3: 5 residues within 4Å: Chain A: L.13, F.260, D.268, V.269, A.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.268, A:A.270, A:A.270 EDO.5: 4 residues within 4Å: Chain A: E.80, F.83, A.84, E.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.80, A:A.84 EDO.6: 3 residues within 4Å: Chain A: Q.23, K.109, W.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.23, A:K.109 EDO.7: 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.8: 7 residues within 4Å: Chain A: L.9, Y.21, R.26, V.205, D.206, S.230, T.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.26, A:T.231 EDO.9: 3 residues within 4Å: Chain A: R.26, R.28, D.206 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: A.149, S.150 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: E.71, I.72, S.73, F.186, G.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.73

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

NAD.10: 27 residues within 4Å: Chain A: G.35, A.36, G.37, T.40, I.44, P.45, D.46, F.47, R.48, S.49, Q.118, N.119, I.120, D.121, H.138, G.212, T.213, S.214, V.217, N.237, K.238, E.239, G.273, E.274, C.275 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, MYR.15 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:A.36, A:F.47 Hydrogen bonds: A:A.36, A:G.37, A:T.40, A:T.40, A:D.46, A:F.47, A:R.48, A:Q.118, A:I.120, A:D.121, A:D.121, A:H.138, A:G.212, A:T.213, A:T.213, A:S.214, A:S.214, A:N.237, A:K.238, A:E.239, A:C.275 Water bridges: A:T.40, A:R.48, A:R.48, A:L.215, A:D.276 Salt bridges: A:R.48

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: F.202, L.203, S.225, K.226, A.227, P.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.202, A:L.203

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 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.15: 12 residues within 4Å: Chain A: F.47, F.70, L.89, Y.90, F.94, I.120, H.138, F.141, V.184, F.186 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, NAD.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.47, A:F.70, A:F.70, A:L.89, A:Y.90, A:F.94, A:I.120, A:I.120, A:F.141, A:F.141 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

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