SMTL ID : 9vge.1

SIRT2 demyristoylation intermediate I structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 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: 11 residues within 4Å: Chain A: H.138, V.184, F.185, F.186, G.187, E.188, L.190, Q.216, V.217, Q.218 Ligands: YDD.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.186, A:L.190, A:Q.218 Hydrogen bonds: A:V.184, A:G.187, A:G.187, A:E.188, A:Q.216, A:Q.216, A:Q.218, A:Q.218

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.2: 10 residues within 4Å: Chain A: A.36, S.39, I.44, P.45, D.46, F.47, N.119, I.120, D.121 Ligands: YDD.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.36, A:I.44, A:F.47 Hydrogen bonds: A:S.39, A:I.120, A:D.121, A:D.121

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: A.270, W.271, L.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.272, A:L.272

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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 YDD: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

YDD.5: 33 residues within 4Å: Chain A: G.35, A.36, G.37, T.40, D.46, R.48, F.70, F.82, A.86, L.89, Y.90, P.91, Q.118, N.119, I.120, D.121, H.138, F.141, I.183, V.184, F.186, G.212, T.213, S.214, L.215, N.237, K.238, E.239, G.273, E.274, C.275 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, NCA.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.70, A:F.70, A:F.82, A:L.89, A:Y.90, A:I.120, A:F.141, A:I.183 Hydrogen bonds: A:A.36, A:G.37, A:T.40, A:F.47, A:R.48, A:Q.118, A:T.213, A:T.213, A:S.214, A:S.214, A:L.215, A:N.237, A:K.238, A:K.238, A:E.274, A:C.275 Salt bridges: 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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