SMTL ID : 9vh0.2 (1 other biounit)

SIRT2-H187A structure in complex with H3K18myr peptide and native NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

PRO-ARG-LYS-GLN-LEU.1: 14 residues within 4Å: Chain A: A.134, V.180, F.181, F.182, G.183, E.184, S.185, L.186, F.191, Q.212, V.213, Q.214 Ligands: NAD.2, MYR.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.180, A:F.182, A:L.186, A:F.191 Hydrogen bonds: A:V.180, A:G.183, A:E.184, A:L.186, A:Q.214, A:Q.214

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

NAD.2: 28 residues within 4Å: Chain A: G.31, A.32, G.33, T.36, I.40, P.41, D.42, F.43, R.44, S.45, Q.114, N.115, I.116, D.117, A.134, G.208, T.209, S.210, L.211, V.213, N.233, K.234, E.235, G.269, E.270, C.271 Ligands: PRO-ARG-LYS-GLN-LEU.1, MYR.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.32, A:F.43 Hydrogen bonds: A:A.32, A:G.33, A:T.36, A:T.36, A:F.43, A:R.44, A:Q.114, A:I.116, A:D.117, A:D.117, A:G.208, A:T.209, A:S.210, A:S.210, A:L.211, A:N.233, A:K.234, A:E.235, A:E.235, A:C.271

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.142, C.147, C.168, C.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.142, A:C.147, A:C.168, A:C.171

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.4: 11 residues within 4Å: Chain A: F.43, L.85, P.87, F.90, I.116, D.117, I.179, V.180, F.182 Ligands: PRO-ARG-LYS-GLN-LEU.1, NAD.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.85, A:F.90, A:I.116

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
B

NAD-dependent protein deacetylase sirtuin-2

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