SMTL ID : 8v5u.1

Human SIRT3 bound to p53-AMC peptide and Honokiol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x GLN- PRO- LYS- ALY- MCM: p53-AMC peptide(Non-covalent)

GLN-PRO-LYS-ALY-MCM.1: 13 residues within 4Å: Chain A: R.41, F.63, H.131, I.174, V.175, F.177, G.178, E.179, L.181, L.186, V.207, E.208, P.209 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.63, A:I.174, A:V.175, A:F.177, A:F.177, A:L.186, A:V.207 Hydrogen bonds: A:R.41, A:R.41, A:V.175, A:G.178, A:E.179, A:L.181, A:E.208

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.139, C.142, C.163, C.166 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.163, A:C.166

1 x Y4T: (1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol(Non-covalent)

Y4T.3: 6 residues within 4Å: Chain A: P.38, D.39, S.45, G.46, L.47, N.50 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.38, A:L.47, A:L.47 Hydrogen bonds: A:S.45, A:G.46, A:L.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guan, X. et al., Computationally Driven Discovery and Characterization of SIRT3-Activating Compounds that Fully Recover Catalytic Activity under ${\mathrm{NAD}}^{+}$ Depletion. Phys. Rev. X (2024)

Release Date

2024-11-06

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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