SMTL ID : 8v15.2 (1 other biounit)

Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x GLN- PRO- LYS- FDL: GLN-PRO-LYS-FDL(Non-covalent)

GLN-PRO-LYS-FDL.1: 14 residues within 4Å: Chain A: F.63, H.131, I.174, V.175, F.176, F.177, G.178, E.179, P.180, L.181, L.186, V.207 Ligands: Y4T.3, CNA.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.63, A:I.174, A:V.207, A:V.207 Hydrogen bonds: A:V.175, A:G.178, A:E.179, A:L.181

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.139, C.142, C.163, V.165, 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: 11 residues within 4Å: Chain A: R.41, E.60, Q.111, T.203, S.204, L.205, E.206, V.207, F.210 Ligands: GLN-PRO-LYS-FDL.1, CNA.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.60, A:V.207, A:V.207, A:F.210 Hydrogen bonds: A:S.204 pi-Cation interactions: A:R.41

1 x CNA: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

CNA.4: 25 residues within 4Å: Chain A: G.28, A.29, G.30, S.32, T.33, I.37, D.39, F.40, R.41, Q.111, N.112, I.113, D.114, H.131, G.202, T.203, S.204, N.227, R.228, D.229, G.247, D.248, V.249 Ligands: GLN-PRO-LYS-FDL.1, Y4T.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.29, A:F.40 Hydrogen bonds: A:A.29, A:G.30, A:S.32, A:T.33, A:D.39, A:Q.111, A:I.113, A:D.114, A:H.131, A:G.202, A:S.204, A:S.204, A:N.227, A:R.228, A:D.248, A:V.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chakrabarti, R. et al., Computationally Driven Discovery and Characterization of SIRT3 Activating Compounds that Fully Recover Catalytic Activity under NAD+ Depletion. biorxiv (2023)

Release Date

2023-12-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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