SMTL ID : 8v2n.1

Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

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

GLN-PRO-LYS-FDL.1: 15 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, F.185, H.188, E.208, P.209 Ligands: CNA.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.63, A:I.174, A:L.181, A:P.209 Hydrogen bonds: A:V.175, A:G.178, A:E.179, A:L.181, A:E.208

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

CNA.2: 27 residues within 4Å: Chain A: G.28, A.29, G.30, S.32, T.33, I.37, P.38, D.39, F.40, R.41, F.63, Q.111, N.112, I.113, D.114, H.131, G.202, T.203, S.204, L.205, V.207, N.227, R.228, G.247, D.248, V.249 Ligands: GLN-PRO-LYS-FDL.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.29, A:I.37, A:F.40, A:F.40, A:V.207 Hydrogen bonds: A:A.29, A:G.30, A:F.40, A:R.41, A:Q.111, A:Q.111, A:I.113, A:D.114, A:D.114, A:D.114, A:T.203, A:S.204, A:S.204, A:L.205, A:N.227, A:R.228, A:R.228, A:R.228, A:D.248, A:V.249 pi-Cation interactions: A:R.228, A:R.228

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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

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
A

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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