SMTL ID : 9ktk.1 (2 other biounits)

Crystal structure of human SIRT3 with its activator SKLB-11A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.142, C.145, C.166, C.169, T.170, G.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.142, A:C.145, A:C.166, A:C.169 ZN.3: 4 residues within 4Å: Chain B: C.142, C.145, C.166, C.169 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.142, B:C.145, B:C.166, B:C.169 ZN.6: 4 residues within 4Å: Chain C: C.142, C.145, C.166, C.169 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.142, C:C.145, C:C.166, C:C.169 ZN.9: 7 residues within 4Å: Chain D: C.142, P.164, C.166, C.169, T.170, G.171, V.173 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.142, D:P.164, D:C.169

4 x 01: methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate

01.2: 10 residues within 4Å: Chain A: R.44, E.63, F.66, I.116, H.134, I.177, V.178, F.179, F.180 Chain C: Y.61 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.63, A:V.178, A:F.180 Hydrogen bonds: A:V.178 Salt bridges: A:H.134 pi-Stacking: A:F.66 pi-Cation interactions: A:H.134 01.5: 12 residues within 4Å: Chain B: F.43, R.44, E.63, F.66, I.116, H.134, I.177, V.178, F.179, F.180 Chain D: P.60, Y.61 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.43, B:E.63, B:V.178, B:F.180 Hydrogen bonds: B:V.178 Salt bridges: B:H.134 pi-Stacking: B:F.66, B:H.134 01.8: 15 residues within 4Å: Chain A: L.184, L.189, V.192 Chain C: R.44, E.63, F.66, Q.114, I.116, A.133, H.134, I.177, V.178, F.179, F.180, V.210 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:L.184, A:L.189, C:E.63, C:V.178, C:F.180, C:V.210 Hydrogen bonds: C:V.178 Salt bridges: C:H.134 pi-Stacking: C:F.66, C:H.134 01.11: 16 residues within 4Å: Chain B: L.184, L.189, V.192 Chain D: E.63, F.66, Q.114, I.116, A.133, H.134, I.177, V.178, F.179, F.180, L.184, P.185, V.210 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain D Hydrophobic interactions: B:L.184, B:L.189, D:E.63, D:V.178, D:F.180, D:F.180, D:V.210 Hydrogen bonds: D:V.178 Salt bridges: D:H.134 pi-Stacking: D:F.66, D:H.134

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain B: F.149 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: P.148, F.149, P.150 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: F.149, P.164, R.165, C.166 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Unraveling Small Molecule-Mediated Sirtuin 3 Activation at a Distinct Binding Site for Cardioprotective Therapies. Acs Cent.Sci. (2025)

Release Date

2025-06-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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