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- PDB-9ktk: Crystal structure of human SIRT3 with its activator SKLB-11A -

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Basic information

Entry
Database: PDB / ID: 9ktk
TitleCrystal structure of human SIRT3 with its activator SKLB-11A
ComponentsNAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsSTRUCTURAL PROTEIN / SIRT3 activator Cardioprotection
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / cellular response to stress / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
: / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsOuyang, L. / Wu, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Cent.Sci. / Year: 2025
Title: Unraveling Small Molecule-Mediated Sirtuin 3 Activation at a Distinct Binding Site for Cardioprotective Therapies.
Authors: Zhang, D. / Zhang, J. / Wu, C. / Xiao, Y. / Ji, L. / Hu, J. / Ding, J. / Li, T. / Zhang, Y. / Ouyang, L.
History
DepositionDec 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,93415
Polymers123,1984
Non-polymers1,73611
Water00
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules

B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,93415
Polymers123,1984
Non-polymers1,73611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area7190 Å2
ΔGint-53 kcal/mol
Surface area44100 Å2
MethodPISA
2
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4557
Polymers61,5992
Non-polymers8565
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-26 kcal/mol
Surface area23850 Å2
MethodPISA
3
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules

C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4798
Polymers61,5992
Non-polymers8806
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1960 Å2
ΔGint-18 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.582, 120.362, 134.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / NAD-dependent protein delactylase sirtuin-3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 30799.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTG7, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1EHU / methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate


Mass: 350.346 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H15FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.49→67.49 Å / Num. obs: 41592 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 2.49→2.63 Å / Num. unique obs: 3187 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→45.47 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3402 1998 4.81 %
Rwork0.2617 --
obs0.2655 41521 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8523 0 111 0 8634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.7591199
X-RAY DIFFRACTIONf_chiral_restr0.0661351
X-RAY DIFFRACTIONf_plane_restr0.0141579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.44451400.35682780X-RAY DIFFRACTION99
2.55-2.620.45951410.34912769X-RAY DIFFRACTION100
2.62-2.70.40871390.3162777X-RAY DIFFRACTION100
2.7-2.790.41931410.30112772X-RAY DIFFRACTION100
2.79-2.890.38071410.30462795X-RAY DIFFRACTION100
2.89-30.36561420.30572812X-RAY DIFFRACTION100
3-3.140.39741420.31922799X-RAY DIFFRACTION100
3.14-3.30.42271400.32912781X-RAY DIFFRACTION100
3.3-3.510.36961430.28482818X-RAY DIFFRACTION100
3.51-3.780.36811430.26462843X-RAY DIFFRACTION100
3.78-4.160.30871420.2512824X-RAY DIFFRACTION100
4.16-4.760.32331460.22012859X-RAY DIFFRACTION100
4.76-60.28091450.23972881X-RAY DIFFRACTION100

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