4bn5

Structure of human SIRT3 in complex with SRT1720 inhibitor

Method: X-RAY DIFFRACTION D_max: 201.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL

HOMO SAPIENS

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
11	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain K； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
12	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain L； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 119–399	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE	Resolution 3.25 Å R-free 0.265

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4BN5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3GLR Crystal Structure of human SIRT3 with acetyl-lysine AceCS2 peptide Deposited 2009-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 4 BCT BICARBONATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 15% (w/v) PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.226
3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Mutation：residues 118-399	ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.244
3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Mutation：residues 118-399	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.244
3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Mutation：residues 118-399	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.244
3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Mutation：residues 118-399	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.244
3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Mutation：residues 118-399	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.244
3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Mutation：residues 118-399	ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.244
3GLT Crystal Structure of Human SIRT3 with ADPR bound to the AceCS2 peptide containing a thioacetyl lysine Deposited 2009-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1 CO3 CARBONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 17% w/v PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.228
3GLU Crystal Structure of Human SIRT3 with AceCS2 peptide Deposited 2009-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 118–399（282 aa） Fragment：Human SIRT3, residues 118-399	Not recorded	SO4 SULFATE ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 17% w/v PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.248
4BN4 Structure of human SIRT3 in complex with ADP-ribose Deposited 2013-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	ZN ZINC ION × 1 NA SODIUM ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 OP2 2-[2-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 30% (V/V) PEG600, 5%(W/V) PEG1000, 10% (V/V) GLYCEROL, 0.1 M MES, PH 6.0	Resolution 1.30 Å R-free 0.179
4BV3 CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD Deposited 2013-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 ZN ZINC ION × 1 NO3 NITRATE ION × 1 GOL GLYCEROL × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M (NH4)2SO4, 20% PEG 3350	Resolution 2.00 Å R-free 0.209
4BVB CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND ADP-RIBOSE Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa）	Not recorded	OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.08 M KH2PO4 18 % PEG 8000 20% GLYCEROL	Resolution 2.00 Å R-free 0.232
4BVE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6	Resolution 2.05 Å R-free 0.208
4BVE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE Deposited 2013-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6	Resolution 2.05 Å R-free 0.208
4BVF CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa） Fragment：;RESIDUES 116-399' ;	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6	Resolution 2.70 Å R-free 0.230
4BVF CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 Deposited 2013-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 116–399（284 aa） Fragment：;RESIDUES 116-399' ;	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6	Resolution 2.70 Å R-free 0.230
4BVG CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 Deposited 2013-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 XYQ (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；0.2 M (NH4)2SO4, 0.1M BISTRIS PH 5.5, 21% PEG 3350	Resolution 2.50 Å R-free 0.248
4BVH CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20% PEG 6000, 0.1 M HEPES PH7	Resolution 1.90 Å R-free 0.226
4BVH CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20% PEG 6000, 0.1 M HEPES PH7	Resolution 1.90 Å R-free 0.226
4BVH CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE Deposited 2013-06-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20% PEG 6000, 0.1 M HEPES PH7	Resolution 1.90 Å R-free 0.226
4C78 Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide Deposited 2013-09-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 116–399（284 aa） Fragment：RESIDUES 116-399	Not recorded	BVB 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；250 MM (NH4)2SO4, 100 MM BISTRIS PH 6, 21% (W/V) PEG 3350	Resolution 2.00 Å R-free 0.241
4C7B Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide Deposited 2013-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 117–399（283 aa） Fragment：RESIDUES 117-399	Not recorded	ZN ZINC ION × 1 BVB 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol × 1 IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；200 MM NACL,100 MM HEPES PH 7, 10% (V/V) ISOPROPANOL	Resolution 2.10 Å R-free 0.234
4FVT Human SIRT3 bound to Ac-ACS peptide and Carba-NAD Deposited 2012-06-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 122–395（274 aa） Fragment：UNP residues 122-395	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SO4 SULFATE ION × 3 ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；0.2M lithium sulfate monohydrate, 15% (w/v) poly-ethylene glycol (PEG) 12000, and 0.1 M Bis-Tris, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.47 Å R-free 0.249
4FZ3 Crystal structure of SIRT3 in complex with acetyl p53 peptide coupled with 4-amino-7-methylcoumarin Deposited 2012-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa） Fragment：residues 118-399	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.85M HEPES-NA, 8.5%(V/V) ISO-PROPANOL, 17%(W/V) PEG4000, 15%(V/V) GLYCEROL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.10 Å R-free 0.282
4HD8 Crystal structure of human Sirt3 in complex with Fluor-de-Lys peptide and piceatannol Deposited 2012-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 116–399（284 aa） Fragment：UNP residues 116-399	Not recorded	ZN ZINC ION × 1 PIT PICEATANNOL × 1 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200 mM NaCl, 100 mM HEPES pH 7, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.240
4JSR Crystal Structure of human SIRT3 with ELT inhibitor 11c [N-{2-[1-(6-carbamoylthieno[3,2-d]pyrimidin-4-yl)piperidin-4-yl]ethyl}-N'-ethylthiophene-2,5-dicarboxamide] Deposited 2013-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–399（282 aa） Fragment：UNP residues 118-399	Not recorded	ZN ZINC ION × 1 1NQ N-{2-[1-(6-carbamoylthieno[3,2-d]pyrimidin-4-yl)piperidin-4-yl]ethyl}-N'-ethylthiophene-2,5-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；0.1M Tris pH 8.0, 20% PEG 4000 or 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.70 Å R-free 0.228
4JT8 Crystal Structure of human SIRT3 with ELT inhibitor 28 [4-(4-{2-[(2,2-dimethylpropanoyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide[ Deposited 2013-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–399（282 aa） Fragment：UNP residues 118-399	Not recorded	ZN ZINC ION × 1 1NR 4-(4-{2-[(2,2-dimethylpropanoyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.26 Å R-free 0.241
4JT9 Crystal Structure of human SIRT3 with ELT inhibitor 3 [14-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide] Deposited 2013-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–399（282 aa） Fragment：UNP residues 118-399	Not recorded	ZN ZINC ION × 1 1NS 4-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide × 1 GOL GLYCEROL × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.24 Å R-free 0.247
4O8Z Crystal structure of human SIRT3 in complex with compound (2-butylbenzofuran-3-yl)(4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl)methanone Deposited 2013-12-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–399（284 aa） Fragment：UNP RESIDUES 116-399	Not recorded	ZN ZINC ION × 1 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.204
5BWN Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine Deposited 2015-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa） Fragment：UNP RESIDUES 118-399	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2M Ammonium tartrate dibasic (pH 7.0), 20% w/v PEG 3350, 0.01M Urea	Resolution 1.94 Å R-free 0.275
5BWO Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide Deposited 2015-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa） Fragment：UNP RESIDUES 118-399	Not recorded	PLM PALMITIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2M Ammonium formate, 20% PEG 3350	Resolution 2.38 Å R-free 0.287
5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350	Resolution 1.83 Å R-free 0.203
5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350	Resolution 1.83 Å R-free 0.203
5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350	Resolution 1.83 Å R-free 0.203
5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 1PE PENTAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350	Resolution 1.83 Å R-free 0.203
5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350	Resolution 1.83 Å R-free 0.203
5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350	Resolution 1.83 Å R-free 0.203
5H4D Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride Deposited 2016-10-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–391（271 aa） Fragment：UNP residues 121-391	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1M HEPES sodium pH 7.5, 10%(v/v) 2-Propanol, 20%(w/v) Polyethylene glycol 4,000	Resolution 3.21 Å R-free 0.372
5H4D Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride Deposited 2016-10-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 121–391（271 aa） Fragment：UNP residues 121-391	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1M HEPES sodium pH 7.5, 10%(v/v) 2-Propanol, 20%(w/v) Polyethylene glycol 4,000	Resolution 3.21 Å R-free 0.372
5Y4H Human SIRT3 in complex with halistanol sulfate Deposited 2017-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa） Fragment：UNP residues 118-399	Not recorded	ZN ZINC ION × 1 8QF [(2~{S},3~{S},5~{S},6~{S},8~{S},9~{S},10~{R},13~{R},14~{R},17~{R})-17-[(2~{R})-6,6-dimethylheptan-2-yl]-10,13-dimethyl-2,3-disulfooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-6-yl] hydrogen sulfate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Potassium phosphate	Resolution 2.60 Å R-free 0.269
5YTK Crystal structure of SIRT3 bound to a leucylated AceCS2 Deposited 2017-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 121–394（274 aa） Chain B 121–394（274 aa） Chain C 121–394（274 aa） Chain D 121–394（274 aa） Chain E 121–394（274 aa） Chain F 121–394（274 aa）	Not recorded	ZN ZINC ION × 6 LEU LEUCINE × 6 LYS LYSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.1M MES monohydrate (pH6.2) and 8% PEG 20,000	Resolution 2.70 Å R-free 0.237
5Z93 Crystal Structure of SIRT3 in complex with H3K9bhb peptide Deposited 2018-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 117–399（283 aa） Fragment：UNP residues 117-399	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M MES pH 6.5, 25% PEG 1000	Resolution 1.95 Å R-free 0.210
5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 117–399（283 aa） Fragment：UNP residues 117-399	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350	Resolution 1.90 Å R-free 0.191
5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 117–399（283 aa） Fragment：UNP residues 117-399	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350	Resolution 1.90 Å R-free 0.191
5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–394（274 aa） Fragment：UNP residues 121-394	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000	Resolution 2.90 Å R-free 0.280
5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 121–394（274 aa） Fragment：UNP residues 121-394	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000	Resolution 2.90 Å R-free 0.280
5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 121–394（274 aa） Fragment：UNP residues 121-394	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000	Resolution 2.90 Å R-free 0.280
5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 121–394（274 aa） Fragment：UNP residues 121-394	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000	Resolution 2.90 Å R-free 0.280
5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 121–394（274 aa） Fragment：UNP residues 121-394	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000	Resolution 2.90 Å R-free 0.280
5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 121–394（274 aa） Fragment：UNP residues 121-394	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000	Resolution 2.90 Å R-free 0.280
6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–394（274 aa）	Not recorded	ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol	Resolution 2.95 Å R-free 0.275
6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 121–394（274 aa）	Not recorded	ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol	Resolution 2.95 Å R-free 0.275
6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 121–394（274 aa）	Not recorded	ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol	Resolution 2.95 Å R-free 0.275
6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 121–394（274 aa）	Not recorded	ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol	Resolution 2.95 Å R-free 0.275
6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 121–394（274 aa）	Not recorded	CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol	Resolution 2.95 Å R-free 0.275
6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 121–394（274 aa）	Not recorded	ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol	Resolution 2.95 Å R-free 0.275
8ANC 14-3-3 sigma sirtuin-3 phospho-peptide complex Deposited 2022-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 98–108（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 6 CA CALCIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M Hepes/NaOH pH 7.5, 0.2 M CaCl2, 26% (v/v) PEG 400, 5% (v/v) glycerol, 1 mM TCEP	Resolution 1.11 Å R-free 0.146
8BBK Crystal structure of human Sirt3 in complex with a fragment of the human AROS protein Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–399（399 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl	Resolution 3.27 Å R-free 0.261
8BBK Crystal structure of human Sirt3 in complex with a fragment of the human AROS protein Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–399（399 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl	Resolution 3.27 Å R-free 0.261
8BBK Crystal structure of human Sirt3 in complex with a fragment of the human AROS protein Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–399（399 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl	Resolution 3.27 Å R-free 0.261
8BBK Crystal structure of human Sirt3 in complex with a fragment of the human AROS protein Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–399（399 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl	Resolution 3.27 Å R-free 0.261
8BBK Crystal structure of human Sirt3 in complex with a fragment of the human AROS protein Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–399（399 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl	Resolution 3.27 Å R-free 0.261
8BBK Crystal structure of human Sirt3 in complex with a fragment of the human AROS protein Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–399（399 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl	Resolution 3.27 Å R-free 0.261
8CCW Crystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate peptide Deposited 2023-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM MES, pH 6.0, 30% (w/v) PEG 200, 5% (w/v) PEG 3000 as reservoir solution.	Resolution 1.65 Å R-free 0.209
8CCZ Crystal structure of human Sirt3 in complex with an inhibiting HIV1 Tat-37-59 peptide Deposited 2023-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM Tat-37-59 in 10% (v/v) DMSO for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM CHES, pH 9.0, 20% (w/v) PEG 8000 as reservoir solution.	Resolution 1.95 Å R-free 0.276
8CCZ Crystal structure of human Sirt3 in complex with an inhibiting HIV1 Tat-37-59 peptide Deposited 2023-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 118–399（282 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM Tat-37-59 in 10% (v/v) DMSO for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM CHES, pH 9.0, 20% (w/v) PEG 8000 as reservoir solution.	Resolution 1.95 Å R-free 0.276
8HLW Crystal structure of SIRT3 in complex with H4K16la peptide Deposited 2022-12-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 119–399（281 aa）	Not recorded	ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350	Resolution 2.50 Å R-free 0.243
8HLY Crystal structure of SIRT3 in complex with H3K23la peptide Deposited 2022-12-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 119–399（281 aa）	Not recorded	GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS pH at 6.5, 28% (w/v) Polyethylene glycol monomethyl ether 2000	Resolution 2.00 Å R-free 0.203
8HN9 Human SIRT3 Recognizing CCNE2K348la peptide Deposited 2022-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 122–395（274 aa） Chain B 122–395（274 aa）	Not recorded	ZN ZINC ION × 2 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.8 M succinic acid, pH 7.0, 0.01M Imidazole	Resolution 3.70 Å R-free 0.218
8V15 Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol Deposited 2023-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa）	Not recorded	ZN ZINC ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).	Resolution 2.40 Å R-free 0.303
8V15 Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol Deposited 2023-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 118–399（282 aa）	Not recorded	ZN ZINC ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 Y4T (1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).	Resolution 2.40 Å R-free 0.303
8V2N Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD Deposited 2023-11-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa）	Not recorded	CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).	Resolution 1.74 Å R-free 0.282
8V5U Human SIRT3 bound to p53-AMC peptide and Honokiol Deposited 2023-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–399（282 aa）	Not recorded	ZN ZINC ION × 1 Y4T (1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).	Resolution 1.48 Å R-free 0.246
9CBT Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10 Deposited 2024-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–399（282 aa）	Not recorded	ZN ZINC ION × 1 5IA 2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4-hydroxy-2-sulfanyloxolan-3-yl]oxy}tetradecylidene)amino]-2-{[(benzyloxy)carbonyl]amino}hexanoyl]amino}-N,N,N-triethylethan-1-aminium (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 7.9, 100 mM MgCl2, 20 % w/v PEG8000, and 17.5 % w/v PEG400	Resolution 1.95 Å R-free 0.239
9CBT Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10 Deposited 2024-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 118–399（282 aa）	Not recorded	ZN ZINC ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 5I7 (phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-6-oxidanyl-2-tridecyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]-1-oxidanylidene-1-[2-(triethyl-$l^{4}-azanyl)ethylamino]hexan-2-yl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 7.9, 100 mM MgCl2, 20 % w/v PEG8000, and 17.5 % w/v PEG400	Resolution 1.95 Å R-free 0.239
9KTK Crystal structure of human SIRT3 with its activator SKLB-11A Deposited 2024-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 118–391（274 aa） Chain B 118–391（274 aa） Chain C 118–391（274 aa） Chain D 118–391（274 aa）	Not recorded	ZN ZINC ION × 4 A1EHU methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate × 4 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5	Resolution 2.49 Å R-free 0.340
9KTK Crystal structure of human SIRT3 with its activator SKLB-11A Deposited 2024-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 118–391（274 aa） Chain D 118–391（274 aa）	Not recorded	ZN ZINC ION × 2 A1EHU methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5	Resolution 2.49 Å R-free 0.340
9KTK Crystal structure of human SIRT3 with its activator SKLB-11A Deposited 2024-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 118–391（274 aa） Chain C 118–391（274 aa）	Not recorded	ZN ZINC ION × 2 A1EHU methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5	Resolution 2.49 Å R-free 0.340
9S27 Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose Deposited 2025-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 118–395（278 aa） Fragment：UNP residues 118-395	Not recorded	ZN ZINC ION × 1 BU3 (R,R)-2,3-BUTANEDIOL × 2 A1JK8 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-(5-dodecyl-3-propyl-1,2,3$l^{4}-triazacyclopenta-2,4-dien-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT3-[LTDi1-ADPR] complex (10.0 mg/mL SIRT3, 15 mM NAD+, 3 mM of LTDi1 with 1.5 % (v/v) final DMSO concentration) formed after 2 days in wells with an equal volume of 300 nL protein solution and 300 nL reservoir solution containing 3 M NaCl in 0.1 M Tris at pH 8.5.	Resolution 1.60 Å R-free 0.194

43 other PDB entries and 79 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SIR3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 119–399 Author chain B； PDBConstruct 1–281； UniProt 119–399 Author chain C； PDBConstruct 1–281； UniProt 119–399 Author chain D； PDBConstruct 1–281； UniProt 119–399 Author chain E； PDBConstruct 1–281； UniProt 119–399 Author chain F； PDBConstruct 1–281； UniProt 119–399 Author chain G； PDBConstruct 1–281； UniProt 119–399 Author chain H； PDBConstruct 1–281； UniProt 119–399 Author chain I； PDBConstruct 1–281； UniProt 119–399 Author chain J； PDBConstruct 1–281； UniProt 119–399 Author chain K； PDBConstruct 1–281； UniProt 119–399 Author chain L； PDBConstruct 1–281； UniProt 119–399

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bn5
Deposition date deposition_date	2013-05-13
Structure title title	Structure of human SIRT3 in complex with SRT1720 inhibitor
Keywords keywords	HYDROLASE, LYSINE DEACETYLASE, ADP RIBOSE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	60.42 Å
Radius of gyration Rg (electron density) rg_electron	60.41 Å
Forward intensity I(0) i0	1934340000.00
Molecular weight molecular_weight	376760.0 kDa
Excluded volume excluded_volume	474690 Å³
Envelope volume envelope_volume	695360 Å³
Hydration-shell volume shell_volume	101130 Å³
Envelope diameter envelope_diameter	205.8 Å
Shell Rg shell_rg	56.20 Å
Envelope Rg envelope_rg	59.30 Å
Shape Rg shape_rg	60.42 Å
Total Rg total_rg	60.28 Å
Total atoms total_atoms	26520
Residues n_residues	3275
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	201.7 Å
Rg (real space) rg_real	60.42 Å
Rg uncertainty (real space) rg_real_error	1.93 Å
I(0) (real space) i0_real	1.9340e+09
I(0) uncertainty (real space) i0_real_error	3.7000e+07
Rg (reciprocal space) rg_reciprocal	60.38 Å
I(0) (reciprocal space) i0_reciprocal	1934000000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	77.6 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.649
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	150500000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.692

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
Molecular weight formula_weight	31253.0 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	26520

DKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	662.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide
Molecular weight formula_weight	469.6 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	4bn5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5G01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5G02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5H01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5I01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5I02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5J01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5J02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5K01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5K02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	4bn5L01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	4bn5L02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

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8. Citations (1)

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Unit-cell length a length_a	227.820 Å
Unit-cell length b length_b	246.060 Å
Unit-cell length c length_c	127.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	48.570 Å
R factor r_factor	0.2107
R_work r_work	0.2079
R_free r_free	0.2653

fit	/app/data/saxs_computation/bn/4bn5/4bn5.fit
pddf	/app/data/pr_computation/bn/4bn5/4bn5.pr.out
profile	/app/data/saxs_computation/bn/4bn5/4bn5.dat