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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 118–395 | Fragment：UNP residues 118-395 | TNFa-derived lysine triazole dodecyl inhibitor × 1 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 |
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 9S27 | 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain J
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain K
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
119–399（281 aa）
|
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 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain I
119–399（281 aa）
|
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 |
| 4BV3 CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD Deposited 2013-06-24 | Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 construct 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 construct 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 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 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 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 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 oligomeric state 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 oligomeric state 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 |
43 other PDB entries and 90 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 4–281； UniProt 118–395 |
