NAD-dependent protein deacylase sirtuin-6
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–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts | Chain K； UniProt 1–355 | Not recorded | Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-J × 2 （P06899） DNA strand 1 × 1 DNA strand 2 × 1 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 3.07 Å |
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 8G57 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3K35 Crystal Structure of Human SIRT6 Deposited 2009-10-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
3–318（316 aa）
Chain B
3–318（316 aa）
Chain C
3–318（316 aa）
Chain D
3–318（316 aa）
Chain E
3–318（316 aa）
Chain F
3–318（316 aa）
|
Not recorded | ZN ZINC ION × 6 APR ADENOSINE-5-DIPHOSPHORIBOSE × 6 SO4 SULFATE ION × 13 UNX UNKNOWN LIGAND × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2M NH4SO4, 2%PEG400, 0.1M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.267 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–355（354 aa）
|
Mutation：K265E | UNX UNKNOWN LIGAND × 2 ZN ZINC 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 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–355（354 aa）
|
Mutation：K265E | UNX UNKNOWN LIGAND × 6 ZN ZINC 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 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
2–355（354 aa）
|
Mutation：K265E | UNX UNKNOWN LIGAND × 7 ZN ZINC 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 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
2–355（354 aa）
|
Mutation：K265E | UNX UNKNOWN LIGAND × 3 ZN ZINC 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 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
2–355（354 aa）
|
Mutation：K265E | UNX UNKNOWN LIGAND × 2 ZN ZINC 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 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
2–355（354 aa）
|
Mutation：K265E | UNX UNKNOWN LIGAND × 6 ZN ZINC 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 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
2–355（354 aa）
Chain B
2–355（354 aa）
Chain C
2–355（354 aa）
|
Mutation：K265E Mutation：K265E Mutation：K265E | UNX UNKNOWN LIGAND × 15 ZN ZINC ION × 3 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 × 3 SO4 SULFATE ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKI Human SIRT6 crystal structure in complex with ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 8 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain D
2–355（354 aa）
Chain E
2–355（354 aa）
Chain F
2–355（354 aa）
|
Mutation：K265E Mutation：K265E Mutation：K265E | UNX UNKNOWN LIGAND × 11 ZN ZINC ION × 3 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 × 3 SO4 SULFATE ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
|
Resolution 2.04 Å R-free 0.213 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–355（354 aa）
|
Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–355（354 aa）
|
Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
2–355（354 aa）
|
Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
2–355（354 aa）
|
Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
2–355（354 aa）
|
Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
2–355（354 aa）
|
Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3PKJ Human SIRT6 crystal structure in complex with 2'-N-Acetyl ADP ribose Deposited 2010-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
2–355（354 aa）
Chain B
2–355（354 aa）
Chain C
2–355（354 aa）
Chain D
2–355（354 aa）
Chain E
2–355（354 aa）
Chain F
2–355（354 aa）
|
Mutation：K267E Mutation：K267E Mutation：K267E Mutation：K267E Mutation：K267E Mutation：K267E | A2N [(2R,3S,4R,5R)-4-(acetylamino)-3,5-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 6 ZN ZINC ION × 6 SO4 SULFATE ION × 12 UNX UNKNOWN LIGAND × 35 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；297 K；2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS PH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
|
Resolution 2.12 Å R-free 0.265 |
| 3ZG6 The novel de-long chain fatty acid function of human sirt6 Deposited 2012-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–296（296 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-296
|
Not recorded | ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 GOL GLYCEROL × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å R-free 0.236 |
| 5MF6 Human Sirt6 in complex with activator UBCS039 Deposited 2016-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
8–308（301 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 PGE TRIETHYLENE GLYCOL × 1 7M2 (4~{R})-4-pyridin-3-yl-4,5-dihydropyrrolo[1,2-a]quinoxaline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, Bis-Tris buffer pH 5.7
|
Resolution 1.87 Å R-free 0.220 |
| 5MF6 Human Sirt6 in complex with activator UBCS039 Deposited 2016-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
8–308（301 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 1 7M2 (4~{R})-4-pyridin-3-yl-4,5-dihydropyrrolo[1,2-a]quinoxaline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, Bis-Tris buffer pH 5.7
|
Resolution 1.87 Å R-free 0.220 |
| 5MFP Human Sirt6 in complex with activator UBCS58 Deposited 2016-11-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
8–308（301 aa）
|
Not recorded | 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 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 7M5 4-pyridin-3-ylpyrrolo[1,2-a]quinoxaline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.98 Å R-free 0.185 |
| 5MFP Human Sirt6 in complex with activator UBCS58 Deposited 2016-11-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
8–308（301 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 7M5 4-pyridin-3-ylpyrrolo[1,2-a]quinoxaline × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.98 Å R-free 0.185 |
| 5MFZ Human Sirt6 in complex with small molecule UBCS40 Deposited 2016-11-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 3 7M9 1-pyrrolo[1,2-a]quinoxalin-4-ylnaphthalen-2-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.10 Å R-free 0.208 |
| 5MFZ Human Sirt6 in complex with small molecule UBCS40 Deposited 2016-11-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.10 Å R-free 0.208 |
| 5MGN Human Sirt6 in complex with activator UBCS38 Deposited 2016-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
8–308（301 aa）
|
Not recorded | 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 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 1 7N2 (4~{R})-4-pyridin-3-yl-5-[3-(trifluoromethyl)phenyl]sulfonyl-4~{H}-pyrrolo[1,2-a]quinoxaline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.07 Å R-free 0.192 |
| 5MGN Human Sirt6 in complex with activator UBCS38 Deposited 2016-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
8–308（301 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.07 Å R-free 0.192 |
| 5X16 Sirt6 apo structure Deposited 2017-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–318（316 aa）
Fragment：UNP residues 3-318
|
Not recorded | 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 TBU TERTIARY-BUTYL ALCOHOL × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol
|
Resolution 1.97 Å R-free 0.232 |
| 5Y2F Human SIRT6 in complex with allosteric activator MDL-801 Deposited 2017-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
3–318（316 aa）
Fragment：UNP RESIDUES 3-318
|
Not recorded | 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 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 ZN ZINC ION × 1 GOL GLYCEROL × 5 SO4 SULFATE ION × 7 PEG DI(HYDROXYETHYL)ETHER × 1 HDR HEXADECANE-1-SULFINIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000
|
Resolution 2.53 Å R-free 0.217 |
| 6HOY Human Sirt6 in complex with ADP-ribose and the inhibitor trichostatin A Deposited 2018-09-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 4 TSN TRICHOSTATIN A × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.70 Å R-free 0.185 |
| 6HOY Human Sirt6 in complex with ADP-ribose and the inhibitor trichostatin A Deposited 2018-09-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 3 TSN TRICHOSTATIN A × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.70 Å R-free 0.185 |
| 6QCD Human Sirt6 in complex with ADP-ribose and the activator quercetin Deposited 2018-12-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 5 QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE × 1 EDO 1,2-ETHANEDIOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.84 Å R-free 0.202 |
| 6QCD Human Sirt6 in complex with ADP-ribose and the activator quercetin Deposited 2018-12-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.84 Å R-free 0.202 |
| 6QCE Human Sirt6 in complex with ADP-ribose and the activator isoquercetin Deposited 2018-12-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 5 HW2 isoquercetin × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.90 Å R-free 0.187 |
| 6QCE Human Sirt6 in complex with ADP-ribose and the activator isoquercetin Deposited 2018-12-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 HW2 isoquercetin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.90 Å R-free 0.187 |
| 6QCH Human Sirt6 in complex with ADP-ribose and the activator cyanidin Deposited 2018-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 4 HWB cyanidin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.10 Å R-free 0.200 |
| 6QCH Human Sirt6 in complex with ADP-ribose and the activator cyanidin Deposited 2018-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 6 HWB cyanidin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.10 Å R-free 0.200 |
| 6QCJ Human Sirt6 in complex with ADP-ribose and the inhibitor catechin gallate Deposited 2018-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
13–308（296 aa）
Chain B
13–308（296 aa）
|
Not recorded | 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 × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 7 XEG (2R,3S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.01 Å R-free 0.199 |
| 6XUY Human Sirt6 13-308 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
|
Resolution 2.13 Å R-free 0.179 |
| 6XUY Human Sirt6 13-308 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
|
Resolution 2.13 Å R-free 0.179 |
| 6XV1 Human Sirt6 13-308 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
|
Resolution 1.95 Å R-free 0.165 |
| 6XV1 Human Sirt6 13-308 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
|
Resolution 1.95 Å R-free 0.165 |
| 6XV6 Human Sirt6 3-318 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–318（316 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 1.75 Å R-free 0.225 |
| 6XV6 Human Sirt6 3-318 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–318（316 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 1.75 Å R-free 0.225 |
| 6XV6 Human Sirt6 3-318 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
3–318（316 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 1.75 Å R-free 0.225 |
| 6XV6 Human Sirt6 3-318 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
3–318（316 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 1.75 Å R-free 0.225 |
| 6XV6 Human Sirt6 3-318 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
3–318（316 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 1.75 Å R-free 0.225 |
| 6XV6 Human Sirt6 3-318 in complex with ADP-ribose Deposited 2020-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
3–318（316 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 1.75 Å R-free 0.225 |
| 6XVG Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
3–318（316 aa）
|
Not recorded | 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 GOL GLYCEROL × 1 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 2.10 Å R-free 0.230 |
| 6XVG Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
3–318（316 aa）
|
Not recorded | 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 GOL GLYCEROL × 1 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 2.10 Å R-free 0.230 |
| 6XVG Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
3–318（316 aa）
|
Not recorded | 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 GOL GLYCEROL × 3 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 2.10 Å R-free 0.230 |
| 6XVG Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
3–318（316 aa）
|
Not recorded | 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 GOL GLYCEROL × 1 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 2.10 Å R-free 0.230 |
| 6XVG Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
3–318（316 aa）
|
Not recorded | 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 GOL GLYCEROL × 2 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 2.10 Å R-free 0.230 |
| 6XVG Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 Deposited 2020-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
3–318（316 aa）
|
Not recorded | 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 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
|
Resolution 2.10 Å R-free 0.230 |
| 6ZU4 Human Sirt6 13-308 in complex with ADP-ribose and the activator fluvastatin Deposited 2020-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
13–308（296 aa）
Chain B
13–308（296 aa）
|
Not recorded | 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 × 2 ZN ZINC ION × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 9 115 (3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
|
Resolution 2.46 Å R-free 0.205 |
| 7CL0 Crystal structure of human SIRT6 Deposited 2020-07-20 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–355（355 aa）
|
Not recorded | 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 SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 8 G4U tetradecanethial × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000
|
Resolution 2.53 Å R-free 0.248 |
| 7CL1 Human SIRT6 in complex with allosteric activator MDL-801 (3.2A) Deposited 2020-07-20 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–355（355 aa）
|
Not recorded | 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 8L9 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid × 1 GOL GLYCEROL × 4 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 G4X hexadecanethial × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000
|
Resolution 3.20 Å R-free 0.220 |
| 8AK5 Human Sirt6 in complex with ADP-ribose and fragment pyroglutamic acid Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PCA PYROGLUTAMIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.12 Å R-free 0.222 |
| 8AK5 Human Sirt6 in complex with ADP-ribose and fragment pyroglutamic acid Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 PCA PYROGLUTAMIC ACID × 1 SO4 SULFATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.12 Å R-free 0.222 |
| 8AK6 Human Sirt6 in complex with ADP-ribose and fragment sulfamethoxazole Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 08D Sulfamethoxazole × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.98 Å R-free 0.222 |
| 8AK6 Human Sirt6 in complex with ADP-ribose and fragment sulfamethoxazole Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 08D Sulfamethoxazole × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.98 Å R-free 0.222 |
| 8AK7 Human Sirt6 in complex with ADP-ribose and fragment 6-O-methylguanine Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 6GO 6-O-methylguanine × 1 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.81 Å R-free 0.233 |
| 8AK7 Human Sirt6 in complex with ADP-ribose and fragment 6-O-methylguanine Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 6GO 6-O-methylguanine × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.81 Å R-free 0.233 |
| 8AK8 Human Sirt6 in complex with ADP-ribose and fragment 4-hydroxybenzamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PEG DI(HYDROXYETHYL)ETHER × 2 P6G HEXAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 4 HBD 4-HYDROXYBENZAMIDE × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.73 Å R-free 0.193 |
| 8AK8 Human Sirt6 in complex with ADP-ribose and fragment 4-hydroxybenzamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 P6G HEXAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 6 HBD 4-HYDROXYBENZAMIDE × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.73 Å R-free 0.193 |
| 8AK9 Human Sirt6 in complex with ADP-ribose and fragment Isatin Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 4 ISN ISATIN × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.95 Å R-free 0.223 |
| 8AK9 Human Sirt6 in complex with ADP-ribose and fragment Isatin Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 PG4 TETRAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 5 ISN ISATIN × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.95 Å R-free 0.223 |
| 8AKA Human Sirt6 in complex with ADP-ribose and fragment cis-resveratrol Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 STL RESVERATROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 6 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.77 Å R-free 0.207 |
| 8AKA Human Sirt6 in complex with ADP-ribose and fragment cis-resveratrol Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 STL RESVERATROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 4 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.77 Å R-free 0.207 |
| 8AKB Human Sirt6 in complex with ADP-ribose and fragment 4-nitrocatechol Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 4NC 4-NITROCATECHOL × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.13 Å R-free 0.261 |
| 8AKB Human Sirt6 in complex with ADP-ribose and fragment 4-nitrocatechol Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 4NC 4-NITROCATECHOL × 1 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.13 Å R-free 0.261 |
| 8AKC Human Sirt6 in complex with ADP-ribose and fragment 3-(acetylamino)thiophene-2-carboxylic acid Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 3 GV9 3-(acetylamino)thiophene-2-carboxylic acid × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.83 Å R-free 0.206 |
| 8AKC Human Sirt6 in complex with ADP-ribose and fragment 3-(acetylamino)thiophene-2-carboxylic acid Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 3 GV9 3-(acetylamino)thiophene-2-carboxylic acid × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.83 Å R-free 0.206 |
| 8AKD Human Sirt6 in complex with ADP-ribose and fragment 1-methyl-L-histidine Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 HIC 4-METHYL-HISTIDINE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.76 Å R-free 0.202 |
| 8AKD Human Sirt6 in complex with ADP-ribose and fragment 1-methyl-L-histidine Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 HIC 4-METHYL-HISTIDINE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.76 Å R-free 0.202 |
| 8AKE Human Sirt6 in complex with ADP-ribose and fragment nicotinamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.82 Å R-free 0.224 |
| 8AKE Human Sirt6 in complex with ADP-ribose and fragment nicotinamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 NCA NICOTINAMIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.82 Å R-free 0.224 |
| 8AKF Human Sirt6 in complex with ADP-ribose and fragment 3-aminobenzamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 4 3AB 3-aminobenzamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.97 Å R-free 0.225 |
| 8AKF Human Sirt6 in complex with ADP-ribose and fragment 3-aminobenzamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 SO4 SULFATE ION × 4 3AB 3-aminobenzamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.97 Å R-free 0.225 |
| 8AKG Human Sirt6 in complex with ADP-ribose and fragment 4-amino-6-chlorobenzene-1,3-disulfonamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 7 I7B 4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.82 Å R-free 0.193 |
| 8AKG Human Sirt6 in complex with ADP-ribose and fragment 4-amino-6-chlorobenzene-1,3-disulfonamide Deposited 2022-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 5 I7B 4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.82 Å R-free 0.193 |
| 8BL0 Human Sirt6 in complex with the inhibitor S6023 and ADP-ribose Deposited 2022-11-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 QTI 3-[4-[[5-(2-fluorophenyl)thiophen-2-yl]methyl]piperazin-1-yl]sulfonylbenzenesulfonamide × 1 SO4 SULFATE ION × 4 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.82 Å R-free 0.239 |
| 8BL0 Human Sirt6 in complex with the inhibitor S6023 and ADP-ribose Deposited 2022-11-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 QTI 3-[4-[[5-(2-fluorophenyl)thiophen-2-yl]methyl]piperazin-1-yl]sulfonylbenzenesulfonamide × 1 SO4 SULFATE ION × 5 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.82 Å R-free 0.239 |
| 8BL1 Human Sirt6 in complex with the inhibitor S6039 and ADP-ribose Deposited 2022-11-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–308（296 aa）
|
Not recorded | 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 QY3 2-azanyl-5-[4-[[5-(2-fluorophenyl)thiophen-2-yl]methyl]piperazin-1-yl]sulfonyl-benzenesulfonamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.06 Å R-free 0.216 |
| 8BL1 Human Sirt6 in complex with the inhibitor S6039 and ADP-ribose Deposited 2022-11-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–308（296 aa）
|
Not recorded | 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 QY3 2-azanyl-5-[4-[[5-(2-fluorophenyl)thiophen-2-yl]methyl]piperazin-1-yl]sulfonyl-benzenesulfonamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.06 Å R-free 0.216 |
| 8CNM Human Sirt6 in complex with the inhibitor S6020 and ADP-ribose Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
13–308（296 aa）
Chain B
13–308（296 aa）
|
Not recorded | 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 × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 8 V7R 4-azanyl-~{N}-(4-oxidanylcyclohexyl)benzenesulfonamide × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.88 Å R-free 0.227 |
| 8CNO Improved complex structure of human Sirtuin 6 with its inhibitor cis-resveratrol Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
13–308（296 aa）
Chain B
13–308（296 aa）
|
Not recorded | 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 × 2 ZN ZINC ION × 2 STL RESVERATROL × 2 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 9 CL CHLORIDE ION × 6 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.75 Å R-free 0.188 |
| 8F86 SIRT6 bound to an H3K9Ac nucleosome Deposited 2022-11-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain K
2–355（354 aa）
|
Not recorded | ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8I2B Human SIRT6 in complex with inhibitor 7702 Deposited 2023-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
13–298（286 aa）
Chain B
13–298（286 aa）
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 9 O5L N1-[[4-(4-aminophenyl)sulfanyl-3-(trifluoromethyl)phenyl]methoxy]benzene-1,4-dicarboxamide × 6 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 × 6 ZN ZINC ION × 6 SO4 SULFATE ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Bis-tris pH 5.7, 1.6 M (NH4)2SO4, 10% PEG400
|
Resolution 2.20 Å R-free 0.238 |
| 8OF4 Nucleosome Bound human SIRT6 (Composite) Deposited 2023-03-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain L
1–355（355 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 8ZVP Human SIRT6 in complex with EGCG Deposited 2024-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
13–308（296 aa）
Chain B
13–308（296 aa）
|
Not recorded | ZN ZINC ION × 6 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 × 6 KDH (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；291.15 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 2.50 Å R-free 0.205 |
| 9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain K
2–355（354 aa）
|
Not recorded | ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9G7H Human Sirt6 in complex with ADP-ribose and the inhibitor 2-Pr Deposited 2024-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
13–308（296 aa）
Chain B
13–308（296 aa）
|
Not recorded | 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 × 6 ZN ZINC ION × 6 A1IIZ 2,4-bis(oxidanylidene)-1-[2-oxidanylidene-2-[[(2S)-3-oxidanylidene-3-(propylamino)-2-[3-(3-pyridin-3-yl-1,2,4-oxadiazol-5-yl)propanoylamino]propyl]amino]ethyl]pyrimidine-5-carboxamide × 3 SO4 SULFATE ION × 21 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
|
Resolution 1.75 Å R-free 0.202 |
44 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SIR6_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain K； PDBConstruct 3–357； UniProt 1–355 |
