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- PDB-8ak8: Human Sirt6 in complex with ADP-ribose and fragment 4-hydroxybenzamide -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ak8 | ||||||
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Title | Human Sirt6 in complex with ADP-ribose and fragment 4-hydroxybenzamide | ||||||
![]() | NAD-dependent protein deacetylase sirtuin-6 | ||||||
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Function / homology | ![]() NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / ketone biosynthetic process / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / regulation of lipid catabolic process / NAD+- protein-lysine ADP-ribosyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | You, W. / Steegborn, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen Authors: You, W. / Steegborn, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ak5C ![]() 8ak6C ![]() 8ak7C ![]() 8ak9C ![]() 8akaC ![]() 8akbC ![]() 8akcC ![]() 8akdC ![]() 8akeC ![]() 8akfC ![]() 8akgC ![]() 8bl0C ![]() 8bl1C ![]() 8cnmC ![]() 8cnoC ![]() 5mf6S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 15 - 297 / Label seq-ID: 9 - 291
NCS oper:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33631.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8N6T7, protein acetyllysine N-acetyltransferase |
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-Non-polymers , 8 types, 223 molecules ![](data/chem/img/AR6.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HBD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HBD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-SO4 / ![]() #7: Chemical | #8: Chemical | ChemComp-CL / ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7 PH range: 5.7-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 5, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.73→45.54 Å / Num. obs: 69954 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 37.049 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.12 / Net I/σ(I): 13.11 | |||||||||||||||
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 0.97 / Num. unique obs: 11245 / CC1/2: 0.4 / Rrim(I) all: 2.61 / % possible all: 99.6 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 5MF6 Resolution: 1.73→45.54 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.438 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.5 Å2 / Biso mean: 37.573 Å2 / Biso min: 19.75 Å2
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Refinement step | Cycle: final / Resolution: 1.73→45.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 2145 / Type: TIGHT THERMAL / Rms dev position: 3.95 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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