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- PDB-6enx: Zebrafish Sirt5 in complex with stalled bicyclic intermediate of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6enx | ||||||
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Title | Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10 | ||||||
![]() | NAD-dependent protein deacylase sirtuin-5, mitochondrial | ||||||
![]() | SIGNALING PROTEIN / Hydrolase / PTM / inhibitor / Sirtuin | ||||||
Function / homology | ![]() Transcriptional activation of mitochondrial biogenesis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent histone deacetylase activity / heterocyclic compound binding ...Transcriptional activation of mitochondrial biogenesis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent histone deacetylase activity / heterocyclic compound binding / NAD+ binding / acyl binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / mitochondrion / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pannek, M. / Steegborn, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Authors: Rajabi, N. / Auth, M. / Troelsen, K.R. / Pannek, M. / Bhatt, D.P. / Fontenas, M. / Hirschey, M.D. / Steegborn, C. / Madsen, A.S. / Olsen, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 53.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.1 KB | Display | ![]() |
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Full document | ![]() | 710.2 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6eo0C ![]() 6eqsC ![]() 4utvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30053.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6DHI5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-BJW / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % / Description: Small cubes |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG8000 0.2 M MgCl2 0.1 M Tris/HCl pH 8.5 0.1 M Glycine PH range: 8.0 - 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 20704 / % possible obs: 99.1 % / Redundancy: 4.1 % / CC1/2: 0.989 / Rrim(I) all: 0.213 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1518 / CC1/2: 0.463 / Rrim(I) all: 1.565 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UTV Resolution: 1.95→49.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.995 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 26.588 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→49.11 Å
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Refine LS restraints |
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