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Yorodumi- PDB-6enx: Zebrafish Sirt5 in complex with stalled bicyclic intermediate of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6enx | ||||||
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Title | Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10 | ||||||
Components | NAD-dependent protein deacylase sirtuin-5, mitochondrial | ||||||
Keywords | SIGNALING PROTEIN / Hydrolase / PTM / inhibitor / Sirtuin | ||||||
Function / homology | Function and homology information 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 / acyl binding / heterocyclic compound binding ...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 / acyl binding / heterocyclic compound binding / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / mitochondrion / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Pannek, M. / Steegborn, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6enx.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6enx.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 6enx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/6enx ftp://data.pdbj.org/pub/pdb/validation_reports/en/6enx | HTTPS FTP |
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-Related structure data
Related structure data | 6eo0C 6eqsC 4utvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Danio rerio (zebrafish) / Gene: sirt5, si:ch211-121a2.1 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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