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Yorodumi- PDB-6eqs: Human Sirt5 in complex with stalled peptidylimidate intermediate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eqs | ||||||
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Title | Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29 | ||||||
Components | NAD-dependent protein deacylase sirtuin-5, mitochondrial | ||||||
Keywords | SIGNALING PROTEIN / Hydrolase / PTM / inhibitor | ||||||
Function / homology | Function and homology information protein demalonylation / protein deglutarylation / 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 protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / 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 protein lysine deacetylase activity / protein deacetylation / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / epigenetic regulation of gene expression / response to nutrient levels / mitochondrion organization / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / transferase activity / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 | 6eqs.cif.gz | 522.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eqs.ent.gz | 430.6 KB | Display | PDB format |
PDBx/mmJSON format | 6eqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eqs_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6eqs_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6eqs_validation.xml.gz | 63.5 KB | Display | |
Data in CIF | 6eqs_validation.cif.gz | 88.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/6eqs ftp://data.pdbj.org/pub/pdb/validation_reports/eq/6eqs | HTTPS FTP |
-Related structure data
Related structure data | 6enxC 6eo0C 3riyS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29913.078 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 6 types, 1119 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BV8 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-BU2 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % / Description: rods and rod-bundles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 30% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol PH range: 5.0 - 6.0 |
-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: 1.32→43.77 Å / Num. obs: 227669 / % possible obs: 91.5 % / Redundancy: 2 % / CC1/2: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.32→1.4 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 35569 / CC1/2: 0.723 / Rrim(I) all: 0.959 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RIY Resolution: 1.32→43.77 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.488 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / 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: 21.373 Å2
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Refinement step | Cycle: 1 / Resolution: 1.32→43.77 Å
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Refine LS restraints |
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