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- PDB-4utz: Crystal structure of zebrafish Sirtuin 5 in complex with adipoyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4utz | ||||||
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Title | Crystal structure of zebrafish Sirtuin 5 in complex with adipoylated CPS1-peptide | ||||||
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![]() | HYDROLASE / SIRTUIN 5 / REGULATORY ENZYME / DEACYLASE / MITOCHONDRIAL / ROSSMANN-FOLD / ZINC-BINDING | ||||||
Function / homology | ![]() carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process / modified amino acid binding / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / homocysteine metabolic process / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / NAD-dependent histone deacetylase activity / cellular response to fibroblast growth factor stimulus / response to growth hormone / glutamate binding / response to food / midgut development / nitric oxide metabolic process / heterocyclic compound binding / response to zinc ion / glutamine metabolic process / response to dexamethasone / cellular response to glucagon stimulus / mitochondrial nucleoid / response to amine / response to starvation / potassium ion binding / NAD+ binding / acyl binding / small molecule binding / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to cAMP / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to toxic substance / phospholipid binding / vasodilation / transferase activity / endopeptidase activity / response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / mitochondrion / zinc ion binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pannek, M. / Gertz, M. / Steegborn, C. | ||||||
![]() | ![]() Title: Chemical Probing of the Human Sirtuin 5 Active Site Reveals its Substrate Acyl Specificity and Peptide-Based Inhibitors. Authors: Roessler, C. / Nowak, T. / Pannek, M. / Gertz, M. / Nguyen, G.T. / Scharfe, M. / Born, I. / Sippl, W. / Steegborn, C. / Schutkowski, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.4 KB | Display | ![]() |
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PDB format | ![]() | 178.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.7 KB | Display | ![]() |
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Full document | ![]() | 492.2 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4utnC ![]() 4utrC ![]() 4utvC ![]() 4utxC ![]() 4uu7C ![]() 4uu8C ![]() 4uuaC ![]() 4uubC ![]() 2nyrS C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.75065, -0.54745, -0.36989), Vector: |
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Components
-Protein / Protein/peptide , 2 types, 3 molecules ABD
#1: Protein | Mass: 30423.785 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE, RESIDUES 30-298 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 #2: Protein/peptide | | Mass: 969.112 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 524-531 / Source method: obtained synthetically Details: BENZOYLATED GLYCINE AT POSITION 1 ADIPOYLATED LYSINE AT POSITION 4 Source: (synth.) ![]() |
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-Non-polymers , 7 types, 37 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/0L1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/0L1.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-EDO / | #8: Chemical | ChemComp-0L1 / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 22% PEG3350, 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91705 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 11477 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.33 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NYR Resolution: 3.3→48.41 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.882 / SU B: 58.47 / SU ML: 0.46 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED STRUCTURE WAS REFINED USING PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. MURSHUDOV 2012 LOW RESOLUTION ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED STRUCTURE WAS REFINED USING PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. MURSHUDOV 2012 LOW RESOLUTION REFINEMENT TOOLS IN REFMAC5. ACTA CRYST. D. MISSING N-TERMINAL RESIDUES ARE DISORDERED RESIDUES A280 TO A281 ARE DISORDERED RESIDUES B 276 TO B2800 ARE DISORDERED
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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: 67.559 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→48.41 Å
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Refine LS restraints |
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