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- PDB-4uu7: Crystal structure of zebrafish Sirtuin 5 in complex with 3-methyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uu7 | ||||||
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Title | Crystal structure of zebrafish Sirtuin 5 in complex with 3-methyl- succinylated 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 | ![]() | 225.2 KB | Display | ![]() |
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PDB format | ![]() | 181.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501 KB | Display | ![]() |
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Full document | ![]() | 509.6 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4utnC ![]() 4utrC ![]() 4utvC ![]() 4utxC ![]() 4utzC ![]() 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: (-0.76013, -0.53985, 0.36161), 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 3S-METHYL-SUCCINYL-LYSINE AND 3R-METHYL-SUCCINYL-LYSINE AT POSITION 4 Source: (synth.) ![]() |
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-Non-polymers , 8 types, 52 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/JO3.gif)
![](data/chem/img/SUH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/JO3.gif)
![](data/chem/img/SUH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-EPE / | #7: Chemical | ChemComp-NA / | #8: Chemical | ChemComp-JO3 / ( | #9: Chemical | ChemComp-SUH / ( | #10: 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: 7.3 / Details: 22% PEG3350, 0.1 M HEPES PH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013 / Details: MIRROR |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 15155 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NYR Resolution: 3→48.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.886 / SU B: 44.939 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MISSING N-TERMINAL RESIDUES OF PROTEIN CHAINS ARE DISORDERED RESIDUES A280 TO A281 ARE DISORDERED. THE PEPTIDE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED MISSING N-TERMINAL RESIDUES OF PROTEIN CHAINS ARE DISORDERED RESIDUES A280 TO A281 ARE DISORDERED. THE PEPTIDE LYSINE IS MODIFIED BY A 3-METHYL-SUCCINYL,WHICH AUTHORS COULD NOT IDENTIFY TO BE S OR R FROM THE DENSITY. RESIDUES CYS274 OF PROTEIN CHAIN A AND B FORM A SS-BRIDGE
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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: 64.248 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.39 Å
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Refine LS restraints |
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