[English] 日本語
Yorodumi- PDB-6fkz: Crystal structure of zebrafish Sirtuin 5 in complex with 3-(pheny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fkz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of zebrafish Sirtuin 5 in complex with 3-(phenylthio)succinyl-CPS1 peptide | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / Sirtuin 5 / Inhibitor / Deacylase | ||||||
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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Pannek, M. / Steegborn, C. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Potent and Selective Inhibitors of Human Sirtuin 5. Authors: Kalbas, D. / Liebscher, S. / Nowak, T. / Meleshin, M. / Pannek, M. / Popp, C. / Alhalabi, Z. / Bordusa, F. / Sippl, W. / Steegborn, C. / Schutkowski, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fkz.cif.gz | 225.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fkz.ent.gz | 181.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fkz ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fkz | HTTPS FTP |
---|
-Related structure data
Related structure data | 6fkyC 6flgC 4utvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 35 - 297 / Label seq-ID: 14 - 276
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31495.012 Da / Num. of mol.: 2 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 |
---|
-Protein/peptide , 2 types, 2 molecules EH
#2: Protein/peptide | Mass: 1210.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
---|---|
#3: Protein/peptide | Mass: 1176.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 4 types, 48 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-EPE / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.4, 20% PEG3350 / PH range: 7.2 - 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2016 / Details: MIRRORS |
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: 3.3→50 Å / Num. obs: 10989 / % possible obs: 99.5 % / Redundancy: 4.1 % / CC1/2: 0.938 / Rrim(I) all: 0.393 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3.3→3.39 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1671 / CC1/2: 0.496 / Rrim(I) all: 1.218 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4utv Resolution: 3.3→48.73 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.902 / SU B: 79.323 / SU ML: 0.596 / Cross valid method: THROUGHOUT / ESU R Free: 0.605 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 61.295 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.3→48.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|