[English] 日本語
Yorodumi- PDB-3ua9: Crystal structure of human tankyrase 2 in complex with a selectiv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ua9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human tankyrase 2 in complex with a selective inhibitor | ||||||
Components | Tankyrase-2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP-RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Narwal, M. / Lehtio, L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Structural basis of selective inhibition of human tankyrases. Authors: Narwal, M. / Venkannagari, H. / Lehtio, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ua9.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ua9.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ua9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ua9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ua9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ua9_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3ua9_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/3ua9 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/3ua9 | HTTPS FTP |
-Related structure data
Related structure data | 3u9hC 3u9yC 3kr7S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 946-1162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase |
---|
-Non-polymers , 5 types, 96 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.33 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M LiSO4, 0.1 M Tris HCl 26 % PEG3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.41 Å / Num. all: 29074 / Num. obs: 29074 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.86 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.18 / Num. unique all: 2072 / % possible all: 96.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KR7 Resolution: 2.15→46.41 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.052 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.373 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→46.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
|