[English] 日本語
![](img/lk-miru.gif)
- PDB-4kzu: Crystal structure of human tankyrase 2 in complex with 4' -bromo ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4kzu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human tankyrase 2 in complex with 4' -bromo flavone | ||||||
![]() | (Tankyrase-2) x 2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / TRANSFERASE / ADP-RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Narwal, M. / Haikarainen, T. / Lehtio, L. | ||||||
![]() | ![]() Title: Discovery of tankyrase inhibiting flavones with increased potency and isoenzyme selectivity. Authors: Narwal, M. / Koivunen, J. / Haikarainen, T. / Obaji, E. / Legala, O.E. / Venkannagari, H. / Joensuu, P. / Pihlajaniemi, T. / Lehtio, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 987.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 989.4 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bs4C ![]() 4kzlC ![]() 4kzqC ![]() 4l09C ![]() 4l0bC ![]() 4l0iC ![]() 4l0sC ![]() 4l0tC ![]() 4l0vC ![]() 4l10C ![]() 4l2fC ![]() 4l2gC ![]() 4l2kC ![]() 4l31C ![]() 4l32C ![]() 4l33C ![]() 4l34C ![]() 3u9hS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 21824.545 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 946-1113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 5493.216 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 1114-1162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 206 molecules ![](data/chem/img/A73.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Li2SO4, 0.1 M Tris HCl 24 % PEG3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Pilatus 2M / Detector: PIXEL / Date: Feb 9, 2013 |
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.9 Å / Num. obs: 31373 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.65 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 6.53 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.44 / Num. unique all: 2120 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3U9H Resolution: 2.1→29.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.885 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.159 / 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: 27.846 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
|