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- PDB-4l09: Crystal structure of human tankyrase 2 in complex with 4-(4-oxo-4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l09 | ||||||
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Title | Crystal structure of human tankyrase 2 in complex with 4-(4-oxo-4H-chromen-2-yl)benzoic acid | ||||||
![]() | (Tankyrase-2![]() | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() XAV939 stabilizes AXIN / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.8 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bs4C ![]() 4kzlC ![]() 4kzqC ![]() 4kzuC ![]() 4l0bC ![]() 4l0iC ![]() 4l0sC ![]() 4l0tC ![]() 4l0vC ![]() 4l10C ![]() 4l2fC ![]() 4l2gC ![]() 4l2kC ![]() 4l31C ![]() 4l32C ![]() 4l33C ![]() 4l34C ![]() 3u9hS 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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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.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 259 molecules ![](data/chem/img/1UR.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 / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.59 % |
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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 |
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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![]() |
Reflection | Resolution: 2.05→29.55 Å / Num. obs: 33649 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.73 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.51 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.76 / Num. unique all: 2450 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3U9H Resolution: 2.05→29.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.066 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.776 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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