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Yorodumi- PDB-4hlm: Crystal structure of Tankyrase 2 in complex with 3',4'-Dihydroxyf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hlm | ||||||
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Title | Crystal structure of Tankyrase 2 in complex with 3',4'-Dihydroxyflavone | ||||||
Components | (Tankyrase-2) x 2 | ||||||
Keywords | TRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP-RIBOSYLATION | ||||||
Function / homology | Function and homology information XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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: 1.95 Å | ||||||
Authors | Narwal, M. / Haikarainen, T. / Lehtio, L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Screening and structural analysis of flavones inhibiting tankyrases. Authors: Narwal, M. / Haikarainen, T. / Fallarero, A. / Vuorela, P.M. / Lehtio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hlm.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hlm.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hlm_validation.pdf.gz | 972.2 KB | Display | wwPDB validaton report |
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Full document | 4hlm_full_validation.pdf.gz | 974.4 KB | Display | |
Data in XML | 4hlm_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4hlm_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hlm ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hlm | HTTPS FTP |
-Related structure data
Related structure data | 4hkiC 4hkkC 4hknC 4hl5C 4hlfC 4hlgC 4hlhC 4hlkC 4hmhC 3u9hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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.) 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 #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.) 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 |
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-Non-polymers , 5 types, 264 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHOR STATES THAT THE BACTERIAL EXPRESSED TANKYRASE 2 CATALYTIC DOMAIN (UNP RESIDUES 946-1162) WAS ...AUTHOR STATES THAT THE BACTERIAL EXPRESSED TANKYRASE 2 CATALYTIC DOMAIN (UNP RESIDUES 946-1162) WAS CLEAVED WITH CHYMOTRYPS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M LiSO4, 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2012 |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.86 Å / Num. all: 39020 / Num. obs: 39020 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.86 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.47 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 4.88 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 4.07 / Num. unique all: 2862 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U9H Resolution: 1.95→19.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.955 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.129 / 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: 22.348 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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