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Yorodumi- PDB-3mhj: Human tankyrase 2 - catalytic PARP domain in complex with 1-methy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mhj | ||||||
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Title | Human tankyrase 2 - catalytic PARP domain in complex with 1-methyl-3-(trifluoromethyl)-5h-benzo[c][1,8]naphtyridine-6-one | ||||||
Components | Tankyrase-2 | ||||||
Keywords | TRANSFERASE / CATALYTIC FRAGMENT / PARP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / ADP-RIBOSYLATION / ANK REPEAT / CHROMOSOMAL PROTEIN / GLYCOSYLTRANSFERASE / GOLGI APPARATUS / MEMBRANE / MRNA TRANSPORT / NAD / NUCLEUS / PHOSPHORYLATION / PROTEIN TRANSPORT / TELOMERE / TRANSLOCATION / TRANSPORT / WNT-SIGNALLING | ||||||
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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / 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 / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Karlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Schutz, P. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Markova, N. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2012 Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mhj.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mhj.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mhj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3mhj_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3mhj_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 3mhj_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mhj ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mhj | HTTPS FTP |
-Related structure data
Related structure data | 3goyC 3mhkC 3p0nC 3p0pC 3p0qC 3se2C 3smiC 3smjC 3kr7S 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
#1: Protein | Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: C-TERMINAL PARP DOMAIN (UNP RESIDUES 946-1162) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 49.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 17% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009 Details: liquid nitrogen cooled channel-cut silicon monochromator and cylindrical grazing incidence mirror |
Radiation | Monochromator: Si monochromator crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.21 Å / Num. all: 49107 / Num. obs: 49107 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.054 / Rsym value: 0.057 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3582 / Rsym value: 0.429 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KR7 Resolution: 1.8→45.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.062 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.106 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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