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Yorodumi- PDB-4k4f: Co-crystal structure of TNKS1 with compound 18 [4-[(4S)-5,5-dimet... -
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-Basic information
Entry | Database: PDB / ID: 4k4f | ||||||
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Title | Co-crystal structure of TNKS1 with compound 18 [4-[(4S)-5,5-dimethyl-2-oxo-4-phenyl-1,3-oxazolidin-3-yl]-N-(quinolin-8-yl)benzamide] | ||||||
Components | Tankyrase-1 | ||||||
Keywords | Transferase/Transferase Inhibitor / PARP / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / 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 ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / 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 / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / spindle assembly / nuclear pore / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huang, X. / Bregman, H. / Wilson, C. / DiMauro, E. / Gunaydin, H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Discovery of novel, induced-pocket binding oxazolidinones as potent, selective, and orally bioavailable tankyrase inhibitors. Authors: Bregman, H. / Chakka, N. / Guzman-Perez, A. / Gunaydin, H. / Gu, Y. / Huang, X. / Berry, V. / Liu, J. / Teffera, Y. / Huang, L. / Egge, B. / Mullady, E.L. / Schneider, S. / Andrews, P.S. / ...Authors: Bregman, H. / Chakka, N. / Guzman-Perez, A. / Gunaydin, H. / Gu, Y. / Huang, X. / Berry, V. / Liu, J. / Teffera, Y. / Huang, L. / Egge, B. / Mullady, E.L. / Schneider, S. / Andrews, P.S. / Mishra, A. / Newcomb, J. / Serafino, R. / Strathdee, C.A. / Turci, S.M. / Wilson, C. / Dimauro, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k4f.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k4f.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/4k4f ftp://data.pdbj.org/pub/pdb/validation_reports/k4/4k4f | HTTPS FTP |
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-Related 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: 25041.332 Da / Num. of mol.: 2 / Fragment: PARP catalytic, UNP residues 1104-1314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95271, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Chemical | |
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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: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2/0.5 M LiCl, 7.5-20% PEG6K, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→41.44 Å / Num. obs: 13114 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.175 |
Reflection shell | Resolution: 2.75→2.85 Å / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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