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Yorodumi- PDB-9grv: Crystal structure of HRP-2 PWWP domain in complex with compound 37 -
+Open data
-Basic information
Entry | Database: PDB / ID: 9grv | ||||||||||||
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Title | Crystal structure of HRP-2 PWWP domain in complex with compound 37 | ||||||||||||
Components | Hepatoma-derived growth factor-related protein 2 | ||||||||||||
Keywords | GENE REGULATION / Inhibitor | ||||||||||||
Function / homology | Function and homology information H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / positive regulation of cell growth ...H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||||||||
Authors | Osipov, E.M. / Paulovcakova, T. / Beelen, S. / Vantieghem, T. / Strelkov, S.V. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2024 Title: Rational fragment-based design of compounds targeting the PWWP domain of the HRP family. Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / ...Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / Veverka, V. / Verwilst, P. / Van Aerschot, A. / Debyser, Z. / Strelkov, S.V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9grv.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9grv.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 9grv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9grv_validation.pdf.gz | 772.9 KB | Display | wwPDB validaton report |
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Full document | 9grv_full_validation.pdf.gz | 776.9 KB | Display | |
Data in XML | 9grv_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 9grv_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/9grv ftp://data.pdbj.org/pub/pdb/validation_reports/gr/9grv | HTTPS FTP |
-Related structure data
Related structure data | 7hg0C 7hg1C 7hg2C 7hg3C 7hg4C 7hg5C 7hg6C 7hg7C 7hg8C 7hg9C 7hgaC 7hgbC 7hgcC 7hgdC 7hgeC 7hgfC 7hggC 7hghC 7hgiC 7hgjC 7hgkC 7hglC 7hgmC 7hgnC 7hgoC 7hgpC 7hgqC 7hgrC 7hgsC 7hgtC 7hguC 7hgvC 7hgwC 7hgxC 7hgyC 7hgzC 7hh0C 7hh1C 7hh2C 7hh3C 7hh4C 7hh5C 7hh6C 7hh7C 7hh8C 7hh9C 7hhaC 7hhbC 7hhcC 7hhdC 7hheC 7hhfC 7hhgC 7hhhC 7hhiC 7hhjC 7hhkC 7hhlC 7hhmC 7hhnC 7hhoC 7hhpC 7hhqC 7hhrC 9g91C 9g94C 9g96C 9grsC 9grtC 9gruC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 10714.236 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z4V5 #2: Chemical | ChemComp-HHN / | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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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: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 2.2 M ammonium sulfate, 0.2 M ammonium iodide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91165 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91165 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→78.83 Å / Num. obs: 40936 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Χ2: 0.67 / Net I/σ(I): 14.6 / Num. measured all: 550814 |
Reflection shell | Resolution: 1.55→1.64 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 1.884 / Num. measured all: 80779 / Num. unique obs: 5839 / CC1/2: 0.679 / Rpim(I) all: 0.519 / Rrim(I) all: 1.955 / Χ2: 0.34 / Net I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→40.52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→40.52 Å
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Refine LS restraints |
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LS refinement shell |
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