+Open data
-Basic information
Entry | Database: PDB / ID: 8g2g | ||||||
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Title | Crystal structure of PRMT3 with compound YD1113 | ||||||
Components | Protein arginine N-methyltransferase 3 | ||||||
Keywords | TRANSFERASE / PRMT3 / YD1113 | ||||||
Function / homology | Function and homology information protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding ...protein-arginine omega-N monomethyltransferase activity / negative regulation of retinoic acid biosynthetic process / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein-arginine N-methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding / methylation / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Song, X. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Deng, Y. / Huang, R. / Min, J. | ||||||
Funding support | 1items
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Citation | Journal: Acta Pharm Sin B / Year: 2023 Title: A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors. Authors: Deng, Y. / Song, X. / Iyamu, I.D. / Dong, A. / Min, J. / Huang, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g2g.cif.gz | 140 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g2g.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 8g2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/8g2g ftp://data.pdbj.org/pub/pdb/validation_reports/g2/8g2g | HTTPS FTP |
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-Related structure data
Related structure data | 8g2fC 8g2hC 8g2iC 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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Unit cell |
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-Components
#1: Protein | Mass: 38281.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT3, HRMT1L3 / Production host: Escherichia coli (E. coli) References: UniProt: O60678, type I protein arginine methyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 53430 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.075 / Χ2: 0.997 / Net I/av σ(I): 25.2 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2619 / CC1/2: 0.693 / CC star: 0.905 / Χ2: 0.811 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→47.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.121 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.148 / 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: 34.889 Å2
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Refinement step | Cycle: 1 / Resolution: 2.02→47.96 Å
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