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Yorodumi- PDB-4qqn: Protein arginine methyltransferase 3 in complex with compound MTV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qqn | ||||||
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Title | Protein arginine methyltransferase 3 in complex with compound MTV044246 | ||||||
Components | PRMT3 protein | ||||||
Keywords | TRANSFERASE / PRMT3 / Structural Genomics / Structural Genomics Consortium / SGC / Epigenetics | ||||||
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 / histone methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines ...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 / histone methyltransferase activity / Protein methylation / negative regulation of protein ubiquitination / methyltransferase activity / RMTs methylate histone arginines / ribosome binding / methylation / chromatin remodeling / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Dong, A. / Dobrovetsky, E. / Tempel, W. / He, H. / Zhao, K. / Smil, D. / Landon, M. / Luo, X. / Chen, Z. / Dai, M. ...Dong, A. / Dobrovetsky, E. / Tempel, W. / He, H. / Zhao, K. / Smil, D. / Landon, M. / Luo, X. / Chen, Z. / Dai, M. / Yu, Z. / Lin, Y. / Zhang, H. / Zhao, K. / Schapira, M. / Brown, P.J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Discovery of Potent and Selective Allosteric Inhibitors of Protein Arginine Methyltransferase 3 (PRMT3). Authors: Kaniskan, H.U. / Eram, M.S. / Zhao, K. / Szewczyk, M.M. / Yang, X. / Schmidt, K. / Luo, X. / Xiao, S. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Li, F. / Dobrovetsky, E. / Smil, D. / Min, S.J. ...Authors: Kaniskan, H.U. / Eram, M.S. / Zhao, K. / Szewczyk, M.M. / Yang, X. / Schmidt, K. / Luo, X. / Xiao, S. / Dai, M. / He, F. / Zang, I. / Lin, Y. / Li, F. / Dobrovetsky, E. / Smil, D. / Min, S.J. / Lin-Jones, J. / Schapira, M. / Atadja, P. / Li, E. / Barsyte-Lovejoy, D. / Arrowsmith, C.H. / Brown, P.J. / Liu, F. / Yu, Z. / Vedadi, M. / Jin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qqn.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qqn.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qqn_validation.pdf.gz | 897 KB | Display | wwPDB validaton report |
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Full document | 4qqn_full_validation.pdf.gz | 895.3 KB | Display | |
Data in XML | 4qqn_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4qqn_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/4qqn ftp://data.pdbj.org/pub/pdb/validation_reports/qq/4qqn | HTTPS FTP |
-Related structure data
Related structure data | 4hsgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38281.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT3 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) Strain (production host): BL21(DE3)-codon plus RIL(Stratagen) References: UniProt: Q8WUV3, UniProt: O60678*PLUS |
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-Non-polymers , 5 types, 171 molecules
#2: Chemical | ChemComp-3BQ / | ||
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#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2 M MgCl2, 0.1 M Tris HCL pH8.5, vapor diffusion hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→50 Å / Num. obs: 27071 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.035 / Net I/σ(I): 25.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HSG Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.614 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 75.44 Å2 / Biso mean: 33.67 Å2 / Biso min: 21.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.078→2.132 Å / Total num. of bins used: 20
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