+Open data
-Basic information
Entry | Database: PDB / ID: 7nr4 | ||||||
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Title | X-RAY STRUCTURE OF PRMT6 IN COMPLEX WITH indazole type inhibitor | ||||||
Components | Protein arginine N-methyltransferase 6 | ||||||
Keywords | TRANSFERASE / Protein Arginine Methyl Transferase 6 | ||||||
Function / homology | Function and homology information histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / base-excision repair / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / RMTs methylate histone arginines / cellular senescence / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Steuber, H. | ||||||
Citation | Journal: Chemmedchem / Year: 2021 Title: Rational Design and Synthesis of Selective PRMT4 Inhibitors: A New Chemotype for Development of Cancer Therapeutics*. Authors: Sutherland, M. / Li, A. / Kaghad, A. / Panagopoulos, D. / Li, F. / Szewczyk, M. / Smil, D. / Scholten, C. / Bouche, L. / Stellfeld, T. / Arrowsmith, C.H. / Barsyte, D. / Vedadi, M. / ...Authors: Sutherland, M. / Li, A. / Kaghad, A. / Panagopoulos, D. / Li, F. / Szewczyk, M. / Smil, D. / Scholten, C. / Bouche, L. / Stellfeld, T. / Arrowsmith, C.H. / Barsyte, D. / Vedadi, M. / Hartung, I.V. / Steuber, H. / Britton, R. / Santhakumar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nr4.cif.gz | 288.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nr4.ent.gz | 231 KB | Display | PDB format |
PDBx/mmJSON format | 7nr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/7nr4 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/7nr4 | HTTPS FTP |
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-Related structure data
Related structure data | 5egsS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42074.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT6, HRMT1L6 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-UO2 / ( #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: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25 % PEG 1500; 0.1 M MMT pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→49.05 Å / Num. obs: 109556 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.997 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.03→2.15 Å / Num. unique obs: 17601 / CC1/2: 0.497 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EGS Resolution: 2.03→49.05 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.262 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.158 / 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: 113.74 Å2 / Biso mean: 38.206 Å2 / Biso min: 19.96 Å2
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Refinement step | Cycle: final / Resolution: 2.03→49.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.082 Å / Rfactor Rfree error: 0
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