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- PDB-5lv4: Crystal structure of mouse PRMT6 in complex with inhibitor LH1236 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lv4 | ||||||
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Title | Crystal structure of mouse PRMT6 in complex with inhibitor LH1236 | ||||||
![]() | Protein arginine N-methyltransferase 6 | ||||||
![]() | TRANSFERASE / S-ADENOSYL-L-METHIONINE | ||||||
Function / homology | ![]() histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / histone binding / methylation / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cura, V. / Marechal, N. / Troffer-Charlier, N. / Halby, L. / Arimondo, P. / Bonnefond, L. / Cavarelli, J. | ||||||
![]() | ![]() Title: Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J. ...Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J.C. / Page, P. / Ferroud, C. / Bonnefond, L. / Guianvarc'h, D. / Cavarelli, J. / Arimondo, P.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.2 KB | Display | ![]() |
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PDB format | ![]() | 162.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.9 KB | Display | ![]() |
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Full document | ![]() | 790 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lv2C ![]() 5lv3C ![]() 5lv5C ![]() 5tbhC ![]() 5tbiC ![]() 5tbjC ![]() 4c07S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44597.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6NZB1, type I protein arginine methyltransferase |
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#2: Chemical | ChemComp-78K / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HEPES NaOH pH 8.0 100 mM PEG 6000 10 % MgCl2 200 mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97779 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→41.08 Å / Num. obs: 44207 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.508 / Mean I/σ(I) obs: 1 / CC1/2: 0.474 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4C07 Resolution: 1.66→41.08 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 19.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→41.08 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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