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Open data
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Basic information
Entry | Database: PDB / ID: 7uy1 | ||||||
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Title | HUMAN PRMT5:MEP50 COMPLEX WITH MTA and Fragment 5 Bound | ||||||
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![]() | TRANSFERASE / MTAP / methyl transferase / fragment-based lead discovery / FBDD | ||||||
Function / homology | ![]() positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / methylosome / protein-arginine N-methyltransferase activity / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / regulation of mitotic nuclear division / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / liver regeneration / DNA-templated transcription termination / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gunn, R.J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits. Authors: Smith, C.R. / Kulyk, S. / Ahmad, M.U.D. / Arkhipova, V. / Christensen, J.G. / Gunn, R.J. / Ivetac, A. / Ketcham, J.M. / Kuehler, J. / Lawson, J.D. / Thomas, N.C. / Wang, X. / Marx, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.1 KB | Display | ![]() |
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PDB format | ![]() | 155.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.2 KB | Display | ![]() |
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Full document | ![]() | 751 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 44.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uyfC ![]() 7zupC ![]() 7zuqC ![]() 7zuuC ![]() 7zuyC ![]() 7zv2C ![]() 7zvlC ![]() 7zvuC ![]() 8csgC ![]() 8ctbC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 73763.625 Da / Num. of mol.: 1 / Fragment: FULL LENGTH Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14744, type II protein arginine methyltransferase |
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#2: Protein | Mass: 37862.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 7 types, 57 molecules ![](data/chem/img/PJ0.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PJ0 / | ||||||
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#4: Chemical | ChemComp-MTA / | ||||||
#5: Chemical | ChemComp-SO4 / | ||||||
#6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: PEG/Buffer/Salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→45.96 Å / Num. obs: 34054 / % possible obs: 93.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.66→2.91 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.44 / Num. unique obs: 8304 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.66→45.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 38.325 / SU ML: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.801 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 130.65 Å2 / Biso mean: 52 Å2 / Biso min: 33.88 Å2
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Refinement step | Cycle: final / Resolution: 2.66→45.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.729 Å / Rfactor Rfree error: 0
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