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- PDB-7t39: Co-crystal structure of human PRMT9 in complex with MT221 inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t39 | ||||||
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Title | Co-crystal structure of human PRMT9 in complex with MT221 inhibitor | ||||||
![]() | Protein arginine N-methyltransferase 9 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() protein-arginine omega-N monomethyltransferase activity / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / protein-arginine N-methyltransferase activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. ...Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Co-crystal structure of human PRMT9 in complex with MT221 inhibitor Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, ...Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.2 KB | Display | ![]() |
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PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pdmS S: Starting model for refinement |
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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: 80486.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q6P2P2, type II protein arginine methyltransferase |
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#2: Chemical | ChemComp-EJB / |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % / Mosaicity: 0.26 ° |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 25%(w/v) PEG3350, 0.2M Ammonium Acetate, 0.1M Bis-Tris pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 16704 / % possible obs: 99.6 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.043 / Rrim(I) all: 0.168 / Χ2: 0.848 / Net I/σ(I): 4 / Num. measured all: 241023 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 6PDM Resolution: 2.81→49.06 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / SU B: 19.837 / SU ML: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416 / 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: 121 Å2 / Biso mean: 54.646 Å2 / Biso min: 29.82 Å2
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Refinement step | Cycle: final / Resolution: 2.81→49.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.88 Å / Rfactor Rfree error: 0
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