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Yorodumi- PDB-5yji: Co-crystal structure of Mouse Nicotinamide N-methyltransferase (N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yji | ||||||
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Title | Co-crystal structure of Mouse Nicotinamide N-methyltransferase (NNMT) with small molecule analog of Nicotinamide | ||||||
Components | Nicotinamide N-methyltransferase | ||||||
Keywords | TRANSFERASE / NNMT / NA / MNA / T2D | ||||||
Function / homology | Function and homology information Methylation / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Nicotinamide salvaging / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / response to organonitrogen compound / methylation ...Methylation / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Nicotinamide salvaging / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / response to organonitrogen compound / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Birudukota, S. / Swaminathan, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Hallur, M.S. / Rajagopal, S. / Ruf, S. / Dhakshinamoorthy, S. / Kannt, A. / Gosu, R. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: A small molecule inhibitor of Nicotinamide N-methyltransferase for the treatment of metabolic disorders. Authors: Kannt, A. / Rajagopal, S. / Kadnur, S.V. / Suresh, J. / Bhamidipati, R.K. / Swaminathan, S. / Hallur, M.S. / Kristam, R. / Elvert, R. / Czech, J. / Pfenninger, A. / Rudolph, C. / Schreuder, ...Authors: Kannt, A. / Rajagopal, S. / Kadnur, S.V. / Suresh, J. / Bhamidipati, R.K. / Swaminathan, S. / Hallur, M.S. / Kristam, R. / Elvert, R. / Czech, J. / Pfenninger, A. / Rudolph, C. / Schreuder, H. / Chandrasekar, D.V. / Mane, V.S. / Birudukota, S. / Shaik, S. / Zope, B.R. / Burri, R.R. / Anand, N.N. / Thakur, M.K. / Singh, M. / Parveen, R. / Kandan, S. / Mullangi, R. / Yura, T. / Gosu, R. / Ruf, S. / Dhakshinamoorthy, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yji.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yji.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 5yji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/5yji ftp://data.pdbj.org/pub/pdb/validation_reports/yj/5yji | HTTPS FTP |
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-Related structure data
Related structure data | 5yjfC 3rodS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31800.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nnmt / Production host: Escherichia coli (E. coli) References: UniProt: O55239, nicotinamide N-methyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.35M Sodium thiocynate, 20% PEG 3350, with 0.01M TMAO as additive |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→47.36 Å / Num. obs: 37822 / % possible obs: 99.6 % / Redundancy: 9.5 % / Net I/σ(I): 14.2 |
Reflection shell | Highest resolution: 1.99 Å / Rmerge(I) obs: 0.52 / Rpim(I) all: 0.182 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ROD Resolution: 1.99→47.36 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.213 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.797 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→47.36 Å
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Refine LS restraints |
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