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Yorodumi- PDB-7bkg: Co-crystal structure of Human Nicotinamide N-methyltransferase (N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bkg | ||||||
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Title | Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the tricyclic inhibitor (2) | ||||||
Components | Nicotinamide N-methyltransferase | ||||||
Keywords | TRANSFERASE / Methyl Transferase / drug discovery / Inhibitor complex / Nicotinamide / metabolic disorders | ||||||
Function / homology | Function and homology information pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / NAD biosynthesis via nicotinamide riboside salvage pathway / positive regulation of protein deacetylation / Methylation / Nicotinamide salvaging / : ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / NAD biosynthesis via nicotinamide riboside salvage pathway / positive regulation of protein deacetylation / Methylation / Nicotinamide salvaging / : / animal organ regeneration / positive regulation of gluconeogenesis / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.326 Å | ||||||
Authors | Schreuder, H.A. / Liesum, A. | ||||||
Citation | Journal: Molecules / Year: 2021 Title: Novel Inhibitors of Nicotinamide- N -Methyltransferase for the Treatment of Metabolic Disorders. Authors: Kannt, A. / Rajagopal, S. / Hallur, M.S. / Swamy, I. / Kristam, R. / Dhakshinamoorthy, S. / Czech, J. / Zech, G. / Schreuder, H. / Ruf, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bkg.cif.gz | 231.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bkg.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bkg_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7bkg_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7bkg_validation.xml.gz | 46.1 KB | Display | |
Data in CIF | 7bkg_validation.cif.gz | 64.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/7bkg ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bkg | HTTPS FTP |
-Related structure data
Related structure data | 7bleC 7nbjC 7nbmC 7nbqC 2iipS 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 31466.033 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE References: UniProt: P40261, nicotinamide N-methyltransferase #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-U0Z / #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: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Human NNMT was crystallized using the following conditions: A protein solution with 6 mg/ml NNMT, 50 mM Tris/HCL, pH 8.0, 1 mM DTT, 86uM S-Adenosyl-L-Homocysteine (SAH), 0.95mM ligand and 5% ...Details: Human NNMT was crystallized using the following conditions: A protein solution with 6 mg/ml NNMT, 50 mM Tris/HCL, pH 8.0, 1 mM DTT, 86uM S-Adenosyl-L-Homocysteine (SAH), 0.95mM ligand and 5% v/v glycerol was equilibrated at room temperature in a hanging drop setup against 2.2 M ammonium sulfate with 0.1 M HEPES/Na, pH 7.6. Small crystal appeared after 1-2 weeks. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.326→106.079 Å / Num. obs: 45768 / % possible obs: 97.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Rrim(I) all: 0.084 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.326→2.334 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 447 / Rpim(I) all: 0.348 / Rrim(I) all: 0.492 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2iip Resolution: 2.326→57.69 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.393 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.403 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.245
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Displacement parameters | Biso mean: 33.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.326→57.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.34 Å
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