+Open data
-Basic information
Entry | Database: PDB / ID: 7ehz | ||||||
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Title | Structure of human NNMT in complex with macrocyclic peptide 2 | ||||||
Components |
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Keywords | TRANSFERASE / Nicotinamide N-methyltransferase | ||||||
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 / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Hayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. ...Hayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Macrocyclic Peptides as a Novel Class of NNMT Inhibitors: A SAR Study Aimed at Inhibitory Activity in the Cell. Authors: Hayashi, K. / Uehara, S. / Yamamoto, S. / Cary, D.R. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M. / Mikamiyama, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ehz.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ehz.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ehz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ehz_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 7ehz_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 7ehz_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7ehz_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/7ehz ftp://data.pdbj.org/pub/pdb/validation_reports/eh/7ehz | HTTPS FTP |
-Related structure data
Related structure data | 7eguC 7ei2C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28891.164 Da / Num. of mol.: 1 / Mutation: E103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli (E. coli) References: UniProt: P40261, nicotinamide N-methyltransferase |
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#2: Protein/peptide | Mass: 1203.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bicine pH9.0, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 7, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 9031 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.077 / Χ2: 1.041 / Net I/σ(I): 13.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.525
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ROD Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.608 / SU ML: 0.259 / SU R Cruickshank DPI: 0.6682 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.668 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 115.61 Å2 / Biso mean: 49.802 Å2 / Biso min: 29.11 Å2
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Refinement step | Cycle: final / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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