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Yorodumi- PDB-7wmc: Crystal structure of macrocyclic peptide 1 bound to human Nicotin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wmc | |||||||||
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Title | Crystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase | |||||||||
Components |
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Keywords | TRANSFERASE / Nicotinamide N-methyltransferase | |||||||||
Function / homology | Function and homology information pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / 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 N-methyltransferase activity / nicotinamide metabolic process / 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) unidentified (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | |||||||||
Authors | Yoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y. | |||||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. Authors: Yoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wmc.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wmc.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wmc_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 7wmc_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 7wmc_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 7wmc_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wmc ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wmc | HTTPS FTP |
-Related structure data
Related structure data | 7wmtC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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.: 2 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 #2: Protein/peptide | Mass: 1211.415 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: synthetic construct (others) #3: 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: 2.62 Å3/Da / Density % sol: 53.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 15%(w/v)PEG3350, 0.1 M sodium malonate pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→75.87 Å / Num. obs: 22069 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.035 / Rrim(I) all: 0.12 / Χ2: 1.084 / Net I/σ(I): 8.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.318
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→75.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.843 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.283 / 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: 99.26 Å2 / Biso mean: 32.468 Å2 / Biso min: 10.49 Å2
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Refinement step | Cycle: final / Resolution: 2.55→75.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.615 Å / Rfactor Rfree error: 0
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