+Open data
-Basic information
Entry | Database: PDB / ID: 7q8t | ||||||
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Title | Crystal structure of NAMPT bound to ligand TSY535(compound 9a) | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Inhibitor / Activator / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of lung blood pressure / Nicotinamide salvaging / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthetic process / heterocyclic compound binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of cellular senescence / negative regulation of autophagy / cytokine activity ...regulation of lung blood pressure / Nicotinamide salvaging / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthetic process / heterocyclic compound binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of cellular senescence / negative regulation of autophagy / cytokine activity / positive regulation of smooth muscle cell proliferation / microglial cell activation / circadian regulation of gene expression / circadian rhythm / cell junction / nuclear speck / nucleotide binding / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Kraemer, A. / Tang, S. / Butterworth, S. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acta Pharm Sin B / Year: 2023 Title: Chemistry-led investigations into the mode of action of NAMPT activators, resulting in the discovery of non-pyridyl class NAMPT activators. Authors: Tang, S. / Garzon Sanz, M. / Smith, O. / Kramer, A. / Egbase, D. / Caton, P.W. / Knapp, S. / Butterworth, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q8t.cif.gz | 212.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q8t.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 7q8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/7q8t ftp://data.pdbj.org/pub/pdb/validation_reports/q8/7q8t | HTTPS FTP |
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-Related structure data
Related structure data | 2gvlS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 8 - 483 / Label seq-ID: 14 - 489
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-Components
#1: Protein | Mass: 56152.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nampt, Pbef1 / Production host: Escherichia coli (E. coli) References: UniProt: Q99KQ4, nicotinamide phosphoribosyltransferase #2: Chemical | #3: Chemical | #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: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 22% PEG 3350 0.1M NaCl 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.99 Å / Num. obs: 54298 / % possible obs: 93.1 % / Redundancy: 2.7 % / CC1/2: 0.964 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.111 / Rrim(I) all: 0.197 / Net I/σ(I): 5.8 / Num. measured all: 148915 / Scaling rejects: 587 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.443 / Num. unique obs: 4629 / CC1/2: 0.763 / Rpim(I) all: 0.314 / Rrim(I) all: 0.546 / % possible all: 96.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GVL Resolution: 2.15→47.03 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.592 / SU ML: 0.194 / SU R Cruickshank DPI: 0.3377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.238 / 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: 67.92 Å2 / Biso mean: 16.858 Å2 / Biso min: 3.94 Å2
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Refinement step | Cycle: final / Resolution: 2.15→47.03 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 15160 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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