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Open data
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Basic information
Entry | Database: PDB / ID: 7pph | ||||||
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Title | CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH Compound 10 | ||||||
![]() | Nicotinamide phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / SMALL MOLECULE INHIBITOR / NMPRTASE | ||||||
Function / homology | ![]() nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hillig, R.C. | ||||||
Funding support | 1items
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![]() | ![]() Title: A Novel NAMPT Inhibitor-Based Antibody-Drug Conjugate Payload Class for Cancer Therapy. Authors: Bohnke, N. / Berger, M. / Griebenow, N. / Rottmann, A. / Erkelenz, M. / Hammer, S. / Berndt, S. / Gunther, J. / Wengner, A.M. / Stelte-Ludwig, B. / Mahlert, C. / Greven, S. / Dietz, L. / ...Authors: Bohnke, N. / Berger, M. / Griebenow, N. / Rottmann, A. / Erkelenz, M. / Hammer, S. / Berndt, S. / Gunther, J. / Wengner, A.M. / Stelte-Ludwig, B. / Mahlert, C. / Greven, S. / Dietz, L. / Jorissen, H. / Barak, N. / Bomer, U. / Hillig, R.C. / Eberspaecher, U. / Weiske, J. / Giese, A. / Mumberg, D. / Nising, C.F. / Weinmann, H. / Sommer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394.9 KB | Display | ![]() |
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PDB format | ![]() | 320.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 43.6 KB | Display | |
Data in CIF | ![]() | 66.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ppeC ![]() 7ppfC ![]() 7ppgC ![]() 7ppiC ![]() 2gvjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 9 - 482 / Label seq-ID: 10 - 483
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Components
#1: Protein | Mass: 55651.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal Gly is a cloning artifact, stems from TEV cleavage site Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % Description: crescent-shaped, plate-shaped crystals, often with very uneven surfaces |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 1 microliter of protein mixed with 1 microliter of reservoir buffer (27-31% PEG 3350 (w/v), 200 mM NaCl, 100 mM sodium dihydrogen phosphate pH 7.6) incubated for 5 min, then streak seeded ...Details: 1 microliter of protein mixed with 1 microliter of reservoir buffer (27-31% PEG 3350 (w/v), 200 mM NaCl, 100 mM sodium dihydrogen phosphate pH 7.6) incubated for 5 min, then streak seeded (with crystals obtained previously under identical conditions). Ligand added prior to crystallization (2 MILLIMOLAR FROM 100 MILLIMOLAR STOCK IN DMSO) and incubated for 1.5 h at 277 K. CRYO BUFFER consisted of RESERVOIR supplemented WITH 2 MILLIMOLAR INHIBITOR AND 10% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→46.53 Å / Num. obs: 104111 / % possible obs: 96.8 % / Redundancy: 4.19 % / Biso Wilson estimate: 22.92 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.197 / Rsym value: 0.172 / Net I/σ(I): 6.66 |
Reflection shell | Resolution: 1.74→1.85 Å / Redundancy: 4.17 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 15703 / CC1/2: 0.409 / Rrim(I) all: 0.914 / Rsym value: 0.802 / % possible all: 90.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GVJ Resolution: 1.74→46.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.093 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 96.79 Å2 / Biso mean: 19.499 Å2 / Biso min: 5.13 Å2
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Refinement step | Cycle: final / Resolution: 1.74→46.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 15443 / 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: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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