+Open data
-Basic information
Entry | Database: PDB / ID: 6azj | ||||||
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Title | Crystal Structure of human NAMPT in complex with NVP-LQN520 | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Weihofen, W.A. / Thigale, S. | ||||||
Citation | Journal: To Be Published Title: Identification and structure based design of cellularly active cyclo-propyl carboxamide Nicotinamide phosphoribosyltransferase (NAMPT) inhibitors Authors: Palacios, D. / Meredith, E. / Kawanami, T. / Adams, C. / Chen, X. / Darsigny, V. / Geno, E. / Palermo, M. / Guy, C. / Hewett, J. / Tierney, L. / THigale, S. / Weihofen, W.A. / Agrikar, U. / ...Authors: Palacios, D. / Meredith, E. / Kawanami, T. / Adams, C. / Chen, X. / Darsigny, V. / Geno, E. / Palermo, M. / Guy, C. / Hewett, J. / Tierney, L. / THigale, S. / Weihofen, W.A. / Agrikar, U. / Boynton, G. / George, E. / Wang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6azj.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6azj.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 6azj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6azj_validation.pdf.gz | 892.7 KB | Display | wwPDB validaton report |
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Full document | 6azj_full_validation.pdf.gz | 906.1 KB | Display | |
Data in XML | 6azj_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 6azj_validation.cif.gz | 52.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6azj ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azj | HTTPS FTP |
-Related structure data
Related structure data | 6atbC 6b75C 6b76C 2e5bS C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 56230.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Hepes pH 6.5, 30-36 % Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→208 Å / Num. obs: 67507 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Redundancy: 6 % / Biso Wilson estimate: 49.63 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.094 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.53→2.65 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9745 / Rpim(I) all: 0.322 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2e5b Resolution: 2.53→96.09 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.8994 / SU R Cruickshank DPI: 0.504 / Cross valid method: THROUGHOUT / σ(F): 2 / SU R Blow DPI: 0.535 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.255
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Displacement parameters | Biso mean: 50.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.261 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.53→96.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.58 Å / Total num. of bins used: 18
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