+Open data
-Basic information
Entry | Database: PDB / ID: 7enq | |||||||||||||||
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Title | Crystal structure of human NAMPT in complex with compound NAT | |||||||||||||||
Components | Nicotinamide phosphoribosyltransferase | |||||||||||||||
Keywords | TRANSFERASE / NAMPT / NAT / NAD | |||||||||||||||
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: 2.20496616708 Å | |||||||||||||||
Authors | Wang, G. / Wu, C. / Liu, M. / Yao, H. / Li, C. / Wang, L. / Tang, Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Cell Res. / Year: 2022 Title: Discovery of small-molecule activators of nicotinamide phosphoribosyltransferase (NAMPT) and their preclinical neuroprotective activity. Authors: Yao, H. / Liu, M. / Wang, L. / Zu, Y. / Wu, C. / Li, C. / Zhang, R. / Lu, H. / Li, F. / Xi, S. / Chen, S. / Gu, X. / Liu, T. / Cai, J. / Wang, S. / Yang, M. / Xing, G.G. / Xiong, W. / Hua, L. ...Authors: Yao, H. / Liu, M. / Wang, L. / Zu, Y. / Wu, C. / Li, C. / Zhang, R. / Lu, H. / Li, F. / Xi, S. / Chen, S. / Gu, X. / Liu, T. / Cai, J. / Wang, S. / Yang, M. / Xing, G.G. / Xiong, W. / Hua, L. / Tang, Y. / Wang, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7enq.cif.gz | 475.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7enq.ent.gz | 312.3 KB | Display | PDB format |
PDBx/mmJSON format | 7enq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7enq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7enq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7enq_validation.xml.gz | 68.2 KB | Display | |
Data in CIF | 7enq_validation.cif.gz | 95 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/7enq ftp://data.pdbj.org/pub/pdb/validation_reports/en/7enq | HTTPS FTP |
-Related structure data
Related structure data | 2e5bS S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56423.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Expression vector pET-mod (others) References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | ChemComp-J7F / #3: Chemical | ChemComp-PO4 / #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: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Sodium phosphate, PEG 3350, NaCl, DTT, BaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.61 Å / Num. obs: 88420 / % possible obs: 88.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 30.14 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Rsym value: 0.14 / Χ2: 0.891 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.20496616708→2.28 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 19.8 / Num. unique obs: 88420 / CC1/2: 0.984 / CC star: 0.996 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Rsym value: 0.14 / Χ2: 0.891 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2e5b Resolution: 2.20496616708→49.61 Å / SU ML: 0.248 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5757 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20496616708→49.61 Å
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Refine LS restraints |
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LS refinement shell |
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