+Open data
-Basic information
Entry | Database: PDB / ID: 8dsm | ||||||
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Title | Human NAMPT in complex with inhibitor ZN-4-3 | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / NAD biosynthesis enzyme:activator complex | ||||||
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: 2.75 Å | ||||||
Authors | Ratia, K. / Xiong, R. / Shen, Z. / Thatcher, G.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: A structural mechanism for positive allosteric modulation of nicotinamide phosphoribosyltransferase to elevate cellular NAD+ Authors: Ratia, K. / Xiong, R. / Shen, Z. / Thatcher, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dsm.cif.gz | 374.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dsm.ent.gz | 305.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dsm_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8dsm_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8dsm_validation.xml.gz | 70.2 KB | Display | |
Data in CIF | 8dsm_validation.cif.gz | 91.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/8dsm ftp://data.pdbj.org/pub/pdb/validation_reports/ds/8dsm | HTTPS FTP |
-Related structure data
Related structure data | 2e5dS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 56666.078 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: Escherichia coli (E. coli) References: UniProt: P43490, nicotinamide phosphoribosyltransferase |
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-Non-polymers , 5 types, 78 molecules
#2: Chemical | ChemComp-TK0 / ( #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl, pH 8, 0.1 M KCl, and 24-28% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 20, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→20.09 Å / Num. obs: 54145 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.074 / Rrim(I) all: 0.202 / Net I/σ(I): 10.1 / Num. measured all: 401692 / Scaling rejects: 59 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E5D Resolution: 2.75→20.088 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.84 / Stereochemistry target values: ML
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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 max: 109.04 Å2 / Biso mean: 59.1358 Å2 / Biso min: 30.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→20.088 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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