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- PDB-8dtj: Human NAMPT in complex with small molecule activator ZN-43-S -

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Basic information

Entry
Database: PDB / ID: 8dtj
TitleHuman NAMPT in complex with small molecule activator ZN-43-S
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAD biosynthesis enzyme:activator complex
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / : / NAD+ biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / : / NAD+ biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / nuclear speck / inflammatory response / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyl transferase / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Chem-TKF / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.118 Å
AuthorsRatia, K. / Xiong, R. / Shen, Z. / Thatcher, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG067771 United States
CitationJournal: Biochemistry / Year: 2023
Title: Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD.
Authors: Ratia, K.M. / Shen, Z. / Gordon-Blake, J. / Lee, H. / Laham, M.S. / Krider, I.S. / Christie, N. / Ackerman-Berrier, M. / Penton, C. / Knowles, N.G. / Musku, S.R. / Fu, J. / Velma, G.R. / ...Authors: Ratia, K.M. / Shen, Z. / Gordon-Blake, J. / Lee, H. / Laham, M.S. / Krider, I.S. / Christie, N. / Ackerman-Berrier, M. / Penton, C. / Knowles, N.G. / Musku, S.R. / Fu, J. / Velma, G.R. / Xiong, R. / Thatcher, G.R.J.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,90710
Polymers113,3322
Non-polymers1,5758
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-62 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.499, 107.483, 83.399
Angle α, β, γ (deg.)90.000, 96.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nicotinamide phosphoribosyltransferase / NAmPRTase / Nampt / Pre-B-cell colony-enhancing factor 1 / Pre-B cell-enhancing factor / Visfatin


Mass: 56666.078 Da / Num. of mol.: 2
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, 415 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TKF / (3S)-N-[(1-benzothiophen-5-yl)methyl]-1-{2-[4-(trifluoromethyl)phenyl]-2H-pyrazolo[3,4-d]pyrimidin-4-yl}piperidine-3-carboxamide


Mass: 536.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H23F3N6OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M NaCl, 20% glycerol and 13-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.118→19.84 Å / Num. obs: 59407 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.12-2.181.80.499720039230.7421.484
9.23-19.843.60.03924366800.99626.589.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2e5d

2e5d


Resolution: 2.118→19.668 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2963 4.99 %
Rwork0.2162 56396 -
obs0.2177 59359 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.12 Å2 / Biso mean: 37.0681 Å2 / Biso min: 15.12 Å2
Refinement stepCycle: final / Resolution: 2.118→19.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7473 0 105 408 7986
Biso mean--42.93 40.3 -
Num. residues----940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.118-2.15250.28681110.3137203474
2.1525-2.18960.33721410.30232683100
2.1896-2.22940.34311360.27272716100
2.2294-2.27220.29761510.27062700100
2.2722-2.31850.30821610.25522697100
2.3185-2.36880.30211460.25812707100
2.3688-2.42380.30861430.23832731100
2.4238-2.48430.27041430.24362686100
2.4843-2.55140.26861270.23762727100
2.5514-2.62630.28181590.22972735100
2.6263-2.71080.25071330.22552678100
2.7108-2.80750.29051640.2292689100
2.8075-2.91950.28861340.23572746100
2.9195-3.05190.28841290.23012726100
3.0519-3.21220.27061420.21512717100
3.2122-3.41250.27111440.21842716100
3.4125-3.67440.21891320.20452728100
3.6744-4.04120.19841370.18712744100
4.0412-4.61940.19881470.17552736100
4.6194-5.79510.1921420.18912712100
5.7951-19.6680.20511410.2094278899

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