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- PDB-8dsd: Human NAMPT in complex with substrate NAM and small molecule acti... -

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Basic information

Entry
Database: PDB / ID: 8dsd
TitleHuman NAMPT in complex with substrate NAM and small molecule activator NP-A1-S
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / 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
Nicotinamide phosphoribosyl transferase / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
NICOTINAMIDE / PHOSPHATE ION / Chem-TIW / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.429 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 22, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,91012
Polymers113,3322
Non-polymers1,57810
Water17,601977
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-78 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.512, 106.691, 82.803
Angle α, β, γ (deg.)90.000, 96.550, 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 , 6 types, 987 molecules

#2: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-TIW / (3S)-1-[2-(4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]-N-{[4-(methylsulfanyl)phenyl]methyl}piperidine-3-carboxamide


Mass: 472.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28N6OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
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: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.429→19.86 Å / Num. obs: 190322 / % possible obs: 98.9 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.451.80.5391356476290.6620.5160.7471.480
7.83-19.863.60.026410511480.9980.0160.0342.693.7

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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: 1.429→19.858 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 9536 5.01 %
Rwork0.1638 180727 -
obs0.1649 190263 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.85 Å2 / Biso mean: 19.7433 Å2 / Biso min: 8.73 Å2
Refinement stepCycle: final / Resolution: 1.429→19.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7450 0 161 977 8588
Biso mean--27.17 30.35 -
Num. residues----934
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4291-1.44540.3182270.3163433971
1.4454-1.46240.28743020.2621602499
1.4624-1.48020.24513360.23026084100
1.4802-1.49890.22953010.2226059100
1.4989-1.51870.23533240.21766078100
1.5187-1.53950.22473420.20916028100
1.5395-1.56140.21953530.1966072100
1.5614-1.58470.23153570.1936005100
1.5847-1.60950.23283180.19186042100
1.6095-1.63590.19983130.18456135100
1.6359-1.66410.2042940.18796087100
1.6641-1.69430.22543390.18216034100
1.6943-1.72690.18852970.1776154100
1.7269-1.76210.23263420.17855995100
1.7621-1.80040.20013270.17256104100
1.8004-1.84220.20673310.17426066100
1.8422-1.88830.20283060.16816062100
1.8883-1.93930.18853360.16696052100
1.9393-1.99630.19422930.16326109100
1.9963-2.06070.17833230.16096077100
2.0607-2.13420.18812960.16266104100
2.1342-2.21960.18473230.15866084100
2.2196-2.32050.20013150.16366105100
2.3205-2.44260.18623280.16416097100
2.4426-2.59530.18523160.16146075100
2.5953-2.79520.17183260.16096071100
2.7952-3.07560.16933280.15896142100
3.0756-3.51850.17523160.14826106100
3.5185-4.42480.14933280.13266107100
4.4248-19.8580.16332990.14886230100

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