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- PDB-8f7l: Human NAMPT in complex with substrate NAM and small molecule acti... -

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Basic information

Entry
Database: PDB / ID: 8f7l
TitleHuman NAMPT in complex with substrate NAM and small molecule activator ZN-29-S
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAD biosynthesis / enzyme activator
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-XI3 / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: To Be Published
Title: Human NAMPT in complex with substrate NAM and small molecule activator ZN-29-S
Authors: Ratia, K. / Xiong, R. / Shen, Z. / Thatcher, G.R.
History
DepositionNov 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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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)114,8039
Polymers113,3322
Non-polymers1,4717
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-51 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.888, 106.997, 83.603
Angle α, β, γ (deg.)90.00, 96.88, 90.00
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, 254 molecules

#2: Chemical ChemComp-NCA / NICOTINAMIDE


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-XI3 / (3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[(2P)-2-(3-fluoro-4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]piperidine-3-carboxamide


Mass: 500.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H25FN6OS / 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.: 247 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2M 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: 0.97872 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: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→65.58 Å / Num. obs: 53951 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.068 / Rrim(I) all: 0.132 / Χ2: 0.96 / Net I/σ(I): 6.8 / Num. measured all: 200876
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 98.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.396 / Num. measured all: 14322 / Num. unique obs: 4609 / CC1/2: 0.867 / Rpim(I) all: 0.263 / Rrim(I) all: 0.478 / Χ2: 1.01 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.16refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→65.58 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 2614 4.85 %
Rwork0.2261 --
obs0.2279 53886 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→65.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 101 247 7830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077766
X-RAY DIFFRACTIONf_angle_d0.97710533
X-RAY DIFFRACTIONf_dihedral_angle_d15.4922839
X-RAY DIFFRACTIONf_chiral_restr0.0771146
X-RAY DIFFRACTIONf_plane_restr0.0051335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.32281330.27232621X-RAY DIFFRACTION98
2.24-2.28310.28891220.25012726X-RAY DIFFRACTION100
2.2831-2.32970.28161220.24622693X-RAY DIFFRACTION100
2.3297-2.38040.29111410.24912672X-RAY DIFFRACTION100
2.3804-2.43570.35141440.24842708X-RAY DIFFRACTION100
2.4357-2.49660.28061460.24592656X-RAY DIFFRACTION100
2.4966-2.56420.28491420.24032683X-RAY DIFFRACTION100
2.5642-2.63960.27681490.2342702X-RAY DIFFRACTION100
2.6396-2.72480.25051450.22982685X-RAY DIFFRACTION100
2.7248-2.82220.31281400.24422661X-RAY DIFFRACTION100
2.8222-2.93520.25531440.2522711X-RAY DIFFRACTION100
2.9352-3.06880.30861410.25272697X-RAY DIFFRACTION100
3.0688-3.23060.30631470.22762712X-RAY DIFFRACTION100
3.2306-3.4330.31671430.2342673X-RAY DIFFRACTION100
3.433-3.6980.22941490.22062698X-RAY DIFFRACTION100
3.698-4.07010.22681420.20522718X-RAY DIFFRACTION100
4.0701-4.65890.22131110.19162743X-RAY DIFFRACTION100
4.6589-5.86920.20871150.20512745X-RAY DIFFRACTION100
5.8692-65.580.23741380.2172768X-RAY DIFFRACTION100

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