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- PDB-8tm7: Human NAMPT in complex with substrate NAM and small molecule acti... -

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Basic information

Entry
Database: PDB / ID: 8tm7
TitleHuman NAMPT in complex with substrate NAM and small molecule activator NP-A3
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAD+ aging enzyme activation
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / : / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD 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 / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRatia, K.M. / Thatcher, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG067771 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Nicotinamide Phosphoribosyltransferase Positive Allosteric Modulators Attenuate Neuronal Oxidative Stress.
Authors: Gordon-Blake, J. / Ratia, K. / Weidig, V. / Velma, G.R. / Ackerman-Berrier, M. / Penton, C. / Musku, S.R. / Alves, E.T.M. / Driver, T. / Tai, L. / Thatcher, G.R.J.
History
DepositionJul 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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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)114,88413
Polymers113,3322
Non-polymers1,55211
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-79 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.560, 106.864, 83.222
Angle α, β, γ (deg.)90.00, 96.71, 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 , 6 types, 446 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Chemical ChemComp-I7Q / N-{2-[(4R)-2,2-dimethyl-4-(propan-2-yl)oxan-4-yl]ethyl}-N-[(4-methoxyphenyl)methyl]furan-2-carboxamide


Mass: 413.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H35NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
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-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.79→52.47 Å / Num. obs: 98774 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Rrim(I) all: 0.102 / Χ2: 0.93 / Net I/σ(I): 8.7
Reflection shellResolution: 1.79→1.82 Å / % possible obs: 97.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.755 / Num. measured all: 10064 / Num. unique obs: 4745 / CC1/2: 0.594 / Rpim(I) all: 0.636 / Rrim(I) all: 0.991 / Χ2: 1.08 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2e5d

2e5d


Resolution: 1.79→52.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.407 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19753 5055 5.1 %RANDOM
Rwork0.17783 ---
obs0.17887 93639 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.233 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-0.41 Å2
2---0.01 Å20 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.79→52.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7450 0 103 435 7988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137726
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177122
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.65310478
X-RAY DIFFRACTIONr_angle_other_deg1.3181.5916572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74423.85374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.951151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5911526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021574
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.111.7933732
X-RAY DIFFRACTIONr_mcbond_other1.1091.7933731
X-RAY DIFFRACTIONr_mcangle_it1.692.6844658
X-RAY DIFFRACTIONr_mcangle_other1.692.6844659
X-RAY DIFFRACTIONr_scbond_it1.8192.0433994
X-RAY DIFFRACTIONr_scbond_other1.8192.0383987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8522.9725809
X-RAY DIFFRACTIONr_long_range_B_refined3.78521.148628
X-RAY DIFFRACTIONr_long_range_B_other3.73221.018568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 372 -
Rwork0.277 6797 -
obs--97.72 %

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