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- PDB-8y55: Crystal Structure of NAMPT-PF403 -

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Basic information

Entry
Database: PDB / ID: 8y55
TitleCrystal Structure of NAMPT-PF403
ComponentsNicotinamide phosphoribosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / NAMPT
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 canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / 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 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
: / DI(HYDROXYETHYL)ETHER / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYu, S.S. / Liu, Y.B. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Pharm Sin B / Year: 2025
Title: Thermal proteome profiling (TPP) reveals NAMPT as the anti-glioma target of phenanthroindolizidine alkaloid PF403.
Authors: Li, F. / Zhang, Z. / Shi, Q. / Wang, R. / Ji, M. / Chen, X. / Li, Y. / Liu, Y. / Yu, S.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 25, 2025Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)112,3138
Polymers111,1902
Non-polymers1,1236
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-27 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.925, 106.424, 83.002
Angle α, β, γ (deg.)90.000, 96.365, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 55594.938 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
#2: Chemical ChemComp-A1D52 / (13~{a}~{S})-6,7-dimethoxy-9,11,12,13,13~{a},14-hexahydrophenanthro[9,10-f]indolizin-3-ol


Mass: 349.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Potassium formate, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 88150 / % possible obs: 99.96 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07574 / Rpim(I) all: 0.04154 / Net I/σ(I): 12.49
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.6836 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8773 / CC1/2: 0.776 / Rpim(I) all: 0.3737 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→41.25 Å / SU ML: 0.1842 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 4326 4.91 %
Rwork0.1645 83824 -
obs0.166 88150 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.38 Å2
Refinement stepCycle: LAST / Resolution: 1.86→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 80 678 8240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01437851
X-RAY DIFFRACTIONf_angle_d1.638410650
X-RAY DIFFRACTIONf_chiral_restr0.09171162
X-RAY DIFFRACTIONf_plane_restr0.01021352
X-RAY DIFFRACTIONf_dihedral_angle_d19.79622914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.25551290.23992775X-RAY DIFFRACTION99.83
1.88-1.90.28081480.23342811X-RAY DIFFRACTION99.7
1.9-1.930.23041320.22152778X-RAY DIFFRACTION100
1.93-1.950.24741230.20782814X-RAY DIFFRACTION99.97
1.95-1.980.24991500.21382806X-RAY DIFFRACTION99.97
1.98-20.2571400.20082727X-RAY DIFFRACTION100
2-2.030.20511450.19122831X-RAY DIFFRACTION100
2.03-2.060.22321460.18222731X-RAY DIFFRACTION99.93
2.06-2.090.2351440.18342806X-RAY DIFFRACTION100
2.09-2.130.20311440.17462794X-RAY DIFFRACTION100
2.13-2.170.19761630.17662741X-RAY DIFFRACTION100
2.17-2.210.22461440.17442781X-RAY DIFFRACTION100
2.21-2.250.20991470.16982828X-RAY DIFFRACTION99.97
2.25-2.290.22721440.16732757X-RAY DIFFRACTION100
2.29-2.340.19681520.16842802X-RAY DIFFRACTION100
2.34-2.40.17531310.15952773X-RAY DIFFRACTION100
2.4-2.460.21651420.16352824X-RAY DIFFRACTION100
2.46-2.520.19621490.15792774X-RAY DIFFRACTION100
2.52-2.60.20241540.15932786X-RAY DIFFRACTION100
2.6-2.680.19021380.15862798X-RAY DIFFRACTION100
2.68-2.780.21411360.16982832X-RAY DIFFRACTION100
2.78-2.890.20341370.17362769X-RAY DIFFRACTION100
2.89-3.020.19331500.1792783X-RAY DIFFRACTION99.97
3.02-3.180.18871630.16862788X-RAY DIFFRACTION100
3.18-3.380.22251580.16932816X-RAY DIFFRACTION100
3.38-3.640.17731480.15742775X-RAY DIFFRACTION100
3.64-4.010.15811410.13932805X-RAY DIFFRACTION99.86
4.01-4.580.15031550.13152806X-RAY DIFFRACTION100
4.59-5.770.16841300.14112838X-RAY DIFFRACTION100
5.77-41.250.16231430.15462875X-RAY DIFFRACTION99.9

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