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- PDB-9iwt: Crystal structure of human NAMPT complexed with AMP -

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Basic information

Entry
Database: PDB / ID: 9iwt
TitleCrystal structure of human NAMPT complexed with AMP
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAMPT / AMP
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / : / Nicotinamide salvage / NAD+ biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian expression / cytokine activity / circadian regulation of gene expression / cell junction ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / : / Nicotinamide salvage / 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
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWang, G. / Wu, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81872874 China
National Natural Science Foundation of China (NSFC)91949101 China
CitationJournal: To Be Published
Title: Crystal structure of human NAMPT complexed with AMP
Authors: Wang, G. / Wu, C.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: 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
C: Nicotinamide phosphoribosyltransferase
D: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,91719
Polymers225,6954
Non-polymers2,22215
Water20,6811148
1
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9469
Polymers112,8482
Non-polymers1,0997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-77 kcal/mol
Surface area31910 Å2
MethodPISA
2
C: Nicotinamide phosphoribosyltransferase
D: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,97110
Polymers112,8482
Non-polymers1,1238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-87 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.170, 93.374, 241.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 56423.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Expression vector pET-mod (others)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1148 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: sodium phosphate, PEG 3350, sodium chloride, DTT, BaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→49.51 Å / Num. obs: 115027 / % possible obs: 89.11 % / Redundancy: 10.5 % / Biso Wilson estimate: 36.15 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.033 / Rrim(I) all: 0.109 / Χ2: 0.921 / Net I/σ(I): 23.2
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 115027 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.109 / Χ2: 0.921 / % possible all: 89.11

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→49.51 Å / SU ML: 0.2349 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 5641 4.9 %
Rwork0.185 109386 -
obs0.1871 115027 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.69 Å2
Refinement stepCycle: LAST / Resolution: 2.02→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14746 0 135 1148 16029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003115224
X-RAY DIFFRACTIONf_angle_d0.603320643
X-RAY DIFFRACTIONf_chiral_restr0.04382262
X-RAY DIFFRACTIONf_plane_restr0.00442601
X-RAY DIFFRACTIONf_dihedral_angle_d12.83535599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.29911430.25922908X-RAY DIFFRACTION72.03
2.04-2.060.30871870.2483681X-RAY DIFFRACTION90.67
2.06-2.090.32941900.24153667X-RAY DIFFRACTION90.97
2.09-2.120.27991760.23633661X-RAY DIFFRACTION90.35
2.12-2.140.28111780.23193605X-RAY DIFFRACTION89.22
2.14-2.170.28671930.2183655X-RAY DIFFRACTION89.89
2.17-2.20.25722230.21423609X-RAY DIFFRACTION89.87
2.2-2.240.26191980.21093657X-RAY DIFFRACTION90.6
2.24-2.270.28882060.21853616X-RAY DIFFRACTION89.15
2.27-2.310.27852020.21553583X-RAY DIFFRACTION89.71
2.31-2.350.26912030.21023610X-RAY DIFFRACTION89.36
2.35-2.390.26661820.20763635X-RAY DIFFRACTION88.71
2.39-2.440.21891690.19763611X-RAY DIFFRACTION89.34
2.44-2.490.26411690.19593616X-RAY DIFFRACTION88.33
2.49-2.540.24182090.20393547X-RAY DIFFRACTION87.57
2.54-2.60.27071930.2053580X-RAY DIFFRACTION87.93
2.6-2.670.26141760.20023543X-RAY DIFFRACTION87.32
2.67-2.740.26961690.19883575X-RAY DIFFRACTION87.66
2.74-2.820.2591880.19873541X-RAY DIFFRACTION86.68
2.82-2.910.23511640.1983562X-RAY DIFFRACTION86.75
2.91-3.010.26231740.20333510X-RAY DIFFRACTION85.77
3.01-3.130.25091890.2023419X-RAY DIFFRACTION83.87
3.13-3.280.24251960.1923528X-RAY DIFFRACTION86.22
3.28-3.450.22281740.18453583X-RAY DIFFRACTION86.41
3.45-3.660.21411480.1713601X-RAY DIFFRACTION87.23
3.67-3.950.20961850.16943753X-RAY DIFFRACTION90.51
3.95-4.340.18462110.15393952X-RAY DIFFRACTION95.44
4.34-4.970.18972100.14664089X-RAY DIFFRACTION98.08
4.97-6.260.17832130.17124105X-RAY DIFFRACTION96.95
6.26-49.510.2012230.18194384X-RAY DIFFRACTION99.52

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