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- PDB-3dkj: Crystal structure of human NAMPT complexed with benzamide and pho... -

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Basic information

Entry
Database: PDB / ID: 3dkj
TitleCrystal structure of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NMPRTase / Visfatin / benzamide / phosphoribosyl pyrophosphate / PRPP / nicotinamide phosphoribosyltransferase / Alternative splicing / Cytoplasm / Glycosyltransferase / Phosphoprotein / Polymorphism / Pyridine nucleotide biosynthesis
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 ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / 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 phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyl transferase / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-PRP / BENZAMIDE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHo, M. / Burgos, E.S. / Almo, S.C. / Schramm, V.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT.
Authors: Burgos, E.S. / Ho, M.C. / Almo, S.C. / Schramm, V.L.
History
DepositionJun 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)110,6336
Polymers109,6102
Non-polymers1,0224
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-41.2 kcal/mol
Surface area33230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.257, 106.811, 83.045
Angle α, β, γ (deg.)90.000, 96.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 54805.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Plasmid: pBAD/DEFT 49 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-UNU / BENZAMIDE


Mass: 121.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200mM NaCl, 100mM Tris-HCl, 15% PEG 3350, 20% Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 74005 / % possible obs: 88.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Χ2: 0.627 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.972.60.25134020.43140.8
1.97-2.052.70.22953330.45264.2
2.05-2.143.10.270470.47884.8
2.14-2.253.50.17380400.50996.2
2.25-2.393.90.14782570.51499.7
2.39-2.584.10.11583510.52100
2.58-2.844.20.08783380.543100
2.84-3.254.20.06783920.702100
3.25-4.084.10.04683730.794100
4.08-204.20.04284720.948100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3DHD

3dhd


Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.502 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3452 5 %RANDOM
Rwork0.168 ---
obs0.17 68540 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.45 Å2 / Biso mean: 24.413 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7450 0 62 398 7910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227693
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9710441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75424.885348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.311151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2531526
X-RAY DIFFRACTIONr_chiral_restr0.0990.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025768
X-RAY DIFFRACTIONr_nbd_refined0.20.23618
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2500
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.28
X-RAY DIFFRACTIONr_mcbond_it0.8061.54782
X-RAY DIFFRACTIONr_mcangle_it1.26727501
X-RAY DIFFRACTIONr_scbond_it2.17733390
X-RAY DIFFRACTIONr_scangle_it3.444.52935
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 194 -
Rwork0.215 3538 -
all-3732 -
obs--70.7 %

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