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- PDB-2gvj: Crystal Structure of Human NMPRTase in complex with FK866 -

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Basic information

Entry
Database: PDB / ID: 2gvj
TitleCrystal Structure of Human NMPRTase in complex with FK866
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NMPRTase / Visfatin / Pbef / cancer / fk866
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / 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 activity / nicotinamide phosphoribosyltransferase / 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-cell signaling / cell junction / 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-DGB / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhan, J.A. / Tao, X. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents.
Authors: Khan, J.A. / Tao, X. / Tong, L.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 9, 2016Group: Non-polymer description

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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)112,2544
Polymers111,4712
Non-polymers7832
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-57 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.780, 105.896, 83.427
Angle α, β, γ (deg.)90.00, 96.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEGLUAA9 - 419 - 41
21PHEGLUBB9 - 419 - 41
12TYRILEAA54 - 48454 - 484
22TYRILEBB54 - 48454 - 484

NCS ensembles :
ID
1
2

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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: 55735.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT / Production host: Escherichia coli (E. coli)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Chemical ChemComp-DGB / (2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide / FK-866


Mass: 391.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: 26% PEG 3350, 200 mM NaCL, BaCl2 as Additive, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.1→82.76 Å / Num. obs: 57137 / % possible obs: 98.25 %
Reflection shellHighest resolution: 2.1 Å / % possible all: 98.25

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→82.76 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.854 / SU B: 6.6 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0.5 / ESU R: 0.312 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29831 3024 5 %RANDOM
Rwork0.24747 ---
obs0.25005 57137 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20.43 Å2
2---0.73 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7431 0 58 775 8264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227669
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.95510388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3224.87347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.195151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2651526
X-RAY DIFFRACTIONr_chiral_restr0.0780.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025776
X-RAY DIFFRACTIONr_nbd_refined0.2140.24086
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2822
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.28
X-RAY DIFFRACTIONr_mcbond_it0.4661.54749
X-RAY DIFFRACTIONr_mcangle_it0.74427474
X-RAY DIFFRACTIONr_scbond_it1.14733418
X-RAY DIFFRACTIONr_scangle_it1.7334.52914
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1283medium positional0.410.5
23420medium positional0.340.5
1283medium thermal0.42
23420medium thermal0.362
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 205 -
Rwork0.263 3652 -
obs--85.62 %

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