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- PDB-4o1b: The crystal structure of a mutant NAMPT (G217R) in complex with a... -

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Basic information

Entry
Database: PDB / ID: 4o1b
TitleThe crystal structure of a mutant NAMPT (G217R) in complex with an inhibitor APO866
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 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 / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsOh, A. / Coons, M. / Brillantes, B. / Wang, W.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors.
Authors: Wang, W. / Elkins, K. / Oh, A. / Ho, Y.C. / Wu, J. / Li, H. / Xiao, Y. / Kwong, M. / Coons, M. / Brillantes, B. / Cheng, E. / Crocker, L. / Dragovich, P.S. / Sampath, D. / Zheng, X. / Bair, ...Authors: Wang, W. / Elkins, K. / Oh, A. / Ho, Y.C. / Wu, J. / Li, H. / Xiao, Y. / Kwong, M. / Coons, M. / Brillantes, B. / Cheng, E. / Crocker, L. / Dragovich, P.S. / Sampath, D. / Zheng, X. / Bair, K.W. / O'Brien, T. / Belmont, L.D.
History
DepositionDec 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Non-polymer description
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)115,93119
Polymers114,0852
Non-polymers1,84617
Water20,3931132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-51 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.579, 106.311, 83.251
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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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: 57042.523 Da / Num. of mol.: 2 / Mutation: G217R
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-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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1132 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.1M Sodium phosphate, pH 8.6, 25% polyethylene glycol 3350, 0.2M NaCl and 1mM compound, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 125404 / Num. obs: 125279 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.65→1.71 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
B3data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→41.373 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 6325 5.06 %
Rwork0.1864 --
obs0.1882 125038 99.55 %
all-125404 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.011 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.828 Å20 Å21.2178 Å2
2--6.9119 Å20 Å2
3---2.8609 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 122 1132 8788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097870
X-RAY DIFFRACTIONf_angle_d1.18210644
X-RAY DIFFRACTIONf_dihedral_angle_d13.1692900
X-RAY DIFFRACTIONf_chiral_restr0.081157
X-RAY DIFFRACTIONf_plane_restr0.0061351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66910.3512030.3053778X-RAY DIFFRACTION95
1.6691-1.68880.32862120.27953971X-RAY DIFFRACTION100
1.6888-1.70930.27772390.25333902X-RAY DIFFRACTION100
1.7093-1.7310.27752090.24024016X-RAY DIFFRACTION100
1.731-1.75380.30262200.24493934X-RAY DIFFRACTION100
1.7538-1.77780.29752090.23263962X-RAY DIFFRACTION100
1.7778-1.80320.24342040.21183960X-RAY DIFFRACTION100
1.8032-1.83010.25392050.20013954X-RAY DIFFRACTION100
1.8301-1.85870.23921980.19823949X-RAY DIFFRACTION100
1.8587-1.88920.26692060.20843969X-RAY DIFFRACTION100
1.8892-1.92170.30871870.30783914X-RAY DIFFRACTION98
1.9217-1.95670.30542190.24063934X-RAY DIFFRACTION99
1.9567-1.99430.22711950.18133952X-RAY DIFFRACTION100
1.9943-2.0350.23461980.1754016X-RAY DIFFRACTION100
2.035-2.07930.24092300.2253926X-RAY DIFFRACTION99
2.0793-2.12760.22762200.18023918X-RAY DIFFRACTION100
2.1276-2.18090.18661930.17123989X-RAY DIFFRACTION100
2.1809-2.23980.23332330.18633912X-RAY DIFFRACTION99
2.2398-2.30570.27922180.24673916X-RAY DIFFRACTION98
2.3057-2.38010.24212010.17433955X-RAY DIFFRACTION100
2.3801-2.46520.20312270.16833950X-RAY DIFFRACTION100
2.4652-2.56390.24832180.17493969X-RAY DIFFRACTION100
2.5639-2.68050.20641900.17173979X-RAY DIFFRACTION100
2.6805-2.82180.22552030.1793982X-RAY DIFFRACTION100
2.8218-2.99860.19872040.1833999X-RAY DIFFRACTION100
2.9986-3.230.1962420.16283969X-RAY DIFFRACTION100
3.23-3.55490.18232040.1653979X-RAY DIFFRACTION100
3.5549-4.06890.18712170.15144001X-RAY DIFFRACTION100
4.0689-5.12490.17092150.14653992X-RAY DIFFRACTION100
5.1249-41.38650.2092060.18014066X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.6837 Å / Origin y: 1.2823 Å / Origin z: 22.7006 Å
111213212223313233
T-0.0111 Å2-0.0033 Å20.0004 Å2-0.0017 Å20.0041 Å2---0.0159 Å2
L0.0232 °2-0.0058 °20.0106 °2-0.0214 °20.0117 °2--0.0579 °2
S0.0238 Å °0.0011 Å °-0.0047 Å °-0.0176 Å °0.0231 Å °-0.0215 Å °0.0019 Å °0.0149 Å °0.1455 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:608 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:609 ) )A8 - 487
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:608 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:609 ) )A603 - 608
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:608 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:609 ) )B8 - 486
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 8:487 OR RESID 603:608 ) ) OR ( CHAIN B AND ( RESID 8:486 OR RESID 603:609 ) )B603 - 609

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