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- PDB-4l4l: Structural Analysis of a Phosphoribosylated Inhibitor in Complex ... -

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Basic information

Entry
Database: PDB / ID: 4l4l
TitleStructural Analysis of a Phosphoribosylated Inhibitor in Complex with Human Nicotinamide Phosphoribosyltransferase
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTransferase/Transferase Inhibitor / Transferase / inhibitor PRPP adduct / active site / Transferase-Transferase Inhibitor complex
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 junction / cell-cell signaling / 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-1XC / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.122 Å
AuthorsOh, A. / Ho, Y. / Zak, M. / Liu, Y. / Yuen, P. / Zheng, X. / Dragovich, S.P. / Wang, W.
CitationJournal: Chembiochem / Year: 2014
Title: Structural and biochemical analyses of the catalysis and potency impact of inhibitor phosphoribosylation by human nicotinamide phosphoribosyltransferase.
Authors: Oh, A. / Ho, Y.C. / Zak, M. / Liu, Y. / Chen, X. / Yuen, P.W. / Zheng, X. / Liu, Y. / Dragovich, P.S. / Wang, W.
History
DepositionJun 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
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)115,73211
Polymers113,8852
Non-polymers1,8479
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-63 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.215, 106.857, 83.021
Angle α, β, γ (deg.)90.00, 96.53, 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: 56942.375 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-1XC / 6-({4-[(3,5-difluorophenyl)sulfonyl]benzyl}carbamoyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)imidazo[1,2-a]pyridin-1-ium


Mass: 640.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25F2N3O10PS
#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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM ligand compound, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K, ...Details: 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM ligand compound, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12719 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12719 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 58875 / Num. obs: 58463 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 %
Reflection shellResolution: 2.12→2.2 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.122→39.85 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 2926 5 %5% random
Rwork0.1872 ---
all0.1891 59007 --
obs0.1891 58463 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.584 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-31.4692 Å20 Å2-0.2145 Å2
2--6.4276 Å2-0 Å2
3----0.1063 Å2
Refinement stepCycle: LAST / Resolution: 2.122→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7548 0 118 470 8136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047843
X-RAY DIFFRACTIONf_angle_d0.83310636
X-RAY DIFFRACTIONf_dihedral_angle_d11.8712871
X-RAY DIFFRACTIONf_chiral_restr0.0581158
X-RAY DIFFRACTIONf_plane_restr0.0041348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1222-2.1570.34231380.28452561X-RAY DIFFRACTION96
2.157-2.19410.30861340.26462567X-RAY DIFFRACTION98
2.1941-2.2340.28011470.24252672X-RAY DIFFRACTION99
2.234-2.2770.2531450.22772570X-RAY DIFFRACTION99
2.277-2.32350.28021460.22422622X-RAY DIFFRACTION99
2.3235-2.3740.25881300.21382656X-RAY DIFFRACTION99
2.374-2.42920.271410.2072619X-RAY DIFFRACTION99
2.4292-2.490.2591570.19642631X-RAY DIFFRACTION99
2.49-2.55730.25561230.1892655X-RAY DIFFRACTION99
2.5573-2.63250.27251350.19572639X-RAY DIFFRACTION99
2.6325-2.71740.2771370.19832660X-RAY DIFFRACTION99
2.7174-2.81450.24791430.19622625X-RAY DIFFRACTION99
2.8145-2.92720.25951350.20262673X-RAY DIFFRACTION100
2.9272-3.06040.23691490.19112636X-RAY DIFFRACTION100
3.0604-3.22170.211210.18132718X-RAY DIFFRACTION100
3.2217-3.42340.19541420.18132629X-RAY DIFFRACTION100
3.4234-3.68760.22361310.17192679X-RAY DIFFRACTION100
3.6876-4.05830.19331440.16772669X-RAY DIFFRACTION100
4.0583-4.64480.16831350.15362693X-RAY DIFFRACTION100
4.6448-5.8490.20031460.15932676X-RAY DIFFRACTION100
5.849-39.85690.19281470.17842687X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.322 Å / Origin y: 1.2252 Å / Origin z: 22.5677 Å
111213212223313233
T-0.0119 Å2-0.0171 Å2-0.0055 Å2--0.0001 Å20.0253 Å2---0.0271 Å2
L0.0827 °20.0097 °20.0006 °2-0.0795 °20.0363 °2--0.1213 °2
S0.0547 Å °-0.0134 Å °-0.0031 Å °-0.05 Å °0.0267 Å °-0.0704 Å °-0.009 Å °0.0906 Å °0.1187 Å °
Refinement TLS groupSelection details: chain A or chain B or chain S or chain L

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