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- PDB-3dkl: Crystal structure of phosphorylated mimic form of human NAMPT com... -

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Basic information

Entry
Database: PDB / ID: 3dkl
TitleCrystal structure of phosphorylated mimic form of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NMPRTase / Visfatin / nicotinamide phosphoribosyltransferase / beryllium fluoride / benzamide / phosphoribosyl pyrophosphate / Alternative splicing / Cytoplasm / Glycosyltransferase / Phosphoprotein / Polymorphism / Pyridine nucleotide biosynthesis
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
BERYLLIUM TRIFLUORIDE ION / Chem-PRP / BENZAMIDE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,86212
Polymers109,6102
Non-polymers1,25210
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-43 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.127, 106.589, 83.240
Angle α, β, γ (deg.)90.000, 96.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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
#5: 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 / Phosphoribosyl pyrophosphate


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

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Non-polymers , 4 types, 431 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UNU / BENZAMIDE / Benzamide


Mass: 121.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 49.93 %
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: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 81779 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.082 / Χ2: 0.808 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.89-1.972.70.35868780.97482
1.97-2.053.20.29277190.66592
2.05-2.143.60.28282191.06998.4
2.14-2.2540.22483930.80799.9
2.25-2.394.10.18283890.884100
2.39-2.584.20.13184000.731100
2.58-2.844.20.183890.725100
2.84-3.254.20.06984550.657100
3.25-4.094.10.04984190.67599.9
4.09-504.10.05485180.9899.7

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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 3DHF

3dhf


Resolution: 1.89→28.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.807 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4084 5 %RANDOM
Rwork0.177 ---
obs0.179 81743 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.34 Å2 / Biso mean: 23.777 Å2 / Biso min: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.89→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7446 0 74 423 7943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227694
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9710439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53524.9349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.123151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8951526
X-RAY DIFFRACTIONr_chiral_restr0.1130.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025768
X-RAY DIFFRACTIONr_nbd_refined0.2080.23721
X-RAY DIFFRACTIONr_nbtor_refined0.310.25252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2524
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.25
X-RAY DIFFRACTIONr_mcbond_it0.9741.54778
X-RAY DIFFRACTIONr_mcangle_it1.5127494
X-RAY DIFFRACTIONr_scbond_it2.69733386
X-RAY DIFFRACTIONr_scangle_it4.1914.52941
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 202 -
Rwork0.298 4364 -
all-4566 -
obs--73.18 %

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