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- PDB-9ulh: Drosophila melanogaster Nicotinamidase in Complex with Inhibitor AAM -

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Basic information

Entry
Database: PDB / ID: 9ulh
TitleDrosophila melanogaster Nicotinamidase in Complex with Inhibitor AAM
Componentsnicotinamidase
KeywordsHYDROLASE / Nicotinamidase / Inhibitor
Function / homology
Function and homology information


nicotinamidase / nicotinamidase activity / NAD+ biosynthetic process via the salvage pathway / response to oxidative stress / negative regulation of neuron apoptotic process / calcium ion binding / cytoplasm / cytosol
Similarity search - Function
: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / : / nicotinamidase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.561 Å
AuthorsLi, G.-B. / Chen, Y.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291; 81502989 China
CitationJournal: To Be Published
Title: Drosophila melanogaster Nicotinamidase in Complex with Inhibitor AAM
Authors: Li, G.-B. / Chen, Y.-T.
History
DepositionApr 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4754
Polymers40,1641
Non-polymers3113
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.930, 70.466, 76.141
Angle α, β, γ (deg.)90.00, 94.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein nicotinamidase / Nicotinamide deamidase


Mass: 40164.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Naam, AAM52663, anon-WO0172774.59, anon-WO0172774.60, CG7444, CG7500, D-NAAM, Dmel\CG31216, dNaam, CG31216, Dmel_CG31216
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VDU7, nicotinamidase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1EPO / 4-(trifluoromethyl)pyridine-3-carboxamide


Mass: 190.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5F3N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 1.0 M Sodium citrate (pH 7.5)

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Mar 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 55268 / % possible obs: 98.8 % / Redundancy: 6.68 % / CC1/2: 0.9718 / Net I/σ(I): 10.83
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
6.9-506620.98371
4.91-6.911740.9791
4.02-4.9114950.97691
3.48-4.0217270.97391
3.12-3.4819910.97881
2.85-3.1221880.97511
2.64-2.8523450.96721
2.47-2.6425300.95981
2.33-2.4727470.06031
2.21-2.3328820.89861
2.11-2.2129520.90981
2.02-2.1131250.2561
1.94-2.0232830.77141
1.87-1.9434140.60321
1.8-1.8735530.38241
1.75-1.835500.25091
1.69-1.7537420.15711
1.65-1.6938710.11181
1.6-1.6539870.06311
1.56-1.640500.01151

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPXdata processing
autoPXdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.561→43.6 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 47.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 1822 3.66 %
Rwork0.226 --
obs0.2272 49791 88.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.561→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 15 60 2665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222675
X-RAY DIFFRACTIONf_angle_d1.1453609
X-RAY DIFFRACTIONf_dihedral_angle_d19.2541585
X-RAY DIFFRACTIONf_chiral_restr0.06395
X-RAY DIFFRACTIONf_plane_restr0.008471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5613-1.60350.5848630.58561480X-RAY DIFFRACTION36
1.6035-1.65070.59411050.59262635X-RAY DIFFRACTION64
1.6507-1.7040.57961190.55993270X-RAY DIFFRACTION79
1.704-1.76490.46551380.51213747X-RAY DIFFRACTION91
1.7649-1.83550.51881650.46163967X-RAY DIFFRACTION96
1.8355-1.91910.4231350.40364086X-RAY DIFFRACTION99
1.9191-2.02020.3951640.33274104X-RAY DIFFRACTION99
2.0202-2.14680.3241560.29084056X-RAY DIFFRACTION97
2.1468-2.31260.32021540.25884089X-RAY DIFFRACTION99
2.3126-2.54530.31651570.26724146X-RAY DIFFRACTION100
2.5453-2.91350.31931520.24214058X-RAY DIFFRACTION98
2.9135-3.67040.26941570.21754171X-RAY DIFFRACTION99
3.6704-43.60.17821570.16764160X-RAY DIFFRACTION98

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