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- PDB-9rlw: Leishmania major N-myristoyltransferase in complex with azetidino... -

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Basic information

Entry
Database: PDB / ID: 9rlw
TitleLeishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-825
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / myristoylation / azetidinopyrimidine / Leishmania / inhibitor
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / metal ion binding / cytosol
Similarity search - Function
Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
: / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.49 Å
AuthorsBrannigan, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Leishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-825
Authors: Bell, A.S.
History
DepositionJun 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6234
Polymers48,1961
Non-polymers1,4273
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.366, 91.721, 53.552
Angle α, β, γ (deg.)90.000, 112.923, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 48195.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: NMT, LMJF_32_0080 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1JHF / ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-1-[5-chloranyl-2-[2-(dimethylamino)ethylamino]pyrimidin-4-yl]azetidine-3-carboxamide


Mass: 424.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23ClF2N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 30% PEG 1500, 0.2 M NaCl, 0.1 M Na cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.49→49.4 Å / Num. obs: 69322 / % possible obs: 98.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.3
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4916 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.49→49.323 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.932 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2269 3437 4.96 %
Rwork0.1855 65856 -
all0.188 --
obs-69293 98.783 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.007 Å2-0 Å2-0.658 Å2
2--0.24 Å20 Å2
3---0.228 Å2
Refinement stepCycle: LAST / Resolution: 1.49→49.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 93 389 3836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123786
X-RAY DIFFRACTIONr_angle_refined_deg2.2571.8735198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.981525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2710635
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.47810184
X-RAY DIFFRACTIONr_chiral_restr0.1460.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022984
X-RAY DIFFRACTIONr_nbd_refined0.2160.21606
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2770.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.236
X-RAY DIFFRACTIONr_mcbond_it2.5742.3031712
X-RAY DIFFRACTIONr_mcangle_it3.6794.1452153
X-RAY DIFFRACTIONr_scbond_it3.4952.6482074
X-RAY DIFFRACTIONr_scangle_it5.1354.6973010
X-RAY DIFFRACTIONr_lrange_it7.19933.2595789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.49-1.5290.3852610.34549160.34851970.9120.92499.61520.344
1.529-1.570.3452480.30847650.3150500.920.94199.26730.302
1.57-1.6160.3192510.2945750.29248800.9370.94998.89340.281
1.616-1.6660.3112240.26442730.26747690.9440.95794.29650.25
1.666-1.720.2722270.22842690.2345850.950.96798.05890.211
1.72-1.7810.2561980.22842600.22944690.9590.96899.75390.209
1.781-1.8480.2712340.20940790.21243240.9570.97299.74560.192
1.848-1.9230.2382100.19939160.20141330.9590.97599.83060.183
1.923-2.0080.2441920.20737620.20939640.9620.97399.74770.194
2.008-2.1060.2681720.20836300.21138310.9570.97499.2430.199
2.106-2.220.2481830.19833890.236020.9620.97899.16710.192
2.22-2.3540.2411490.18431380.18734400.9650.9895.55230.18
2.354-2.5160.2141590.17530200.17731970.9720.98199.4370.173
2.516-2.7170.2241550.18528720.18730270.970.9781000.185
2.717-2.9760.2541310.18926440.19227750.9610.9781000.195
2.976-3.3260.1981230.17223500.17324870.9740.98299.43710.183
3.326-3.8370.1831070.14820910.1522190.9810.98799.05360.164
3.837-4.6920.15720.1317470.13118800.9860.9996.75530.153
4.692-6.6060.199830.15713830.15914660.9820.9881000.187
6.606-49.3230.208580.1797770.1818350.9790.9861000.211

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