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

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Basic information

Entry
Database: PDB / ID: 9rly
TitleLeishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-929
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: 1.36 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-929
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)49,6644
Polymers48,1961
Non-polymers1,4683
Water10,106561
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)47.590, 91.471, 52.887
Angle α, β, γ (deg.)90.000, 111.828, 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-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1JHH / 1-[5-chloranyl-2-(4-methyl-1,4-diazepan-1-yl)pyrimidin-4-yl]-~{N}-(isoquinolin-4-ylmethyl)azetidine-3-carboxamide


Mass: 465.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28ClN7O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.36→49.2 Å / Num. obs: 82971 / % possible obs: 92.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.6
Reflection shellResolution: 1.36→1.38 Å / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3483

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.36→49.095 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.193 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.204 4119 4.972 %
Rwork0.1687 78732 -
all0.17 --
obs-82851 92.066 %
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: 15.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.355 Å2-0 Å2-0.303 Å2
2--0.234 Å20 Å2
3---0.275 Å2
Refinement stepCycle: LAST / Resolution: 1.36→49.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 97 561 4012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123842
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.875289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.704525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51310664
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.00810186
X-RAY DIFFRACTIONr_chiral_restr0.1250.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023022
X-RAY DIFFRACTIONr_nbd_refined0.2150.21714
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2398
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.268
X-RAY DIFFRACTIONr_mcbond_it1.541.221738
X-RAY DIFFRACTIONr_mcangle_it2.3132.1972193
X-RAY DIFFRACTIONr_scbond_it2.3411.4742104
X-RAY DIFFRACTIONr_scangle_it3.5262.5823052
X-RAY DIFFRACTIONr_lrange_it5.20122.6226229
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
1.36-1.3950.2981780.28234830.28266360.9390.94855.16880.271
1.395-1.4330.3042310.26443880.26664610.9440.95671.49050.25
1.433-1.4750.2822980.24954710.25162900.950.95891.7170.232
1.475-1.520.2432930.21655330.21860850.9620.96895.74360.2
1.52-1.570.2392780.19554260.19759390.9640.97596.04310.181
1.57-1.6250.2442800.19452080.19756940.9650.97696.38220.18
1.625-1.6860.232720.17850820.18155380.9660.97996.67750.165
1.686-1.7550.2212490.16949130.17153280.9680.98296.88440.158
1.755-1.8330.2072680.17147240.17351320.9720.98197.2720.163
1.833-1.9230.1992360.16244920.16448550.9750.98397.38410.157
1.923-2.0260.1972160.16843350.16946630.9780.98497.59810.167
2.026-2.1490.1762020.16541130.16644020.9810.98598.02360.168
2.149-2.2970.1821950.15738710.15841380.9810.98698.260.161
2.297-2.4810.1811880.1535800.15238190.9780.98698.66460.158
2.481-2.7170.2141710.16533530.16735610.9740.98398.9610.176
2.717-3.0360.2051500.16130370.16332110.9750.98399.25260.176
3.036-3.5040.21340.15226780.15528420.9760.98598.94440.174
3.504-4.2860.1481170.12522950.12624290.9860.99199.30010.147
4.286-6.0380.156890.14617700.14718650.9860.98999.67830.174
6.038-49.0950.259740.2169810.21910690.9760.9898.69040.243

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