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- PDB-6tw7: Leishmania major N-myristoyltransferase in complex with indazole ... -

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Basic information

Entry
Database: PDB / ID: 6tw7
TitleLeishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-918
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / myristoylation / indazole / Leishmania
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
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 / Chem-NZB / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsBrannigan, J.A.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
CitationJournal: To Be Published
Title: Leishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-918
Authors: Brannigan, J.A.
History
DepositionJan 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5884
Polymers48,1961
Non-polymers1,3933
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-27 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.379, 91.899, 53.609
Angle α, β, γ (deg.)90.000, 113.697, 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-NZB / [(5-{4-fluoro-2-[2-(pyridin-3-yl)ethoxy]phenyl}-1H-indazol-3-yl)methyl]dimethylamine / 1-[5-[4-fluoranyl-2-(2-pyridin-3-ylethoxy)phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 390.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23FN4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→49 Å / Num. obs: 83675 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 14.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3809 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2434 4182 5.002 %
Rwork0.205 --
all0.207 --
obs-83602 99.205 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.823 Å2-0 Å2-0.286 Å2
2--1.115 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 93 406 3853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123709
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.6795086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3422.129202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24415621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7791524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022911
X-RAY DIFFRACTIONr_nbd_refined0.2140.21738
X-RAY DIFFRACTIONr_nbtor_refined0.320.22500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.239
X-RAY DIFFRACTIONr_mcbond_it2.2672.2561696
X-RAY DIFFRACTIONr_mcangle_it3.043.3822130
X-RAY DIFFRACTIONr_scbond_it2.8792.4932013
X-RAY DIFFRACTIONr_scangle_it4.1123.6282930
X-RAY DIFFRACTIONr_lrange_it5.42331.3825854
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
1.4-1.4360.3592980.36654670.36662140.6980.68392.77440.359
1.436-1.4760.3593270.33357080.33560560.7070.72799.65320.314
1.476-1.5180.3172980.30455790.30558890.7940.80699.79620.279
1.518-1.5650.3062770.2854200.28157120.8420.83799.73740.252
1.565-1.6160.3172840.26852430.27155350.8310.84899.85550.241
1.616-1.6730.312700.25851000.26153780.8430.86799.85120.231
1.673-1.7360.3172620.24949080.25251760.8430.87599.88410.225
1.736-1.8070.2932260.24647420.24949750.8760.88899.85930.227
1.807-1.8870.2732600.22344990.22547660.8950.91499.85310.208
1.887-1.9790.2732180.22943570.23145800.90.91299.89080.217
1.979-2.0860.2542000.22541610.22643740.9140.92299.70280.219
2.086-2.2120.2892120.22538860.22841010.8880.91599.92680.223
2.212-2.3650.2831720.21236850.21538690.8930.91499.68980.214
2.365-2.5540.2361850.19634300.19836320.9310.93999.53190.202
2.554-2.7970.2351630.20131330.20333080.9270.93499.63720.212
2.797-3.1250.211420.19728620.19730170.9320.93899.56910.214
3.125-3.6060.1991250.16925100.17126480.9530.9699.50910.188
3.606-4.4110.21080.14821410.1522610.9540.96799.46930.174
4.411-6.2130.158860.15316620.15317580.9690.97199.43120.186
6.213-49.0890.216690.1869260.1889980.9580.9699.69940.226

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