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- PDB-6tw8: Leishmania major N-myristoyltransferase in complex with indazole ... -

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Basic information

Entry
Database: PDB / ID: 6tw8
TitleLeishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-917
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
Chem-9M2 / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.79 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 indazole inhibitor IMP-917
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
CCC: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2398
Polymers96,3922
Non-polymers2,8476
Water11,422634
1
AAA: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6194
Polymers48,1961
Non-polymers1,4243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CCC: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6194
Polymers48,1961
Non-polymers1,4243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.020, 89.820, 97.180
Angle α, β, γ (deg.)90.000, 104.270, 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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-9M2 / 1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 421.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28FN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.49 Å3/Da / Density % sol: 51 %
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: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→65 Å / Num. obs: 82872 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.7
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 4 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4573 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.79→65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2645 4145 5.003 %
Rwork0.2181 --
all0.22 --
obs-82848 99.676 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.058 Å2-0 Å20.446 Å2
2---0.412 Å20 Å2
3---0.216 Å2
Refinement stepCycle: LAST / Resolution: 1.79→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 190 634 7532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127414
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.67910167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60722.334407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.834151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9551546
X-RAY DIFFRACTIONr_chiral_restr0.1180.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025826
X-RAY DIFFRACTIONr_nbd_refined0.2190.23494
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2533
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.236
X-RAY DIFFRACTIONr_mcbond_it1.8312.0023384
X-RAY DIFFRACTIONr_mcangle_it2.8142.9984248
X-RAY DIFFRACTIONr_scbond_it2.1452.1034030
X-RAY DIFFRACTIONr_scangle_it3.1583.0715871
X-RAY DIFFRACTIONr_lrange_it5.27226.67311684
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
1.79-1.8360.3162830.31558420.31561400.830.82199.75570.297
1.836-1.8870.3112970.28956270.2959410.840.85399.71390.266
1.887-1.9410.2883110.26454660.26557960.8690.87699.67220.239
1.941-2.0010.2892770.2453340.24256240.8760.89799.76880.211
2.001-2.0670.2762630.23252090.23454820.8880.90399.81760.205
2.067-2.1390.2742500.22950400.23153060.8920.90799.69850.203
2.139-2.220.272340.21848500.2250920.9040.91999.84290.192
2.22-2.310.2892510.21446620.21849250.8880.91999.75630.189
2.31-2.4130.2842470.21144750.21547250.8960.92499.93650.188
2.413-2.5310.2462220.21242770.21445060.9160.92299.84470.189
2.531-2.6670.2832350.21740510.22142920.90.91799.86020.198
2.667-2.8290.2622040.21638350.21940480.9050.92199.77770.201
2.829-3.0240.2582030.2135900.21338070.9190.9399.63230.198
3.024-3.2650.2471750.20833850.2135750.9280.93699.58040.2
3.265-3.5760.2351510.19631350.19832960.9380.95199.69660.193
3.576-3.9970.2271550.18327910.18629540.9450.95899.72920.185
3.997-4.6120.2151290.17224820.17426190.9520.96199.69450.179
4.612-5.6410.2351080.1821170.18322400.9530.96399.33040.192
5.641-7.9480.324940.25616400.2617470.9060.92399.25590.263
7.948-650.317560.3048950.30510010.920.92395.0050.352

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