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- PDB-6tw5: Plasmodium vivax N-myristoyltransferase with bound indazole inhib... -

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Basic information

Entry
Database: PDB / ID: 6tw5
TitlePlasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-917
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / myristoylation / malaria / indazole inhibitor
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 speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsBrannigan, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Plasmodium vivax N-myristoyltransferase with bound 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
BBB: Glycylpeptide N-tetradecanoyltransferase
CCC: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,01021
Polymers136,1103
Non-polymers4,90018
Water30,0131666
1
AAA: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0998
Polymers45,3701
Non-polymers1,7297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9076
Polymers45,3701
Non-polymers1,5375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0037
Polymers45,3701
Non-polymers1,6336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.472, 121.655, 178.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules AAABBBCCC

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 45369.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_085815 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 7 types, 1684 molecules

#2: 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.: 3 / Source method: obtained synthetically / Formula: C24H28FN5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1666 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M AS, 25% PEG 3350, 0.1 M Bis-Tris pH 6.0

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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 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→49 Å / Num. obs: 181592 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8856 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→49 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1982 9126 5.029 %
Rwork0.1645 --
all0.166 --
obs-181478 99.882 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0 Å2
2--0.108 Å20 Å2
3---0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9401 0 315 1666 11382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01210702
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.67514669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30651342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61223.363565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.249151950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.021547
X-RAY DIFFRACTIONr_chiral_restr0.1220.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028196
X-RAY DIFFRACTIONr_nbd_refined0.210.24812
X-RAY DIFFRACTIONr_nbtor_refined0.3160.27099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.21150
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.2109
X-RAY DIFFRACTIONr_mcbond_it1.4431.4174794
X-RAY DIFFRACTIONr_mcangle_it2.1962.1256048
X-RAY DIFFRACTIONr_scbond_it2.2941.655908
X-RAY DIFFRACTIONr_scangle_it3.3682.3788520
X-RAY DIFFRACTIONr_lrange_it4.97420.56817216
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
1.55-1.590.3066850.267125650.269132770.8320.85299.79660.251
1.59-1.6340.2776550.248123010.249129600.870.8899.96910.229
1.634-1.6810.2386470.219119460.22125960.9030.90699.97620.198
1.681-1.7330.2485970.208116780.21122760.9040.91699.99190.186
1.733-1.790.2175800.181113190.183119070.9290.93899.93280.16
1.79-1.8520.1975670.161109340.163115050.9410.95199.96520.143
1.852-1.9220.1975780.16105480.162111350.9420.95199.91920.143
1.922-2.0010.2035260.162101660.164106960.9450.95499.96260.147
2.001-2.090.1935610.16396880.165102580.9510.95799.91230.151
2.09-2.1920.2124610.16493940.16698660.9410.95699.88850.153
2.192-2.310.24530.1689200.16293810.9490.95999.91470.151
2.31-2.450.1934170.15384480.15588740.9520.96299.89860.144
2.45-2.6190.1964210.15879530.1683870.9480.95999.8450.15
2.619-2.8290.1913830.15474170.15678080.9540.96399.89750.148
2.829-3.0990.1863920.15368080.15572090.9550.96499.87520.15
3.099-3.4640.1753690.14161550.14365420.9630.9799.72490.141
3.464-3.9990.142880.12955280.12958230.9740.97699.87980.133
3.999-4.8960.1522360.12747200.12849620.9750.97999.87910.134
4.896-6.9160.2152000.18336940.18439000.9520.96599.84620.188
6.916-100.5050.3091100.23221710.23522820.9340.94899.95620.239

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