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- PDB-6tw6: Plasmodium vivax N-myristoyltransferase with bound indazole inhib... -

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Basic information

Entry
Database: PDB / ID: 6tw6
TitlePlasmodium vivax N-myristoyltransferase with bound indazole inhibitor IMP-923
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
2-oxopentadecyl-CoA / Chem-NZE / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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-923
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)140,81220
Polymers136,1103
Non-polymers4,70217
Water29,0941615
1
AAA: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9757
Polymers45,3701
Non-polymers1,6056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8796
Polymers45,3701
Non-polymers1,5095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9577
Polymers45,3701
Non-polymers1,5876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.608, 121.785, 178.831
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 Sal-1 (eukaryote) / Gene: PVX_085815 / Plasmid: pET28 derivative / 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, 1632 molecules

#2: Chemical ChemComp-NHW / 2-oxopentadecyl-CoA


Mass: 991.916 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H64N7O17P3S
#3: Chemical ChemComp-NZE / [(5-{4-fluoro-2-[2-(1H-imidazol-1-yl)ethoxy]phenyl}-1H-indazol-3-yl)methyl]dimethylamine / 1-[5-[4-fluoranyl-2-(2-imidazol-1-ylethoxy)phenyl]-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 379.431 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H22FN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1615 / 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50.381 Å / Num. obs: 139024 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2 / Num. unique obs: 6789 / % 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: 1.7→50.381 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2085 6960 5.01 %
Rwork0.1682 --
all0.17 --
obs-138925 99.94 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.138 Å20 Å20 Å2
2---0.038 Å20 Å2
3---0.176 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9400 0 303 1615 11318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01210732
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.67314704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28951355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13923.44564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.344151969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.841546
X-RAY DIFFRACTIONr_chiral_restr0.1180.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028219
X-RAY DIFFRACTIONr_nbd_refined0.2120.24697
X-RAY DIFFRACTIONr_nbtor_refined0.3150.27056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.21128
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.2121
X-RAY DIFFRACTIONr_mcbond_it1.3121.3974816
X-RAY DIFFRACTIONr_mcangle_it2.0222.0916082
X-RAY DIFFRACTIONr_scbond_it1.8561.5665916
X-RAY DIFFRACTIONr_scangle_it2.7422.2748520
X-RAY DIFFRACTIONr_lrange_it4.57819.61417057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3295020.3089646X-RAY DIFFRACTION99.8524
1.744-1.7920.2854830.2639421X-RAY DIFFRACTION100
1.792-1.8440.2534770.2229158X-RAY DIFFRACTION99.9792
1.844-1.9010.2184870.1858896X-RAY DIFFRACTION99.9787
1.901-1.9630.2284440.1818606X-RAY DIFFRACTION99.989
1.963-2.0320.2144580.1728340X-RAY DIFFRACTION99.9773
2.032-2.1080.2224440.1748083X-RAY DIFFRACTION100
2.108-2.1940.2273880.1687797X-RAY DIFFRACTION99.9878
2.194-2.2920.2143780.1657511X-RAY DIFFRACTION99.9747
2.292-2.4040.1953690.1577172X-RAY DIFFRACTION99.947
2.404-2.5340.2263430.1616794X-RAY DIFFRACTION99.972
2.534-2.6870.1963390.1556442X-RAY DIFFRACTION99.9853
2.687-2.8730.2063240.1576112X-RAY DIFFRACTION100
2.873-3.1030.1913200.1545639X-RAY DIFFRACTION100
3.103-3.3980.1853180.1485222X-RAY DIFFRACTION99.9459
3.398-3.7990.1692500.1364756X-RAY DIFFRACTION99.9601
3.799-4.3860.1462160.1244242X-RAY DIFFRACTION100
4.386-5.3690.1721830.1353606X-RAY DIFFRACTION100
5.369-7.5820.2411550.1992847X-RAY DIFFRACTION99.9334
7.582-100.337820.2381675X-RAY DIFFRACTION99.4904

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