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- PDB-9npj: Structural studies of reaction hijacking inhibition of a malaria ... -

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Basic information

Entry
Database: PDB / ID: 9npj
TitleStructural studies of reaction hijacking inhibition of a malaria parasite aspartyl-tRNA synthetase.
Componentsaspartate--tRNA ligase
KeywordsLIGASE / t-RNA synthetase / Malaria / inhibitor
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / cytosol
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / aspartate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsKhandokar, Y. / Ketprasit, K. / Tai, C.W. / Xie, S. / Tilley, L. / Griffin, M.D.W. / Panjikar, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Plos Pathog. / Year: 2025
Title: Natural product-mediated reaction hijacking mechanism validates Plasmodium aspartyl-tRNA synthetase as an antimalarial drug target.
Authors: Ketprasit, N. / Tai, C.W. / Sharma, V.K. / Manickam, Y. / Khandokar, Y. / Ye, X. / Dogovski, C. / Hilko, D.H. / Morton, C.J. / Braun, A.C. / Leeming, M.G. / Siddharam, B. / Shami, G.J. / ...Authors: Ketprasit, N. / Tai, C.W. / Sharma, V.K. / Manickam, Y. / Khandokar, Y. / Ye, X. / Dogovski, C. / Hilko, D.H. / Morton, C.J. / Braun, A.C. / Leeming, M.G. / Siddharam, B. / Shami, G.J. / Pradeepkumar, P.I. / Panjikar, S. / Poulsen, S.A. / Griffin, M.D.W. / Sharma, A. / Tilley, L. / Xie, S.C.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct_ref / struct_ref_seq
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aspartate--tRNA ligase
B: aspartate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4386
Polymers124,2582
Non-polymers1,1804
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-50 kcal/mol
Surface area39730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.045, 140.045, 273.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-937-

HOH

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Components

#1: Protein aspartate--tRNA ligase / Aspartyl-tRNA synthetase


Mass: 62128.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax / Gene: PVX_081610 / Production host: Escherichia coli (E. coli) / References: UniProt: A5K9Y2, aspartate-tRNA ligase
#2: Chemical ChemComp-A1B0L / 9-(5-O-{[(1R,2R)-2-amino-3-carboxy-1-hydroxypropyl]sulfamoyl}-beta-D-lyxofuranosyl)-2-chloro-9H-purin-6-amine


Mass: 497.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20ClN7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 3000, 20% (v/v) 1,2,4-butanetriol, 1% (w/v) nondetergent sulfobetaine (NDSB) 256, 0.5 mM manganese chloride, 0.5 mM cobalt chloride, and 0.5 mM zinc chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.36→48.88 Å / Num. obs: 65749 / % possible obs: 99.7 % / Redundancy: 40.5 % / Biso Wilson estimate: 50.43 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.01836 / Rsym value: 0.1154 / Net I/σ(I): 24.15
Reflection shellResolution: 2.36→2.38 Å / Num. unique obs: 1952 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→48.88 Å / SU ML: 0.3034 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 2000 3.04 %
Rwork0.1876 63749 -
obs0.1884 65749 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.16 Å2
Refinement stepCycle: LAST / Resolution: 2.36→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7973 0 76 332 8381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00748225
X-RAY DIFFRACTIONf_angle_d0.849411115
X-RAY DIFFRACTIONf_chiral_restr0.05161218
X-RAY DIFFRACTIONf_plane_restr0.00591418
X-RAY DIFFRACTIONf_dihedral_angle_d20.8833073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.410.30551350.28024310X-RAY DIFFRACTION95.8
2.41-2.480.29241400.25654456X-RAY DIFFRACTION100
2.48-2.550.30251410.23684503X-RAY DIFFRACTION100
2.55-2.640.29021400.21394476X-RAY DIFFRACTION100
2.64-2.730.25071420.19834504X-RAY DIFFRACTION100
2.73-2.840.22881410.20064498X-RAY DIFFRACTION99.96
2.84-2.970.24991430.2064538X-RAY DIFFRACTION99.98
2.97-3.120.25131410.21364518X-RAY DIFFRACTION99.98
3.12-3.320.22441430.19624544X-RAY DIFFRACTION100
3.32-3.580.2051440.18584569X-RAY DIFFRACTION100
3.58-3.940.17881430.1774578X-RAY DIFFRACTION99.98
3.94-4.510.17081450.15374628X-RAY DIFFRACTION100
4.51-5.670.1941460.17034674X-RAY DIFFRACTION100
5.68-48.880.22261560.18754953X-RAY DIFFRACTION99.98
Refinement TLS params.Method: refined / Origin x: -18.5047580178 Å / Origin y: -54.9548657329 Å / Origin z: 13.3184819143 Å
111213212223313233
T0.362365365223 Å20.0122154709463 Å2-0.0883179582394 Å2-0.311337800688 Å20.00295269187155 Å2--0.30121908014 Å2
L0.89696718857 °20.240896253192 °20.0200101008289 °2-1.00278569385 °20.0253159566318 °2--0.476700402897 °2
S-0.0333108116265 Å °-0.0298862582082 Å °-0.033654357043 Å °0.211239942129 Å °0.0196376890697 Å °-0.093435969253 Å °0.0447739289411 Å °-0.031297561557 Å °0.00666409697439 Å °
Refinement TLS groupSelection details: all

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