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- PDB-9r3r: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 9r3r
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01827593
ComponentsLysine--tRNA ligase
KeywordsLIGASE / inhibitor
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / 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. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / 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
: / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDawson, A. / Baragana, B. / Forte, B. / Robinson, D.A.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP129505 United States
Other privateMMV16-1022
Global Health Innovative Technology FundG2020-115 Japan
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structure-Guided Optimization of Novel Inhibitors of Plasmodium Lysyl-tRNA Synthetase with Multistage Activity against Malaria Parasites.
Authors: Forte, B. / Bellany, F. / Campbell, P.S. / Chemi, G. / Dawson, A. / Anderson, M. / Aniweh, Y. / Burkhard, A.Y. / Aguiar, A.C.C. / Churchyard, A. / Cooper, C.A. / Dos Santos Ferreira, A. / ...Authors: Forte, B. / Bellany, F. / Campbell, P.S. / Chemi, G. / Dawson, A. / Anderson, M. / Aniweh, Y. / Burkhard, A.Y. / Aguiar, A.C.C. / Churchyard, A. / Cooper, C.A. / Dos Santos Ferreira, A. / Famodimu, M.T. / Fang, F.G. / Hu, X. / Huijs, T. / Baud, D. / Jansen, C. / Jimenez Diaz, M.B. / Bonnert, R. / Boyd, S. / Crespo-Fernandez, B. / Mitasev, B. / Montagna, S. / Mok, S. / Murugesan, D. / Narwal, S.K. / Norcross, N.R. / Okombo, J. / Park, H. / Peet, C. / Pereira, D.B. / Post, J.M. / Reader, J. / Riley, J. / Robinson, D.A. / Shinkyo, R. / Simeons, F.R.C. / Simpson, L. / Smith, A. / Smith, D. / Striepen, J. / Teles, C.B.G. / van der Laak, R. / Uhlemann, A.C. / Vantaux, A. / Wilson, C. / Witkowski, B. / Wood, G. / Yeo, T. / Zuccotto, F. / Angulo-Barturen, I. / Baum, J. / Bolscher, J.M. / Guido, R.V.C. / Birkholtz, L.M. / Delves, M.J. / Dembele, L. / Fidock, D.A. / Gamo, F.J. / Kyle, D.E. / Maher, S.P. / Popovici, J. / Walpole, C. / Gusovsky, F. / Willis, P.A. / Read, K.D. / Gilbert, I.H. / Baragana, B.
History
DepositionMay 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2026Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 24, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,0397
Polymers122,9182
Non-polymers1,1215
Water16,934940
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-55 kcal/mol
Surface area39440 Å2
Unit cell
Length a, b, c (Å)72.759, 116.265, 142.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 45 - 544 / Label seq-ID: 21 - 520

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 61459.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd4_2370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CR27, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-A1JC9 / 6-azanyl-2-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-4-(trifluoromethyl)-1~{H}-pyrrolo[3,4-c]pyridin-3-one


Mass: 365.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16F5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.44 Å3/Da / Density % sol: 49.69 % / Description: rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5 % glycerol, 2 mM TCEP, pH 7, 5 mM lysine Reservoir: 25% PEG 3350, 0.2 M Li sulfate, 0.1 M tris pH 7.8
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.5→47.36 Å / Num. obs: 191914 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rpim(I) all: 0.044 / Rsym value: 0.057 / Net I/σ(I): 11.4
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9494 / CC1/2: 0.542 / Rpim(I) all: 0.655 / Rsym value: 0.851 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.618 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.307 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1806 9709 5.061 %
Rwork0.1576 182124 -
all0.159 --
obs-191833 99.579 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.714 Å20 Å2-0 Å2
2--0.928 Å2-0 Å2
3----0.214 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8059 0 75 940 9074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128352
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167869
X-RAY DIFFRACTIONr_angle_refined_deg1.971.86611283
X-RAY DIFFRACTIONr_angle_other_deg0.6511.77118225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.04552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.586101512
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.0810394
X-RAY DIFFRACTIONr_chiral_restr0.1010.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021882
X-RAY DIFFRACTIONr_nbd_refined0.2170.21512
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.27405
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24109
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2704
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.222
X-RAY DIFFRACTIONr_nbd_other0.1840.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.253
X-RAY DIFFRACTIONr_mcbond_it2.0252.0843991
X-RAY DIFFRACTIONr_mcbond_other2.0252.0843992
X-RAY DIFFRACTIONr_mcangle_it2.8193.7344978
X-RAY DIFFRACTIONr_mcangle_other2.8183.7344979
X-RAY DIFFRACTIONr_scbond_it3.982.5194361
X-RAY DIFFRACTIONr_scbond_other3.9812.5194358
X-RAY DIFFRACTIONr_scangle_it6.0664.3966304
X-RAY DIFFRACTIONr_scangle_other6.0684.3956299
X-RAY DIFFRACTIONr_lrange_it7.06322.7799610
X-RAY DIFFRACTIONr_lrange_other6.94321.0829350
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.0516555
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.069740.05009
12AX-RAY DIFFRACTIONLocal ncs0.069740.05009
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
1.5-1.5390.36950.274134230.275141230.9350.94499.96460.257
1.539-1.5810.2636770.247130830.248137760.9470.95699.88390.228
1.581-1.6270.2596900.238125940.239133580.9540.95999.4460.215
1.627-1.6770.246140.214121650.216129810.9630.96898.44390.188
1.677-1.7320.2156490.198119430.199126450.970.97499.58090.171
1.732-1.7920.2036310.183115400.184121880.9730.97899.86050.156
1.792-1.860.1985620.168112070.17117960.9740.98299.77110.145
1.86-1.9360.1795950.157107550.158113520.9790.98499.98240.136
1.936-2.0220.1815540.148103500.15109230.9790.98699.82610.132
2.022-2.120.1755420.14998380.15103960.9820.98799.84610.137
2.12-2.2350.1645120.14394020.14499370.9830.98899.76850.134
2.235-2.370.1774530.13989160.14194400.9830.98899.24790.132
2.37-2.5330.1624280.13984100.1488650.9840.98899.69540.133
2.533-2.7350.1914210.14878400.1582790.9780.98699.78260.145
2.735-2.9950.1783950.15772310.15876360.980.98599.8690.158
2.995-3.3470.1853550.16365570.16469490.9790.98499.46760.169
3.347-3.8620.153130.13757630.13861510.9870.98998.78070.148
3.862-4.7210.132640.12249350.12352590.990.99198.85910.138
4.721-6.6430.192340.16138810.16341390.9830.98899.42020.178
6.643-46.6180.1961250.1722910.17124410.980.98398.97580.186

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