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- PDB-9qc3: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 9qc3
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593
ComponentsLysine--tRNA ligase 1
KeywordsLIGASE / inhibitor
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
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 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDawson, A. / Cleghorn, L.A.T. / Davis, S.H.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1066891 United States
Bill & Melinda Gates FoundationOPP1191579 United States
Wellcome Trust100195/Z/12/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design and Development of Lysyl tRNA Synthetase Inhibitors, for the Treatment of Tuberculosis.
Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. ...Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. / Ray, P.C. / Epemolu, O. / Lopez-Roman, E.M. / Lopez, L.G. / Engelhart, C.A. / Kim, J. / Pino, P.A. / Schnappinger, D. / Read, K.D. / Encinas, L. / Bates, R.H. / Wyatt, P.G. / Green, S.R. / Cleghorn, L.A.T.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6293
Polymers58,1901
Non-polymers4402
Water1,47782
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2586
Polymers116,3792
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)83.669, 83.669, 147.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 58189.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lysS1, lysS, Rv3598c, MTCY07H7B.24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU9, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-A1I50 / 2-azanyl-4-methoxy-6-[(1~{R},2~{S})-2-oxidanylcycloheptyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 292.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir: 0.25 M NaOAc, 14% W/V PEG 3350 Protein buffer: 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM DTT, pH 7
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 2.28→147.26 Å / Num. obs: 24663 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.043 / Net I/σ(I): 11.1
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.702 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1193 / CC1/2: 0.894 / Rpim(I) all: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→72.853 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.223 / SU ML: 0.253 / Cross valid method: FREE R-VALUE / ESU R: 0.327 / ESU R Free: 0.256
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2769 1232 5.011 %
Rwork0.214 23355 -
all0.217 --
obs-24587 99.951 %
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: 66.897 Å2
Baniso -1Baniso -2Baniso -3
1-2.656 Å20 Å20 Å2
2--2.656 Å20 Å2
3----5.311 Å2
Refinement stepCycle: LAST / Resolution: 2.28→72.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3591 0 31 82 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163577
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.8355005
X-RAY DIFFRACTIONr_angle_other_deg0.5011.7618196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7465457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.2445.34144
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.854101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47310613
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.12210165
X-RAY DIFFRACTIONr_chiral_restr0.0660.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02856
X-RAY DIFFRACTIONr_nbd_refined0.2040.2782
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.23423
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21755
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.240
X-RAY DIFFRACTIONr_nbd_other0.160.2159
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2990.222
X-RAY DIFFRACTIONr_mcbond_it4.9756.7241846
X-RAY DIFFRACTIONr_mcbond_other4.9746.7231846
X-RAY DIFFRACTIONr_mcangle_it7.44712.0582297
X-RAY DIFFRACTIONr_mcangle_other7.44512.0562298
X-RAY DIFFRACTIONr_scbond_it4.9687.0491841
X-RAY DIFFRACTIONr_scbond_other4.977.051840
X-RAY DIFFRACTIONr_scangle_it7.69212.8162708
X-RAY DIFFRACTIONr_scangle_other7.6912.8142709
X-RAY DIFFRACTIONr_lrange_it10.22466.9214067
X-RAY DIFFRACTIONr_lrange_other10.22366.9054055
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
2.28-2.3390.3061060.34416720.34117790.8550.87999.94380.327
2.339-2.4030.304830.31716510.31717350.90.90799.94240.295
2.403-2.4730.3371030.27815820.28216850.9160.9311000.254
2.473-2.5490.355700.27515670.27916370.9310.9381000.243
2.549-2.6320.326720.26315300.26616020.9260.9461000.223
2.632-2.7250.29780.25414620.25615410.950.95399.93510.218
2.725-2.8270.323620.2514320.25314940.9360.9521000.214
2.827-2.9430.337860.23913570.24514430.9360.9591000.2
2.943-3.0730.351640.23313140.23913790.9180.96299.92750.203
3.073-3.2230.379740.22412670.23113410.9120.9661000.197
3.223-3.3970.276660.20811910.21112570.9550.9731000.189
3.397-3.6020.275530.21311650.21512180.9520.9751000.198
3.602-3.850.3550.21110720.21511270.9390.9731000.196
3.85-4.1580.216510.18110130.18210640.9730.9791000.17
4.158-4.5530.218560.1589300.1619860.9740.9841000.161
4.553-5.0880.263450.1858570.1889020.9580.981000.185
5.088-5.8710.253300.1987740.28040.9740.9791000.199
5.871-7.1780.26310.1756670.1786990.9540.9899.85690.181
7.178-10.1030.228300.1755250.1785550.9670.9811000.204
10.103-72.8530.26170.2813270.283510.9740.93898.00570.349

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