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- PDB-9r32: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 9r32
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01887015
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDawson, A. / Baragana, B. / Forte, B.
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 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: 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
B: Lysine--tRNA ligase
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,68030
Polymers245,8364
Non-polymers3,84426
Water24,7891376
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,83815
Polymers122,9182
Non-polymers1,92013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-38 kcal/mol
Surface area39070 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,84215
Polymers122,9182
Non-polymers1,92413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-31 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.153, 119.425, 142.760
Angle α, β, γ (deg.)90.000, 90.308, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 45 - 545 / Label seq-ID: 21 - 521

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 61459.094 Da / Num. of mol.: 4
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

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Non-polymers , 7 types, 1402 molecules

#2: Chemical
ChemComp-A1JCT / 2-azanyl-6-[[(1~{S},3~{S})-1-oxidanyl-3-(trifluoromethyl)cyclohexyl]methyl]-4-(trifluoromethyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 398.304 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16F6N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1376 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.48 % / Description: rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM TCEP, pH 7 Reservoir: 25% PEG 3350, 0.1 M tris pH 7.8, 0.2 M Li sulfate
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 8, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.9→142.76 Å / Num. obs: 187306 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.767 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.055 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.658 / Num. unique obs: 8580 / CC1/2: 0.706 / Rpim(I) all: 0.514 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→91.768 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.474 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2064 9337 4.986 %
Rwork0.1802 177917 -
all0.181 --
obs-187254 97.166 %
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: 21.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.439 Å2-0 Å2-0.495 Å2
2--1.227 Å20 Å2
3----0.783 Å2
Refinement stepCycle: LAST / Resolution: 1.9→91.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16196 0 255 1376 17827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01216854
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615863
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.85522744
X-RAY DIFFRACTIONr_angle_other_deg0.5221.7736725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8252006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.4455104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.113103022
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.8210795
X-RAY DIFFRACTIONr_chiral_restr0.0760.22433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023785
X-RAY DIFFRACTIONr_nbd_refined0.2090.23040
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.214424
X-RAY DIFFRACTIONr_nbtor_refined0.180.28111
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.28655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.216
X-RAY DIFFRACTIONr_nbd_other0.1970.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.246
X-RAY DIFFRACTIONr_mcbond_it1.8512.1038038
X-RAY DIFFRACTIONr_mcbond_other1.852.1038036
X-RAY DIFFRACTIONr_mcangle_it2.6413.76910025
X-RAY DIFFRACTIONr_mcangle_other2.643.76910026
X-RAY DIFFRACTIONr_scbond_it2.872.4138816
X-RAY DIFFRACTIONr_scbond_other2.8662.4128813
X-RAY DIFFRACTIONr_scangle_it4.4934.27512716
X-RAY DIFFRACTIONr_scangle_other4.4914.27312711
X-RAY DIFFRACTIONr_lrange_it5.61321.77118976
X-RAY DIFFRACTIONr_lrange_other5.55821.28118609
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.0516724
X-RAY DIFFRACTIONr_ncsr_local_group_20.0450.0516762
X-RAY DIFFRACTIONr_ncsr_local_group_30.0530.0516685
X-RAY DIFFRACTIONr_ncsr_local_group_40.0570.0516666
X-RAY DIFFRACTIONr_ncsr_local_group_50.0390.0516809
X-RAY DIFFRACTIONr_ncsr_local_group_60.0570.0516696
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.04530.05009
12AX-RAY DIFFRACTIONLocal ncs0.04530.05009
23AX-RAY DIFFRACTIONLocal ncs0.044710.05009
24AX-RAY DIFFRACTIONLocal ncs0.044710.05009
35AX-RAY DIFFRACTIONLocal ncs0.052910.05009
36AX-RAY DIFFRACTIONLocal ncs0.052910.05009
47AX-RAY DIFFRACTIONLocal ncs0.056590.05009
48AX-RAY DIFFRACTIONLocal ncs0.056590.05009
59AX-RAY DIFFRACTIONLocal ncs0.038620.05009
510AX-RAY DIFFRACTIONLocal ncs0.038620.05009
611AX-RAY DIFFRACTIONLocal ncs0.057250.05009
612AX-RAY DIFFRACTIONLocal ncs0.057250.05009
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
1.9-1.9490.2656530.26122080.26142130.9480.9590.48760.242
1.949-2.0030.2546150.234122060.235138840.9550.9692.34370.21
2.003-2.0610.2446470.221120350.222134460.9580.96794.3180.194
2.061-2.1240.2416550.22119220.221130930.950.96796.0590.194
2.124-2.1940.2226820.202116500.203126940.9660.97397.14830.174
2.194-2.2710.2186590.191113210.192122880.9640.97697.49350.164
2.271-2.3560.2146180.184109380.186118300.9720.97897.68390.156
2.356-2.4530.2085170.174106790.176113910.9730.98198.28810.148
2.453-2.5620.2035030.175102330.176108890.9750.98298.59490.148
2.562-2.6860.24730.17998800.18104930.9760.98298.66580.152
2.686-2.8320.2214960.18192990.18399290.9730.98298.65040.154
2.832-3.0030.2194260.17789400.17994280.9720.98299.34240.153
3.003-3.210.2064380.17183620.17388710.9750.98299.19960.153
3.21-3.4670.1964010.17378220.17482480.9780.98399.69690.164
3.467-3.7980.1863510.17272210.17375940.9820.98599.71030.167
3.798-4.2450.1763760.15665100.15768970.9840.98799.84050.155
4.245-4.90.1612920.12858020.12960950.9870.99299.98360.133
4.9-5.9970.1972610.17248890.17351500.9820.9881000.17
5.997-8.4630.2091720.17538420.17640140.9830.9881000.175
8.463-91.7680.1791020.17121580.17122670.9820.98499.69120.183

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