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- PDB-8qic: Structure-based identification of salicylic acid derivatives as m... -

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Basic information

Entry
Database: PDB / ID: 8qic
TitleStructure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / threonyl tRNA-synthetase / malaria / Plasmodium falciparum / salicylic acid
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / Beta-grasp domain superfamily
Similarity search - Domain/homology
: / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli O8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRodriguez, J.A. / Parisini, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/19/A/019European Union
CitationJournal: Plos One / Year: 2024
Title: Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors.
Authors: Bobrovs, R. / Bolsakova, J. / Buitrago, J.A.R. / Varaceva, L. / Skvorcova, M. / Kanepe, I. / Rudnickiha, A. / Parisini, E. / Jirgensons, A.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine--tRNA ligase
D: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,40210
Polymers93,1362
Non-polymers1,2668
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-17 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.780, 110.500, 113.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine--tRNA ligase


Mass: 46567.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O8 (bacteria) / Gene: thrS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7M1C7
#2: Chemical ChemComp-VL0 / 2-oxidanyl-5-[[4-(phenylmethyl)phenyl]sulfamoyl]benzoic acid


Mass: 383.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H17NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 297 K / Method: evaporation / pH: 5.9
Details: 10% (w/v) PEG 4000, 18% (v/v) MPD, and 0.1 M sodium citrate pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→79.34 Å / Num. obs: 47446 / % possible obs: 72.64 % / Redundancy: 11.1 % / CC1/2: 0.996 / Net I/σ(I): 11.2
Reflection shellResolution: 2.085→2.139 Å / Num. unique obs: 47446 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
DIALSV1.0data reduction
xia2V1.0data scaling
PHASERV1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→79.33 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.512 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23312 1932 5.2 %RANDOM
Rwork0.19493 ---
obs0.1969 35571 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.614 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→79.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 80 47 6659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0166752
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166308
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.7979090
X-RAY DIFFRACTIONr_angle_other_deg0.461.56614520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585.35858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.102206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.304101220
X-RAY DIFFRACTIONr_chiral_restr0.0610.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
X-RAY DIFFRACTIONr_mcbond_it2.4281.8033198
X-RAY DIFFRACTIONr_mcbond_other2.4161.8043198
X-RAY DIFFRACTIONr_mcangle_it3.6953.2373994
X-RAY DIFFRACTIONr_mcangle_other3.6963.2393995
X-RAY DIFFRACTIONr_scbond_it4.2752.3123554
X-RAY DIFFRACTIONr_scbond_other4.2742.3143555
X-RAY DIFFRACTIONr_scangle_other6.3254.0185097
X-RAY DIFFRACTIONr_long_range_B_refined8.80717.867420
X-RAY DIFFRACTIONr_long_range_B_other8.80617.867418
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 159 -
Rwork0.283 2509 -
obs--96.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9773-0.18640.62991.14190.0411.1321-0.0436-0.12820.07470.1656-0.0201-0.0888-0.0683-0.02220.06370.18050.010.01460.02860.00060.0178-22.13-21.42226.839
21.4041-0.0365-0.56720.6792-0.03211.0330.0297-0.01-0.08420.0988-0.0279-0.010.10620.0661-0.00180.1784-0.0112-0.02910.0316-0.00450.0107-16.614-44.91822.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D2 - 401
2X-RAY DIFFRACTION2A2 - 401

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