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- PDB-9vci: Crystal structure of Escherichia coli tryptophanyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 9vci
TitleCrystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with an inhibitor
ComponentsTryptophan--tRNA ligase
KeywordsLYASE / tryptophanyl-tRNA synthetase / an inhibitor / complex
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / : / Tryptophan-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / CHLORZOXAZONE / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsXia, K. / Peng, X. / Xiao, L. / Huang, Q. / Gu, Q. / Chen, B. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
CitationJournal: Bioorg.Chem. / Year: 2025
Title: Structure-based design of tirabrutinib derivatives as inhibitors of bacterial tryptophanyl-tRNA synthetase.
Authors: Xia, K. / Peng, X. / Xiao, L. / Huang, Q. / Xu, J. / Chen, B. / Zhou, H.
History
DepositionJun 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,43810
Polymers76,7472
Non-polymers1,6918
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-90 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.495, 79.532, 77.651
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 38373.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_ ...Gene: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035
Production host: Escherichia coli (E. coli) / References: UniProt: E2QFN4, tryptophan-tRNA ligase

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Non-polymers , 5 types, 514 molecules

#2: Chemical ChemComp-A1ERR / ~{N}-[[5-[4-(6-azanyl-8-oxidanylidene-9-piperidin-4-yl-purin-7-yl)phenoxy]-2-fluoranyl-4-oxidanyl-phenyl]methyl]ethanamide


Mass: 507.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26FN7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CLW / CHLORZOXAZONE / 5-CHLORO-2-BENZOXAZOLONE


Mass: 169.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4ClNO2
#5: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.15 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.88→59.16 Å / Num. obs: 57750 / % possible obs: 98.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.6
Reflection shellResolution: 1.88→1.98 Å / Rmerge(I) obs: 0.653 / Num. unique obs: 8331

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→59.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2861 5 %RANDOM
Rwork0.19381 ---
obs0.19503 54869 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å2-0 Å20.07 Å2
2--1.7 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.88→59.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 110 506 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135213
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174702
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6337089
X-RAY DIFFRACTIONr_angle_other_deg2.3491.58810873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4355652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02823.266248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45515828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3251524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025993
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021047
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0652.7522620
X-RAY DIFFRACTIONr_mcbond_other2.0642.7522619
X-RAY DIFFRACTIONr_mcangle_it2.5634.113268
X-RAY DIFFRACTIONr_mcangle_other2.5634.1113269
X-RAY DIFFRACTIONr_scbond_it2.872.8952593
X-RAY DIFFRACTIONr_scbond_other2.8142.8792574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6494.2253792
X-RAY DIFFRACTIONr_long_range_B_refined4.16633.7786157
X-RAY DIFFRACTIONr_long_range_B_other4.13933.4666033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.882→1.931 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 215 -
Rwork0.276 3917 -
obs--95.65 %

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