9TWV | pdb_00009twv

Complex of E. coli leucyl-tRNA synthetase AN3365-resistant mutant D345A bound to tRNA(leu)

• PDB DOI: https://doi.org/10.2210/pdb9TWV/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2026-01-15 Released: 2026-09-02 
• Deposition Author(s): Hoffmann, G., Palencia, A., Muller, B.
• Funding Organization(s): iNEXT-Discovery, Grenoble Instruct-ERIC Center (ISBG), Agence Nationale de la Recherche (ANR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.252 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Mechanisms of Resistance to an Antibiotic Targeting Bacterial Leucyl-tRNA Synthetase

Muller, B., Fries, F., Huber, A.L., Risch, T., Mohamadyar-Toupkanlou, F., Hoffmann, G., Dulic, M., Herrmann, J., Guic Sovulj, I., Muller, R., Palencia, A.

(2026) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 127.94 kDa 
• Atom Count: 8,702 
• Modeled Residue Count: 894 
• Deposited Residue Count: 967 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine--tRNA ligase	A	880	Escherichia coli	Mutation(s): 1  Gene Names: leuS, b0642, JW0637 EC: 6.1.1.4
UniProt
Find proteins for P07813 (Escherichia coli (strain K12)) Explore P07813  Go to UniProtKB:  P07813

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNA(leu)	B	87	Escherichia coli

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JX6( Subject of Investigation/LOI)	C [auth A]	(2~{S})-2-azanyl-~{N}-[azanyl-(3-fluorophenyl)-oxidanylidene-$l^{6}-sulfanylidene]-4-methyl-pentanamide C12 H18 F N3 O2 S UIYQWUQZPSKJIH-WLRWDXFRSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.252 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.799	α = 90
b = 118.955	β = 90
c = 140.713	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Hoffmann, G., Palencia, A., Muller, B.

---

Funding Organization	Location	Grant Number
iNEXT-Discovery	European Union	45625
Grenoble Instruct-ERIC Center (ISBG)	France	27604
Agence Nationale de la Recherche (ANR)	France	ANR-20-AMRB-0003
Agence Nationale de la Recherche (ANR)	France	ANR-22-CE44-0040

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release