6MES | pdb_00006mes

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1907)

• PDB DOI: https://doi.org/10.2210/pdb6MES/pdb

• Classification: ligase/ligase inhibitor
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-09-07 Released: 2019-09-18 
• Deposition Author(s): Barros-Alvarez, X., Hol, W.G.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Structure-guided discovery of selective methionyl-tRNA synthetase inhibitors with potent activity against Trypanosoma brucei

Zhang, Z., Barros-Alvarez, X., Gillespie, J.R., Ranade, R.M., Huang, W., Shibata, S., Molasky, N.M.R., Faghih, O., Mushtaq, A., Choy, R.K.M., de Hostos, E., Hol, W.G.J., Verlinde, C.L.M.J., Buckner, F.S.B., Fan, E.

(2020) RSC Med Chem 

• DOI: https://doi.org/10.1039/D0MD00057D

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.28 kDa 
• Atom Count: 8,770 
• Modeled Residue Count: 1,052 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	A, B	542	Trypanosoma brucei brucei TREU927	Mutation(s): 6  Gene Names: Tb10.70.6470 EC: 6.1.1.10
UniProt
Find proteins for Q38C91 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38C91  Go to UniProtKB:  Q38C91

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JFA	D [auth B]	1-[(1H-benzimidazol-2-yl)methyl]-4-[(2,4-dichlorophenyl)methyl]-1,3-dihydro-2H-imidazol-2-one C18 H14 Cl2 N4 O ZHAMKWDXQMODPF-UHFFFAOYSA-N
MET	C [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.64	α = 90
b = 106.13	β = 90
c = 207.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Barros-Alvarez, X., Hol, W.G.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI084004

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2020-09-09
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Refinement description