7F96

Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95

• PDB DOI: https://doi.org/10.2210/pdb7F96/pdb

• Classification: LIGASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-04 Released: 2023-01-04 
• Deposition Author(s): Mishra, S., Malhotra, N., Yogavel, M., Sharma, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.191 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development

Mishra, S., Malhotra, N., Laleu, B., Chakraborti, S., Yogavel, M., Sharma, A.

(2024) iScience 27

• DOI: https://doi.org/10.1016/j.isci.2024.110049

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.29 kDa 
• Atom Count: 4,057 
• Modelled Residue Count: 487 
• Deposited Residue Count: 497 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A	497	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: proRS, PFL0670c EC: 6.1.1.15
UniProt
Find proteins for Q8I5R7 (Plasmodium falciparum (isolate 3D7)) Explore Q8I5R7  Go to UniProtKB:  Q8I5R7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JE6 (Subject of Investigation/LOI)	B [auth A]	~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide C22 H22 N4 O2 FLWLQSFDWRRFDA-JOCHJYFZSA-N
PRO	C [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.191 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.61	α = 90
b = 103.61	β = 90
c = 128.04	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-04 
Deposition Author(s): Mishra, S., Malhotra, N., Yogavel, M., Sharma, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-04
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2024-07-31
  Changes: Database references, Structure summary