8YLW | pdb_00008ylw

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with Lys-AMS

• PDB DOI: https://doi.org/10.2210/pdb8YLW/pdb

• Classification: LIGASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-03-07 Released: 2025-09-10 
• Deposition Author(s): Sharma, V.K., Manickam, Y., Bagale, S., Pradeepkumar, P.I., Sharma, A.
• Funding Organization(s): Department of Biotechnology (DBT, India), Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with Lys-AMS

Sharma, V.K., Manickam, Y., Bagale, S., Pradeepkumar, P.I., Sharma, A.

To be published.

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 236.73 kDa 
• Atom Count: 15,701 
• Modeled Residue Count: 1,935 
• Deposited Residue Count: 2,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A [auth B], B [auth A], C [auth D], D [auth C]	507	Plasmodium falciparum	Mutation(s): 0  Gene Names: PF3D7_1350100 EC: 6.1.1.6
UniProt
Find proteins for Q8IDJ8 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDJ8  Go to UniProtKB:  Q8IDJ8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KAA (Subject of Investigation/LOI)	E [auth B], F [auth A], G [auth D], H [auth C]	5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE C16 H26 N8 O7 S NARKTLKJPPMFJF-LEJQEAHTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.36	α = 90
b = 302.19	β = 90
c = 141.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Sharma, V.K., Manickam, Y., Bagale, S., Pradeepkumar, P.I., Sharma, A.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	PR32713
Department of Science & Technology (DST, India)	India	JC Bose Fellowship Award

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release