6L4Q | pdb_00006l4q

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-B

• PDB DOI: https://doi.org/10.2210/pdb6L4Q/pdb

• Classification: STRUCTURAL PROTEIN/INHIBITOR
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-19 Released: 2021-05-19 
• Deposition Author(s): Babbar, P., Sharma, A., Manickam, Y., Mishra, S., Harlos, K.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B

Babbar, P., Sato, M., Manickam, Y., Mishra, S., Harlos, K., Gupta, S., Parvez, S., Kikuchi, H., Sharma, A.

(2021) Chembiochem 

• DOI: https://doi.org/10.1002/cbic.202100212

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: 118.29 kDa 
• Atom Count: 8,049 
• Modeled Residue Count: 972 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A [auth B], B [auth A]	507	Plasmodium falciparum 3D7	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E5R	C [auth B], E [auth A]	(3R)-3-[[(3R)-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one C16 H21 N O4 ZNIKUZOBPQNYBK-ZWNOBZJWSA-N
LYS	D [auth B], F [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.181	α = 90
b = 121.833	β = 90
c = 179.695	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
DIALS	data reduction
PDB_EXTRACT	data extraction
xia2	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Babbar, P., Sharma, A., Manickam, Y., Mishra, S., Harlos, K.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	PR13636

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary