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)

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
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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IDJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KAA (Subject of Investigation/LOI) Query on KAA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth D] SDF format, chain H [auth C] SDF format, chain F [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A]	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		Interactions Focus chain E [auth B] Focus chain F [auth A] Focus chain G [auth D] Focus chain H [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth A] Focus chain G [auth D] Focus chain H [auth C]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Pradeepkumar, P.I.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.