9JKL | pdb_00009jkl

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE

PDB DOI: https://doi.org/10.2210/pdb9JKL/pdb

Classification: LIGASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-16 Released: 2025-09-10
Deposition Author(s): Jani, J., Mochi, J., Shah, S., Das, A., Patel, D., Pananghat, G., Pappachan, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.215 (DCC)
R-Value Work:
0.204 (Depositor), 0.191 (DCC)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE

Jani, J., Mochi, J., Shah, S., Das, A., Patel, D., Pananghat, G., Pappachan, A.

To be published.

Macromolecule Content

Total Structure Weight: 60.64 kDa
Atom Count: 4,394
Modeled Residue Count: 488
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A	523	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: lysS, SAV0517 EC: 6.1.1.6
UniProt
Find proteins for Q2G0Q3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0Q3 Go to UniProtKB: Q2G0Q3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G0Q3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]