9KWD | pdb_00009kwd

Crystal structure of E.coli LysU complexing with LysSA and ATP

PDB DOI: https://doi.org/10.2210/pdb9KWD/pdb

Classification: LIGASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-05 Released: 2025-12-10
Deposition Author(s): Xia, M., Hei, Z., Fang, P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.49 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.224 (Depositor), 0.225 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of E.coli LysU complexing with LysSA and ATP

Xia, M., Hei, Z., Fang, P.

To be published.

Macromolecule Content

Total Structure Weight: 59.18 kDa
Atom Count: 3,974
Modeled Residue Count: 489
Deposited Residue Count: 504
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, heat inducible	A	504	Escherichia coli K-12	Mutation(s): 0 Gene Names: lysU, b4129, JW4090 EC: 6.1.1.6
UniProt
Find proteins for P0A8N5 (Escherichia coli (strain K12)) Explore P0A8N5 Go to UniProtKB: P0A8N5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
KAA (Subject of Investigation/LOI) Query on KAA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE C₁₆ H₂₆ N₈ O₇ S NARKTLKJPPMFJF-LEJQEAHTSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]