9HEH | pdb_00009heh

Structure of the ligand binding domain of the chemoreceptor MkcA (DSOMK10_RS0100305) of Dickeya solani MK10 in complex with choline

PDB DOI: https://doi.org/10.2210/pdb9HEH/pdb

Classification: SIGNALING PROTEIN
Organism(s): Dickeya solani MK10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-14 Released: 2025-08-06
Deposition Author(s): Gavira, J.A., Rico-Jimenez, M., Matilla, M.A.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.202 (Depositor), 0.199 (DCC)
R-Value Work:
0.174 (Depositor), 0.171 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: in silico
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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

Acetylcholine Chemotaxis in Global Bacterial Plant PathogensRunning title: Acetylcholine chemotaxis in phytopathogenic bacteria

Gavira, J.A., Gilabert, M.J., Santamaria-Hernando, S., Molina-Ollero, A., Rico-Jimenez, M., Cabrera, J.J., Lopez-Solanilla, E., Matilla, M.A.

(2025) Microbiol Res

DOI: https://doi.org/10.1016/j.micres.2025.128294

Macromolecule Content

Total Structure Weight: 34.38 kDa
Atom Count: 2,650
Modeled Residue Count: 284
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-accepting chemotaxis protein	A	306	Dickeya solani MK10	Mutation(s): 0 Gene Names: trg_19, FGLHLNJM_03480, HAT90_03954, I2625_07850, O0557_07220
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHT (Subject of Investigation/LOI) Query on CHT 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]	CHOLINE ION C₅ H₁₄ N O OEYIOHPDSNJKLS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A]	C [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]