8PS7

Crystal structure of Medicago truncatula LYR4 kinase domain

PDB DOI: https://doi.org/10.2210/pdb8PS7/pdb

Classification: PLANT PROTEIN
Organism(s): Medicago truncatula
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-13 Released: 2024-11-06
Deposition Author(s): Simonsen, B., Gysel, K., Laursen, M., Andersen, K.R.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269
R-Value Work: 0.221
R-Value Observed: 0.225

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

The Medicago truncatula LYR4 intracellular domain serves as a scaffold in immunity signaling independent of its phosphorylation activity

Simonsen, B., Rubsam, H., Kolte, M.V., Larsen, M.M., Kronauer, C., Gysel, K., Laursen, M., Feng, F., Kaya, G., Oldroyd, G.E.D., Stougaard, J., Fort, S., Radutoiu, S., Andersen, K.R.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.10.23.619817

Macromolecule Content

Total Structure Weight: 68.34 kDa
Atom Count: 4,646
Modelled Residue Count: 553
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysM-domain receptor-like kinase	A, B	297	Medicago truncatula	Mutation(s): 0 Gene Names: 11433363, MTR_5g085790, MtrunA17_Chr5g0439331
UniProt
Find proteins for G7K7K0 (Medicago truncatula) Explore G7K7K0 Go to UniProtKB: G7K7K0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G7K7K0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	C [auth A], E [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B]