8PS7

Crystal structure of Medicago truncatula LYR4 kinase domain


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysM-domain receptor-like kinase
A, B
297Medicago truncatulaMutation(s): 0 
Gene Names: 11433363MTR_5g085790MtrunA17_Chr5g0439331
UniProt
Find proteins for G7K7K0 (Medicago truncatula)
Explore G7K7K0 
Go to UniProtKB:  G7K7K0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7K7K0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.684α = 90
b = 78.242β = 90.4
c = 70.365γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF18OC0052855

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release