9GFZ

Crystal structure of Medicago Truncatula LYK3 kinase domain D459N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.257 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Two residues reprogram immunity receptor kinases to signal in nitrogen-fixing symbiosis

Tsitsikli, M.Simonsen, B.W.Larsen, M.M.Andersen, C.G.Gysel, K.Lironi, D.Kronauer, C.Rubsam, H.Luu, T.B.Hansen, S.B.Kaya, G.Stougaard, J.Andersen, K.R.Radutoiu, S.

(2024) bioRxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysM domain receptor-like kinase 3
A, B
296Medicago truncatulaMutation(s): 1 
Gene Names: LYK3HCLRLK3MTR_5g086130
EC: 2.7.11.1
UniProt
Find proteins for Q6UD73 (Medicago truncatula)
Explore Q6UD73 
Go to UniProtKB:  Q6UD73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UD73
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.98α = 99.905
b = 59.84β = 105.75
c = 61.24γ = 119.799
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF18OC0052855

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release