Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.

Fernandes, H.Pasternak, O.Bujacz, G.Bujacz, A.Sikorski, M.M.Jaskolski, M.

(2008) J Mol Biol 378: 1040-1051

  • DOI: https://doi.org/10.1016/j.jmb.2008.03.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Plant pathogenesis-related (PR) proteins of class 10 (PR-10) are small and cytosolic. The main feature of their three-dimensional structure is a large cavity between a seven-stranded antiparallel beta-sheet and a long C-terminal alpha-helix. Although PR-10 proteins are abundant in plants, their physiological role remains unknown. Recent data have indicated ligand binding as their possible biological function. The article describes the structure of a complex between a classic PR-10 protein (yellow lupine LlPR-10.2B) and the plant hormone, trans-zeatin. Previously, trans-zeatin binding has been reported in a structurally related cytokinin-specific binding protein, which has a distant sequence relation with classic PR-10 proteins. In the present 1.35 A resolution crystallographic model, three perfectly ordered zeatin molecules are found in the binding cavity of the protein. The fact that three zeatin molecules are bound by the protein when only a fourfold molar excess of the ligand was used indicates an unusual type of affinity for this ligand and suggests that LlPR-10.2B, and perhaps other PR-10 proteins as well, acts as a reservoir of cytokinin molecules in the aqueous environment of the cell.

  • Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PR10.2B158Lupinus luteusMutation(s): 0 
Gene Names: pr10.2bYpr10.2b
Find proteins for Q9LLQ2 (Lupinus luteus)
Explore Q9LLQ2 
Go to UniProtKB:  Q9LLQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LLQ2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.822α = 90
b = 73.822β = 90
c = 67.212γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description