Crystal structure of cytokinin-specific binding protein from mung bean in complex with cytokinin

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.190 
  • R-Value Observed: 0.157 

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Crystal Structure of Vigna radiata Cytokinin-Specific Binding Protein in Complex with Zeatin.

Pasternak, O.Bujacz, G.D.Fujimoto, Y.Hashimoto, Y.Jelen, F.Otlewski, J.Sikorski, M.M.Jaskolski, M.

(2006) Plant Cell 18: 2622-2634

  • DOI: https://doi.org/10.1105/tpc.105.037119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The cytosolic fraction of Vigna radiata contains a 17-kD protein that binds plant hormones from the cytokinin group, such as zeatin. Using recombinant protein and isothermal titration calorimetry as well as fluorescence measurements coupled with ligand displacement, we have reexamined the K(d) values and show them to range from approximately 10(-6) M (for 4PU30) to 10(-4) M (for zeatin) for 1:1 stoichiometry complexes. In addition, we have crystallized this cytokinin-specific binding protein (Vr CSBP) in complex with zeatin and refined the structure to 1.2 A resolution. Structurally, Vr CSBP is similar to plant pathogenesis-related class 10 (PR-10) proteins, despite low sequence identity (<20%). This unusual fold conservation reinforces the notion that classic PR-10 proteins have evolved to bind small-molecule ligands. The fold consists of an antiparallel beta-sheet wrapped around a C-terminal alpha-helix, with two short alpha-helices closing a cavity formed within the protein core. In each of the four independent CSBP molecules, there is a zeatin ligand located deep in the cavity with conserved conformation and protein-ligand interactions. In three cases, an additional zeatin molecule is found in variable orientation but with excellent definition in electron density, which plugs the entrance to the binding pocket, sealing the inner molecule from contact with bulk solvent.

  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cytokinin-specific binding protein
A, B, C, D
155Vigna radiataMutation(s): 0 
Gene Names: vrcsbp
Find proteins for A0A1S3THR8 (Vigna radiata var. radiata)
Explore A0A1S3THR8 
Go to UniProtKB:  A0A1S3THR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3THR8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZEA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D]
C10 H13 N5 O
Query on NA

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
ZEA PDBBind:  2FLH Kd: 1.06e+5 (nM) from 1 assay(s)
Binding MOAD:  2FLH Kd: 1.06e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.190 
  • R-Value Observed: 0.157 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.79α = 90
b = 113.79β = 90
c = 86.98γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations