2WRZ

Crystal structure of an arabinose binding protein with designed serotonin binding site in open, ligand-free state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The Computational Design of Ligand Binding is not a Solved Problem

Schreier, B.Stumpp, C.Wiesner, S.Hocker, B.

(2009) Proc Natl Acad Sci U S A 106: 18491

  • DOI: https://doi.org/10.1073/pnas.0907950106
  • Primary Citation of Related Structures:  
    2WRZ

  • PubMed Abstract: 

    Computational design has been very successful in recent years: multiple novel ligand binding proteins as well as enzymes have been reported. We wanted to know in molecular detail how precise the predictions of the interactions of protein and ligands are. Therefore, we performed a structural analysis of a number of published receptors designed onto the periplasmic binding protein scaffold that were reported to bind to the new ligands with nano- to micromolar affinities. It turned out that most of these designed proteins are not suitable for structural studies due to instability and aggregation. However, we were able to solve the crystal structure of an arabinose binding protein designed to bind serotonin to 2.2 A resolution. While crystallized in the presence of an excess of serotonin, the protein is in an open conformation with no serotonin bound, although the side-chain conformations in the empty binding pocket are very similar to the conformations predicted. During subsequent characterization using isothermal titration calorimetry, CD, and NMR spectroscopy, no indication of binding could be detected for any of the tested designed receptors, whereas wild-type proteins bound their ligands as expected. We conclude that although the computational prediction of side-chain conformations appears to be working, it does not necessarily confer binding as expected. Hence, the computational design of ligand binding is not a solved problem and needs to be revisited.


  • Organizational Affiliation

    The Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-ARABINOSE-BINDING PERIPLASMIC PROTEIN
A, B
306Escherichia coli K-12Mutation(s): 9 
UniProt
Find proteins for P02924 (Escherichia coli (strain K12))
Explore P02924 
Go to UniProtKB:  P02924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02924
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.76α = 90
b = 86.3β = 90
c = 116.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
CCP4Iphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description