1L3P

CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE MAJOR GRASS POLLEN ALLERGEN Phl p 5b

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

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This is version 1.6 of the entry. See complete history. 


Literature

Structure of the functional domain of the major grass-pollen allergen Phlp 5b.

Rajashankar, K., Bufe, A., Weber, W., Eschenburg, S., Lindner, B., Betzel, C.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1175-1181

  • DOI: https://doi.org/10.1107/s0907444902007254
  • Primary Citation of Related Structures:  
    1L3P

  • PubMed Abstract: 

    The major allergen Phlp 5b from timothy grass pollen induces allergic rhinitis and bronchial asthma in millions of allergic patients worldwide. As an important step towards understanding the interactions between the pollen protein and components of the human immune system, the structure of the C-terminal key domain of Phlp 5b has been determined at 2.0 A resolution and refined to an R value of 19.7%. This is the first known allergen composed entirely of alpha-helices. The protein forms a dimer stabilized by one intermolecular disulfide bridge. Sequence homology suggests that at least all group V and group VI grass-pollen allergens belong to this new class of 'four-helix-bundle allergens'.

    • Organizational Affiliation: 

    Institut für Medizinische Biochemie und Molekularbiologie, Universitätsklinikum Hamburg-Eppendorf, c/o DESY, Gebäude 22a, Notkestrasse 85, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLLEN ALLERGEN Phl p 5b102Phleum pratenseMutation(s): 0 
UniProt
Find proteins for Q40963 (Phleum pratense)
Explore Q40963 
Go to UniProtKB:  Q40963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ40963
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.975α = 90
b = 50.355β = 90
c = 107.804γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2017-02-08
    Changes: Database references
  • Version 1.5: 2017-10-11
    Changes: Refinement description
  • Version 1.6: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description