1L3P

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

• PDB DOI: https://doi.org/10.2210/pdb1L3P/pdb

• Classification: ALLERGEN
• Organism(s): Phleum pratense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-02-28 Released: 2003-02-28 
• Deposition Author(s): Rajashankar, K.R., Bufe, A., Weber, W., Eschenburg, S., Lindner, B., Betzel, C.

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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 

Starting Model: experimental

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

• PubMed: 12077438 
• 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'.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 10.73 kDa 
• Atom Count: 841 
• Modelled Residue Count: 102 
• Deposited Residue Count: 102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLLEN ALLERGEN Phl p 5b	A	102	Phleum pratense	Mutation(s): 0
UniProt
Find proteins for Q40963 (Phleum pratense) Explore Q40963  Go to UniProtKB:  Q40963

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	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 = 38.975	α = 90
b = 50.355	β = 90
c = 107.804	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
CCP4	model building
CNS	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-28 
Deposition Author(s): Rajashankar, K.R., Bufe, A., Weber, W., Eschenburg, S., Lindner, B., Betzel, C.

Revision History  

• 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