1QNX | pdb_00001qnx

Ves v 5, an allergen from Vespula vulgaris venom

• PDB DOI: https://doi.org/10.2210/pdb1QNX/pdb

• Classification: ALLERGEN
• Organism(s): Vespula vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-10-25 Released: 2000-10-26 
• Deposition Author(s): Henriksen, A., Gajhede, M., Spangfort, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.236 (Depositor) 
• R-Value Work: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Major Venom Allergen of Yellow Jackets, Ves V 5: Structural Characterization of a Pathogenesis-Related Protein Superfamily.

Henriksen, A., King, T.P., Mirza, O., Monsalve, R.I., Meno, K., Ipsen, H., Larsen, J.N., Gajhede, M., Spangfort, M.D.

(2001) Proteins 45: 438

• PubMed: 11746691 
• DOI: https://doi.org/10.1002/prot.1160
• Primary Citation Related Structures: 
  1QNX


• PubMed Abstract: 
  

  Ves v 5 is one of three major allergens found in yellow-jacket venom: phospholipase A(1) (Ves v 1), hyaluronidase (Ves v 2), and antigen 5 (Ves v 5). Ves v 5 is related by high amino acid sequence identity to pathogenesis-related proteins including proteins from mammals, reptiles, insects, fungi, and plants. The crystal structure of Ves v 5 has been solved and refined to a resolution of 1.9 A. The majority of residues conserved between the pathogenesis-related proteins can be rationalized in terms of hydrogen bonding patterns and hydrophobic interactions defining an alpha-beta-alpha sandwich core structure. A small number of consensus residues are solvent exposed (including two adjacent histidines) and located in an elongated cavity that forms a putative active site. The site has no structural resemblance to previously characterized enzymes. Homologous antigen 5's from a large number of different yellow jackets, hornets, and paper wasps are known and patients show varying extents of cross-reactivity to the related antigen 5's. The structure of Ves v 5 allows a detailed analysis of the epitopes that may participate in antigenic cross-reactivity, findings that are useful for the development of a vaccine for treatment of insect allergy.

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Organizational Affiliation: 
• Protein Structure Group, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 23.89 kDa 
• Atom Count: 1,928 
• Modeled Residue Count: 209 
• Deposited Residue Count: 209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VES V 5	A	209	Vespula vulgaris	Mutation(s): 0
UniProt
Find proteins for Q05110 (Vespula vulgaris) Explore Q05110  Go to UniProtKB:  Q05110

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.236 (Depositor) 
• R-Value Work:  0.209 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.359	α = 90
b = 62.179	β = 90
c = 82.777	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-10-26 
Deposition Author(s): Henriksen, A., Gajhede, M., Spangfort, M.D.

Revision History  

• Version 1.0: 2000-10-26
  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: 2018-01-17
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary