3TSH

Crystal structure of Phl p 4, a grass pollen allergen with glucose dehydrogenase activity

• PDB DOI: https://doi.org/10.2210/pdb3TSH/pdb

• Classification: ALLERGEN, OXIDOREDUCTASE
• Organism(s): Phleum pratense
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2011-09-13 Released: 2012-09-19 
• Deposition Author(s): Zafred, D., Nandy, A., Keller, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Crystal structure and immunologic characterization of the major grass pollen allergen Phl p 4.

Zafred, D., Nandy, A., Pump, L., Kahlert, H., Keller, W.

(2013) J Allergy Clin Immunol 132: 696-703.e10

• PubMed: 23683465 
• DOI: https://doi.org/10.1016/j.jaci.2013.03.021
• Primary Citation of Related Structures:  
  3TSH, 3TSJ


• PubMed Abstract: 
  

  Phl p 4 is a major pollen allergen but exhibits lower allergenicity than other major allergens. The natural protein is glycosylated and shows cross-reactivity with related and structurally unrelated allergens.

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Organizational Affiliation: 

Institute for Molecular Biosciences (IMB), University of Graz, Graz, Austria.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 56.7 kDa 
• Atom Count: 4,516 
• Modelled Residue Count: 490 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pollen allergen Phl p 4	A	500	Phleum pratense	Mutation(s): 2  Gene Names: phlp4
UniProt
Find proteins for Q2I6V7 (Phleum pratense) Explore Q2I6V7  Go to UniProtKB:  Q2I6V7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA	B [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
MLI	F [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	C [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.077	α = 90
b = 117.077	β = 90
c = 202.09	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Zafred, D., Nandy, A., Keller, W.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2017-06-21
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description