3ZS3 | pdb_00003zs3

High resolution structure of Mal d 2, the thaumatin like food allergen from apple

• PDB DOI: https://doi.org/10.2210/pdb3ZS3/pdb

• Classification: ALLERGEN
• Organism(s): Malus domestica
• Mutation(s): No 


• Deposited: 2011-06-22 Released: 2012-07-11 
• Deposition Author(s): Kopec, J., Smole, U., Pavkov, T., Breiteneder, H., Keller, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

High Resolution Structure of Mal D 2, the Thaumatin Like Food Allergen from Apple

Kopec, J., Smole, U., Pavkov, T., Breiteneder, H., Keller, W.

To be published.

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: 23.78 kDa 
• Atom Count: 1,816 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THAUMATIN-LIKE PROTEIN	A	222	Malus domestica	Mutation(s): 0
UniProt
Find proteins for Q9FSG7 (Malus domestica) Explore Q9FSG7  Go to UniProtKB:  Q9FSG7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	B [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
ACY	H [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	G [auth A], I [auth A], J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.662	α = 90
b = 54.06	β = 113.81
c = 45.239	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Kopec, J., Smole, U., Pavkov, T., Breiteneder, H., Keller, W.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary