6AX0 | pdb_00006ax0

Structure of PR-10 Allergen Ara h 8.01 in complex with epicatechin

• PDB DOI: https://doi.org/10.2210/pdb6AX0/pdb

• Classification: PROTEIN BINDING
• Organism(s): Arachis hypogaea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-06 Released: 2018-09-12 
• Deposition Author(s): Offermann, L.R., Yarbrough, J., McBride, J., Hurlburt, B.K., Maleki, S.J., Pote, S.S., Chruszcz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Structure of PR-10 Allergen Ara h 8.01.

Offermann, L.R., Yarbrough, J., McBride, J., Hurlburt, B.K., Maleki, S.J., Pote, S.S., Chruszcz, M.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.57 kDa 
• Atom Count: 2,398 
• Modeled Residue Count: 312 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ara h 8 allergen	A, B	157	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for Q6VT83 (Arachis hypogaea) Explore Q6VT83  Go to UniProtKB:  Q6VT83

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
28E (Subject of Investigation/LOI)	D [auth A], F [auth B]	(2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol C15 H14 O6 PFTAWBLQPZVEMU-UKRRQHHQSA-N
NA (Subject of Investigation/LOI)	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.435	α = 90
b = 92.068	β = 91.79
c = 39.489	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
HKL-3000	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Offermann, L.R., Yarbrough, J., McBride, J., Hurlburt, B.K., Maleki, S.J., Pote, S.S., Chruszcz, M.

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description