6B1D | pdb_00006b1d

Structure of PR 10 Allergen Ara h 8.01 with Quercetin

• PDB DOI: https://doi.org/10.2210/pdb6B1D/pdb

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


• Deposited: 2017-09-18 Released: 2018-09-19 
• 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: 2.51 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structure of PR 10 Allergen Ara h 8.01 with Quercetin

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.31 kDa 
• Atom Count: 3,620 
• Modeled Residue Count: 468 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ara h 8 allergen	A, B, C	156	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
QUE	D [auth A], E [auth C]	3,5,7,3',4'-PENTAHYDROXYFLAVONE C15 H10 O7 REFJWTPEDVJJIY-UHFFFAOYSA-N
BGC	F [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.938	α = 90
b = 52	β = 97.71
c = 55.62	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-19 
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: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary