6AWS | pdb_00006aws

Structure of PR 10 Allergen Ara h 8.01 in complex with quercetin

PDB DOI: https://doi.org/10.2210/pdb6AWS/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., McBride, J., Hurlburt, B.K., Maleki, S.J., Pote, S.S., Perdue, M., Chruszcz, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 52.84 kDa
Atom Count: 3,640
Modeled Residue Count: 468
Deposited Residue Count: 471
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ara h 8 allergen	A, B, C	157	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for Q6VT83 (Arachis hypogaea) Explore Q6VT83 Go to UniProtKB: Q6VT83
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VT83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QUE (Subject of Investigation/LOI) Query on QUE Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A]	E [auth A] I [auth A] J [auth A] N [auth C] O [auth C] E [auth A], I [auth A], J [auth A], N [auth C], O [auth C], P [auth C]	3,5,7,3',4'-PENTAHYDROXYFLAVONE C₁₅ H₁₀ O₇ REFJWTPEDVJJIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B], M [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain M [auth C]
UNL (Subject of Investigation/LOI) Query on UNL Download Ideal Coordinates CCD File	F [auth A], G [auth A], H [auth A]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.568	α = 90
b = 52.318	β = 94.51
c = 57.497	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Revision History (Full details and data files)

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