6AWT | pdb_00006awt

Structure of PR 10 Allergen in complex with epicatechin

PDB DOI: https://doi.org/10.2210/pdb6AWT/pdb

Classification: PLANT PROTEIN
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., Perdue, M., McBride, J., Hurlburt, B.K., Maleki, S.J., Pote, S.S., Chruszcz, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.252 (Depositor), 0.260 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (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: 69.3 kDa
Atom Count: 4,958
Modeled Residue Count: 624
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR 10 protein	A, B, C, D	156	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
28E Query on 28E Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] J [auth C] K [auth C] E [auth A], F [auth A], H [auth B], J [auth C], K [auth C], M [auth D]	(2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol C₁₅ H₁₄ O₆ PFTAWBLQPZVEMU-UKRRQHHQSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	G [auth A], I [auth B], L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252 (Depositor), 0.260 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.451	α = 90
b = 62.507	β = 90
c = 186.585	γ = 90

Software Package:

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

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Help and Resources

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Structure of PR 10 Allergen in complex with epicatechin

Structure of PR-10 Allergen Ara h 8.01.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations