7OXE

Crystal structure of the KDEL receptor bound to HDEF peptide at pH 6.0

• PDB DOI: https://doi.org/10.2210/pdb7OXE/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Gallus gallus, Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2021-06-22 Released: 2022-07-13 
• Deposition Author(s): Newstead, S., Parker, J.L.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.288 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Literature

Crystal structure of the KDEL receptor bound to HDEF peptide at pH 6.0

Newstead, S., Parker, J.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.75 kDa 
• Atom Count: 1,926 
• Modelled Residue Count: 216 
• Deposited Residue Count: 219 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ER lumen protein-retaining receptor 2	A	212	Gallus gallus	Mutation(s): 0  Gene Names: KDELR2, RCJMB04_8l23 Membrane Entity: Yes
UniProt
Find proteins for Q5ZKX9 (Gallus gallus) Explore Q5ZKX9  Go to UniProtKB:  Q5ZKX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-ALA-GLU-HIS-ASP-GLU-PHE	B	7	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	C [auth A], D [auth A], E [auth A], F [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.288 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.383	α = 90
b = 37.533	β = 95.22
c = 62.685	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Newstead, S., Parker, J.L.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	219531/Z/19/Z

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description