7Q5D

Structure of EPCR in a non-canonical conformation

• PDB DOI: https://doi.org/10.2210/pdb7Q5D/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-11-03 Released: 2022-09-14 
• Deposition Author(s): Lopez-Sagaseta, J., Erausquin, E.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure of EPCR in a non-canonical conformation

Erausquin, E., Rodriguez-Fernandez, A., Lopez-Sagaseta, J.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.12.16.472967

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

Macromolecule Content

• Total Structure Weight: 24 kDa 
• Atom Count: 1,575 
• Modelled Residue Count: 173 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial protein C receptor	A	195	Homo sapiens	Mutation(s): 0  Gene Names: PROCR, EPCR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNN8 (Homo sapiens) Explore Q9UNN8  Go to UniProtKB:  Q9UNN8
PHAROS:  Q9UNN8 GTEx:  ENSG00000101000
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q9UNN8-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTY	E [auth A]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
CYS	D [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.47	α = 90
b = 70.47	β = 90
c = 96.635	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Lopez-Sagaseta, J., Erausquin, E.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PGC2018-094894-B-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	RYC-2017-21683

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary