8F5X

Crystal structure of human eosinophil-derived neurotoxin (EDN, ribonuclease 2) in complex with 5'-adenosine monophosphate (AMP)

• PDB DOI: https://doi.org/10.2210/pdb8F5X/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-15 Released: 2023-11-29 
• Deposition Author(s): Tran, T.T.Q., Pham, N.T.H., Calmettes, C., Doucet, N.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Fonds de Recherche du Quebec - Sante (FRQS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.197 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Crystal structure of human eosinophil-derived neurotoxin (EDN, ribonuclease 2) in complex with 5'-adenosine monophosphate (AMP)

Thi Thanh, Q.T., Pham, N.T.H., Calmettes, C., Doucet, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.56 kDa 
• Atom Count: 1,276 
• Modelled Residue Count: 135 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-secretory ribonuclease	A	135	Homo sapiens	Mutation(s): 0  Gene Names: RNASE2, EDN, RNS2
UniProt & NIH Common Fund Data Resources
Find proteins for P10153 (Homo sapiens) Explore P10153  Go to UniProtKB:  P10153
PHAROS:  P10153 GTEx:  ENSG00000169385

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	E [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SIN	B [auth A], C [auth A], G [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
EDO	D [auth A], F [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.197 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.78	α = 90
b = 52.45	β = 90
c = 56.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Tran, T.T.Q., Pham, N.T.H., Calmettes, C., Doucet, N.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN202204368
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN201706091
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	CREATE511956
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	251848
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	281993

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release