8QEW | pdb_00008qew

Eosinophil Derived Neurotoxin/RNase 2 in complex with Tartrate

PDB DOI: https://doi.org/10.2210/pdb8QEW/pdb

Classification: IMMUNE SYSTEM
Organism(s): Escherichia coli 'BL21-Gold(DE3)pLysS AG
Expression System: Cloning vector pET-T7p(-14G)-SpacerA-GFP-LVA
Mutation(s): No

Deposited: 2023-09-01 Released: 2024-09-11
Deposition Author(s): Li, J., Kang, X., Prats-Ejarque, G., Boix, E.
Funding Organization(s): Agencia Estatal de Investigacion (AEI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for saccharide binding by human RNase 2/EDN, a protein combining enzymatic and lectin properties

Kang, X., Prats-Ejarque, G., Boix, E., Li, J.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.03.20.713198

Macromolecule Content

Total Structure Weight: 16.06 kDa
Atom Count: 1,299
Modeled Residue Count: 135
Deposited Residue Count: 135
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-secretory ribonuclease	A	135	Escherichia coli 'BL21-Gold(DE3)pLysS AG	Mutation(s): 0 Gene Names: RNASE2, EDN, RNS2 EC: 4.6.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P10153 (Homo sapiens) Explore P10153 Go to UniProtKB: P10153
PHAROS: P10153 GTEx: ENSG00000169385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA (Subject of Investigation/LOI) Query on TLA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.193 (Depositor), 0.193 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.793	α = 90
b = 52.677	β = 90
c = 56.421	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Prats-Ejarque, G.

Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	PID2019-106123GB-I00

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary
Version 1.2: 2026-04-22
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.