8QEW

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
R-Value Work: 0.174
R-Value Observed: 0.175

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Eosinophil Derived Neurotoxin/RNase 2 in complex with Tartrate

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

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.193
R-Value Work: 0.174
R-Value Observed: 0.175
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

View Full Validation Report

Ligand Structure Quality Assessment

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

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 R01GM133198.