1GQV | pdb_00001gqv

Atomic Resolution (0.98A) Structure of Eosinophil-Derived Neurotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 
    0.144 (Depositor) 
  • R-Value Work: 
    0.169 (DCC) 
  • R-Value Observed: 
    0.116 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Atomic Resolution (0.98 A) Structure of Eosinophil-Derived Neurotoxin

Swaminathan, G.J.Holloway, D.E.Veluraja, K.Acharya, K.R.

(2002) Biochemistry 41: 3341

  • DOI: https://doi.org/10.1021/bi015911f
  • Primary Citation Related Structures: 
    1GQV

  • PubMed Abstract: 

    Human eosinophil-derived neurotoxin (EDN) is a small, basic protein that belongs to the ribonuclease A superfamily. EDN displays antiviral activity and causes the neurotoxic Gordon phenomenon when injected into rabbits. Although EDN and ribonuclease A have appreciable structural similarity and a conserved catalytic triad, their peripheral substrate-binding sites are not conserved. The crystal structure of recombinant EDN (rEDN) has been determined at 0.98 A resolution from data collected at a low temperature (100 K). We have refined the crystallographic model of the structure using anisotropic displacement parameters to a conventional R-factor of 0.116. This represents the highest resolution structure of rEDN determined to date and is only the second ribonuclease structure to be determined at a resolution greater than 1.0 A. The structure provides a detailed picture of the conformational freedom at the various subsites of rEDN, and the water structure accounts for more than 50% of the total solvent content of the unit cell. This information will be crucial for the design of tight-binding inhibitors to restrain the ribonucleolytic activity of rEDN.


  • Organizational Affiliation
    • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.

Macromolecule Content 

  • Total Structure Weight: 15.67 kDa 
  • Atom Count: 1,396 
  • Modeled Residue Count: 135 
  • Deposited Residue Count: 135 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EOSINOPHIL-DERIVED NEUROTOXIN135Homo sapiensMutation(s): 0 
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10153
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT

Query on ACT



Download:Ideal Coordinates CCD File
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free:  0.144 (Depositor) 
  • R-Value Work:  0.169 (DCC) 
  • R-Value Observed: 0.116 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.024α = 90
b = 57.477β = 90
c = 42.398γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary