Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.91 kDa 
• Atom Count: 1422 
• Residue Count: 136 
• Unique protein chains: 1

1K2A

Modified Form of Eosinophil-derived Neurotoxin

• DOI: 10.2210/pdb1K2A/pdb

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


• Deposited: 2001-09-26 Released: 2002-04-03 
• Deposition Author(s): Chang, C., Newton, D.L., Rybak, S.M., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.169 
• R-Value Work: 0.132 
• R-Value Observed: 0.135 

Literature

Crystallographic and functional studies of a modified form of eosinophil-derived neurotoxin (EDN) with novel biological activities.

Chang, C., Newton, D.L., Rybak, S.M., Wlodawer, A.

(2002) J Mol Biol 317: 119-130

• PubMed: 11916383 
• DOI: 10.1006/jmbi.2002.5406
• Primary Citation of Related Structures:  
  1K2A


• PubMed Abstract: 
  

The crystal structure of a post-translationally modified form of eosinophil-derived neurotoxin (EDN) with four extra residues on its N terminus ((-4)EDN) has been solved and refined at atomic resolution (1 A). Two of the extra residues can be placed unambiguously, while the density corresponding to two others is poor. The modified N terminus appears to influence the position of the catalytically important His129, possibly explaining the diminished catalytic activity of this variant. However, (-4)EDN has been shown to be cytotoxic to a Kaposi's sarcoma tumor cell line and other endothelial cell lines. Analysis of the structure and function suggests that the reason for cytotoxicity is most likely due to cellular recognition by the N-terminal extension, since the intrinsic activity of the enzyme is not sufficient for cytotoxicity and the N-terminal extension does not affect the conformation of EDN.

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Organizational Affiliation: 

Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eosinophil-derived neurotoxin	A	136	Homo sapiens	Mutation(s): 0  Gene Names: RNASE2, EDN, RNS2 EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P10153 (Homo sapiens) Explore P10153  Go to UniProtKB:  P10153
NIH Common Fund Data Resources
PHAROS:  P10153 GTEx:  ENSG00000169385

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.169 
• R-Value Work: 0.132 
• R-Value Observed: 0.135 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.138	α = 90
b = 52.558	β = 90
c = 56.627	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-26 
• Released Date: 2002-04-03 
Deposition Author(s): Chang, C., Newton, D.L., Rybak, S.M., Wlodawer, A.

Revision History 

• Version 1.0: 2002-04-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance