3P7O

Rat Insulin Degrading Enzyme (Insulysin) E111F mutant with two bound peptides

• PDB DOI: https://doi.org/10.2210/pdb3P7O/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-10-12 Released: 2011-07-27 
• Deposition Author(s): Rodgers, D.W., Noinaj, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.285 
• R-Value Work: 0.208 
• R-Value Observed: 0.215 

Literature

Identification of the allosteric regulatory site of insulysin.

Noinaj, N., Bhasin, S.K., Song, E.S., Scoggin, K.E., Juliano, M.A., Juliano, L., Hersh, L.B., Rodgers, D.W.

(2011) PLoS One 6: e20864-e20864

• PubMed: 21731629 
• DOI: https://doi.org/10.1371/journal.pone.0020864
• Primary Citation of Related Structures:  
  3P7L, 3P7O


• PubMed Abstract: 
  

  Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the Aβ peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP.

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Organizational Affiliation: 

Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 119.2 kDa 
• Atom Count: 8,094 
• Modelled Residue Count: 973 
• Deposited Residue Count: 1,034 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A	1,019	Rattus norvegicus	Mutation(s): 1  Gene Names: Ide EC: 3.4.24.56
UniProt
Find proteins for P35559 (Rattus norvegicus) Explore P35559  Go to UniProtKB:  P35559

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
active site bound peptide	B	8	Rattus norvegicus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
distal site bound peptide	C	7	Rattus norvegicus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.285 
• R-Value Work: 0.208 
• R-Value Observed: 0.215 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.52	α = 90
b = 70.91	β = 92.97
c = 114.36	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Rodgers, D.W., Noinaj, N.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2024-02-21
  Changes: Advisory, Data collection, Database references