3P7L

Rat Insulin Degrading Enzyme (Insulysin)

PDB DOI: https://doi.org/10.2210/pdb3P7L/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-10-12 Released: 2011-07-20
Deposition Author(s): Rodgers, D.W., Noinaj, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.269
R-Value Work: 0.202
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

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

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 113.37 kDa
Atom Count: 8,030
Modelled Residue Count: 954
Deposited Residue Count: 978
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A	978	Rattus norvegicus	Mutation(s): 0 Gene Names: Ide EC: 3.4.24.56
UniProt
Find proteins for P35559 (Rattus norvegicus) Explore P35559 Go to UniProtKB: P35559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.269
R-Value Work: 0.202
R-Value Observed: 0.206
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.61	α = 90
b = 70.98	β = 92.66
c = 114	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Rodgers, D.W.

Noinaj, N.

Revision History (Full details and data files)

Version 1.0: 2011-07-20
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, Derived calculations