3H44

Crystal Structure of Insulin Degrading Enzyme in Complex with macrophage inflammatory protein 1 alpha

• PDB DOI: https://doi.org/10.2210/pdb3H44/pdb

• Classification: Hydrolase/Cytokine
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-17 Released: 2010-04-14 
• Deposition Author(s): Ren, M., Guo, Q., Tang, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Macrophage Inflammatory Protein-1 Is A Novel High Affinity Substrate For Human Insulin Degrading Enzyme

Ren, M., Guo, Q., Tang, W.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 245.37 kDa 
• Atom Count: 15,937 
• Modelled Residue Count: 1,929 
• Deposited Residue Count: 2,120 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	990	Homo sapiens	Mutation(s): 14  Gene Names: IDE EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens) Explore P14735  Go to UniProtKB:  P14735
PHAROS:  P14735 GTEx:  ENSG00000119912

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-C motif chemokine 3	C, D	70	Homo sapiens	Mutation(s): 0  Gene Names: CCL3, G0S19-1, MIP1A, MIP1alpha, SCYA3
UniProt & NIH Common Fund Data Resources
Find proteins for P10147 (Homo sapiens) Explore P10147  Go to UniProtKB:  P10147
PHAROS:  P10147 GTEx:  ENSG00000277632

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
ZN	H [auth B], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 262.737	α = 90
b = 262.737	β = 90
c = 90.502	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Ren, M., Guo, Q., Tang, W.J.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description