4M1C | pdb_00004m1c

Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40)

• PDB DOI: https://doi.org/10.2210/pdb4M1C/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-02 Released: 2014-08-06 
• Deposition Author(s): McCord, L.M., Liang, W., Farcasanu, M., Scherpelz, K., Meredith, S.C., Koide, S., Tang, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40)

McCord, L.A., Liang, W., Farcasanu, M., Scherpelz, K., Meredith, S.C., Koide, S., Tang, W.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 346.29 kDa 
• Atom Count: 21,509 
• Modeled Residue Count: 2,692 
• Deposited Residue Count: 3,064 
• Unique protein chains: 4

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, Insulin Degrading Enzyme 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
Fab-bound IDE, heavy chain	C, E	263	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-bound IDE, light chain	D, F	239	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	G, H	40	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.583	α = 90
b = 135.324	β = 90
c = 368.524	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): McCord, L.M., Liang, W., Farcasanu, M., Scherpelz, K., Meredith, S.C., Koide, S., Tang, W.J.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Source and taxonomy
• Version 1.2: 2014-10-08
  Changes: Derived calculations
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary