Alzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd-substituted Thermolysin

Experimental Data Snapshot

  • Resolution: 1.17 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Alzheimer's A beta1-40peptide degradation by thermolysin: evidence of inhibition by a C-terminal A beta product.

Leite, J.P.Gales, L.

(2019) FEBS Lett 593: 128-137

  • DOI: https://doi.org/10.1002/1873-3468.13285
  • Primary Citation of Related Structures:  
    5ONP, 5ONQ, 5ONR, 6GHX

  • PubMed Abstract: 

    The interaction of the amyloid-β peptide (Aβ) with thermolysin (TLN) was investigated by X-ray crystallography. Structural models of the complexes of TLN with several Aβ fragments show that, despite the numerous possible cleavage sites of the Aβ sequence, the C-terminal product of Ala30-Ile31 cleavage does not dissociate, thus inhibiting the enzyme. The high similarity between the TLN structural motif and neprilysin (NEP), the most extensively studied peptidase associated with Aβ clearance, suggests that NEP should be more efficient against Aβ polymorphs where Ala30-Ile31 is inaccessible, which is in agreement with studies in living mice that point to the limited role of NEP in degrading soluble Aβ and its higher ability to degrade insoluble and/or oligomeric Aβ forms, producing only the Aβ 10-37 intermediate.

  • Organizational Affiliation

    i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolysin316Geobacillus stearothermophilusMutation(s): 0 
Find proteins for P43133 (Geobacillus stearothermophilus)
Explore P43133 
Go to UniProtKB:  P43133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43133
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid-beta A4 protein5Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
GTEx:  ENSG00000142192 
Entity Groups  
UniProt GroupP05067
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.17 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.488α = 90
b = 93.488β = 90
c = 129.558γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description