5ONQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1002/1873-3468.13285
  • Primary Citation of Related Structures:  

  • 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 sequ ...

    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

    IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Geobacillus stearothermophilusMutation(s): 0 
Gene Names: nprS (nprM)
EC: 3.4.24.27
Find proteins for P43133 (Geobacillus stearothermophilus)
Go to UniProtKB:  P43133
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amyloid-beta A4 protein
B
5Homo sapiensMutation(s): 0 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.163 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.488α = 90.00
b = 93.488β = 90.00
c = 129.558γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-08-04 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Leite, J.P., Gales, L.

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references