6GHX

Alzheimer's Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd-substituted Thermolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
View more details

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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolysin316Geobacillus stearothermophilusMutation(s): 0 
EC: 3.4.24.27
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ILE
Query on ILE

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
F [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.06α = 90
b = 93.06β = 90
c = 130.29γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
PortugalSFRH/BD/129921/2017

Revision History  (Full details and data files)

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