5ONP

Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd-substituted Thermolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 

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


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: 1.34 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.412α = 90.00
b = 93.412β = 90.00
c = 130.149γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

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