5OM7

Crystal structure of Alpha1-antichymotrypsin variant DBS-II: a drug-binding serpin for doxorubicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report



Literature

Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein.

Schmidt, K.Gardill, B.R.Kern, A.Kirchweger, P.Borsch, M.Muller, Y.A.

(2018) Proc Natl Acad Sci U S A 115: 5744-5749

  • DOI: 10.1073/pnas.1716666115
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The allosteric interplay between distant functional sites present in a single protein provides for one of the most important regulatory mechanisms in biological systems. While the design of ligand-binding sites into proteins remains challenging, this ...

    The allosteric interplay between distant functional sites present in a single protein provides for one of the most important regulatory mechanisms in biological systems. While the design of ligand-binding sites into proteins remains challenging, this holds even truer for the coupling of a newly engineered binding site to an allosteric mechanism that regulates the ligand affinity. Here it is shown how computational design algorithms enabled the introduction of doxycycline- and doxorubicin-binding sites into the serine proteinase inhibitor (serpin) family member α1-antichymotrypsin. Further engineering allowed exploitation of the proteinase-triggered serpin-typical S-to-R transition to modulate the ligand affinities. These design variants follow strategies observed in naturally occurring plasma globulins that allow for the targeted delivery of hormones in the blood. By analogy, we propose that the variants described in the present study could be further developed to allow for the delivery of the antibiotic doxycycline and the anticancer compound doxorubicin to tissues/locations that express specific proteinases, such as bacterial infection sites or tumor cells secreting matrix metalloproteinases.


    Organizational Affiliation

    Department of Biotechnology, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany; yves.muller@fau.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-1-antichymotrypsinA369Homo sapiensMutation(s): 17 
Gene Names: SERPINA3AACTGIG24GIG25
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
NIH Common Fund Data Resources
PHAROS  P01011
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Alpha-1-antichymotrypsinB40Homo sapiensMutation(s): 7 
Gene Names: SERPINA3AACTGIG24GIG25
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
NIH Common Fund Data Resources
PHAROS  P01011
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM2
Query on DM2

Download CCD File 
A
DOXORUBICIN
C27 H29 N O11
AOJJSUZBOXZQNB-TZSSRYMLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.463α = 90
b = 84.463β = 90
c = 98.322γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK-1962

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 2.0: 2018-06-06
    Changes: Atomic model, Data collection, Database references