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 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1073/pnas.1716666115
  • Primary Citation of Related Structures:  
    5OM2, 5OM3, 5OM5, 5OM6, 5OM7, 5OM8, 6FTP

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsin369Homo sapiensMutation(s): 17 
Gene Names: SERPINA3AACTGIG24GIG25
UniProt & NIH Common Fund Data Resources
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
PHAROS:  P01011
GTEx:  ENSG00000196136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01011
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1-antichymotrypsin40Homo sapiensMutation(s): 7 
Gene Names: SERPINA3AACTGIG24GIG25
UniProt & NIH Common Fund Data Resources
Find proteins for P01011 (Homo sapiens)
Explore P01011 
Go to UniProtKB:  P01011
PHAROS:  P01011
GTEx:  ENSG00000196136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01011
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DM2
Query on DM2

Download Ideal Coordinates CCD File 
C [auth A]DOXORUBICIN
C27 H29 N O11
AOJJSUZBOXZQNB-TZSSRYMLSA-N
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

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK-1962

Revision History  (Full details and data files)

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