5OM3

Crystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MMP14-cleavable drug-binding serpin for doxycycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1073/pnas.1716666115
  • Primary Citation of Related Structures:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-1-antichymotrypsin
A
369Homo sapiensMutation(s): 14 
Gene Names: SERPINA3 (AACT)
Find proteins for P01011 (Homo sapiens)
Go to Gene View: SERPINA3
Go to UniProtKB:  P01011
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Alpha-1-antichymotrypsin
B
40Homo sapiensMutation(s): 8 
Gene Names: SERPINA3 (AACT)
Find proteins for P01011 (Homo sapiens)
Go to Gene View: SERPINA3
Go to UniProtKB:  P01011
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DXT
Query on DXT

Download SDF File 
Download CCD File 
B
(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
DOXYTETRACYCLINE, DOXYCYCLINE
C22 H24 N2 O8
JBIWCJUYHHGXTC-AKNGSSGZSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.321α = 90.00
b = 84.321β = 90.00
c = 98.156γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 1.1: 2018-06-06
    Type: Data collection, Database references