4KTS

Bovine trypsin in complex with microviridin J at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.106 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Harnessing the evolvability of tricyclic microviridins to dissect protease-inhibitor interactions.

Weiz, A.R.Ishida, K.Quitterer, F.Meyer, S.Kehr, J.C.Muller, K.M.Groll, M.Hertweck, C.Dittmann, E.

(2014) Angew.Chem.Int.Ed.Engl. 53: 3735-3738

  • DOI: 10.1002/anie.201309721
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Understanding and controlling proteolysis is an important goal in therapeutic chemistry. Among the natural products specifically inhibiting proteases microviridins are particularly noteworthy. Microviridins are ribosomally produced and posttranslatio ...

    Understanding and controlling proteolysis is an important goal in therapeutic chemistry. Among the natural products specifically inhibiting proteases microviridins are particularly noteworthy. Microviridins are ribosomally produced and posttranslationally modified peptides that are processed into a unique, cagelike architecture. Here, we report a combined rational and random mutagenesis approach that provides fundamental insights into selectivity-conferring moieties of microviridins. The potent variant microviridin J was co-crystallized with trypsin, and for the first time the three-dimensional structure of microviridins was determined and the mode of inhibition revealed.


    Organizational Affiliation

    Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm (Germany).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Microviridin
B
14Microcystis aeruginosa MRCMutation(s): 0 
Gene Names: mdnA
Find proteins for B2G3C8 (Microcystis aeruginosa MRC)
Go to UniProtKB:  B2G3C8
Small Molecules
Ligands 2 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
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001086
Query on PRD_001086
BMicroviridin JCyclic peptide / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.106 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.330α = 90.00
b = 64.490β = 90.00
c = 71.210γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references