4KTS

Bovine trypsin in complex with microviridin J at pH 8.5

• PDB DOI: https://doi.org/10.2210/pdb4KTS/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bos taurus, Microcystis aeruginosa MRC
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-21 Released: 2014-04-02 
• Deposition Author(s): Quitterer, F., Groll, M., Hertweck, C., Dittmann, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.128 
• R-Value Work: 0.106 
• R-Value Observed: 0.107 

Starting Model: experimental

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

• PubMed: 24591244 
• DOI: https://doi.org/10.1002/anie.201309721
• Primary Citation of Related Structures:  
  4KTS, 4KTU


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.2 kDa 
• Atom Count: 2,107 
• Modelled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microviridin	B	14	Microcystis aeruginosa MRC	Mutation(s): 1  Gene Names: mdnA
UniProt
Find proteins for B2G3C8 (Microcystis aeruginosa MRC) Explore B2G3C8  Go to UniProtKB:  B2G3C8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001086	B	Microviridin J	Cyclic peptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.128 
• R-Value Work: 0.106 
• R-Value Observed: 0.107 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.33	α = 90
b = 64.49	β = 90
c = 71.21	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Quitterer, F., Groll, M., Hertweck, C., Dittmann, E.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary