4GUX

Crystal structure of trypsin:MCoTi-II complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.803 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural insights into the role of the cyclic backbone in a squash trypsin inhibitor

Daly, N.L., Thorstholm, L., Greenwood, K.P., King, G.J., Rosengren, K.J., Heras, B., Martin, J.L., Craik, D.J.

(2013) J.Biol.Chem. 288: 36141-36148

  • DOI: 10.1074/jbc.M113.528240

  • PubMed Abstract: 

    • MCoTI-II is a head-to-tail cyclic peptide with potent trypsin inhibitory activity and, on the basis of its exceptional proteolytic stability, is a valuable template for the design of novel drug leads. Insights into inhibitor dynamics and interactions ...

    MCoTI-II is a head-to-tail cyclic peptide with potent trypsin inhibitory activity and, on the basis of its exceptional proteolytic stability, is a valuable template for the design of novel drug leads. Insights into inhibitor dynamics and interactions with biological targets are critical for drug design studies, particularly for protease targets. Here, we show that the cyclization and active site loops of MCoTI-II are flexible in solution, but when bound to trypsin, the active site loop converges to a single well defined conformation. This finding of reduced flexibility on binding is in contrast to a recent study on the homologous peptide MCoTI-I, which suggested that regions of the peptide are more flexible upon binding to trypsin. We provide a possible explanation for this discrepancy based on degradation of the complex over time. Our study also unexpectedly shows that the cyclization loop, not present in acyclic homologues, facilitates potent trypsin inhibitory activity by engaging in direct binding interactions with trypsin.

    Organizational Affiliation: 

    From the Institute for Molecular Bioscience and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A, B, C
246Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trypsin inhibitor 2
D, E, F
34Momordica cochinchinensisMutation(s): 0 
Find proteins for P82409 (Momordica cochinchinensis)
Go to UniProtKB:  P82409
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000750
Query on PRD_000750		D,E,FCYCLIC KNOTTIN TRYPSIN INHIBITOR IICyclic peptide / Antimicrobial, Antitumor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.803 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.139α = 90.00
b = 71.852β = 119.76
c = 108.460γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
Blu-Icedata collection
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references