9CT1 | pdb_00009ct1

Complex between the porcine trypsin and M271 a Kunitz-STI from Solanum tuberosum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.244 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CT1

This is version 1.1 of the entry. See complete history

Literature

Structural determination of a new non-canonical inhibition complex between porcine trypsin and M271 a potato Kunitz-STI inhibitor.

Campuzano-Gonzalez, A.Gil-Rodriguez, P.Quintana-Armas, A.X.Guerra, Y.Perez, Y.Rudino-Pinera, E.

(2025) Biochem Biophys Res Commun 768: 151818-151818

  • DOI: https://doi.org/10.1016/j.bbrc.2025.151818
  • Primary Citation Related Structures: 
    9CSZ, 9CT1

  • PubMed Abstract: 

    The Kunitz-Soybean Trypsin Inhibitor (Kunitz-STI) is a protein family found in different plants. Several of its members have been experimentally described as inhibitors of various classes of proteases from several organisms. Even though most of the previous crystallographic studies describing the protease inhibition interactions present by different Kunitz-STI family members have been focused on serine proteases, the protein family has been proposed as a promising scaffold for multifunctional protease inhibitor design with a wide range of applications. In this work, a crystallographic complex formed between M271, a Kunitz-STI inhibitor obtained from Solanum tuberosum, and porcine trypsin shows a new inhibitory ensemble in which inhibitor's loops β1-β2 and β3-β4 play a central role. Additionally, the structural analysis demonstrates that the inhibition described here follows a non-canonical mechanism in which the inhibitor loops block the trypsin active site. Our findings expand the repertoire of protease-binding loops in which a Kunitz-STI inhibitor can inhibit trypsin, emphasizing the role of the dynamic characteristics of this protein family member on the protease inhibition process. This work also gives a new example of the remarkable plasticity of the Kunitz-STI fold, in which an arrangement with eleven highly sequence-variable loops projected to the solvent demonstrates a simple answer for a multifunctional evolutionary tool to inhibit proteases.


  • Organizational Affiliation
    • Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Morelos, Mexico. Electronic address: alexis.campuzano@ibt.unam.mx.

Macromolecule Content 

  • Total Structure Weight: 92.39 kDa 
  • Atom Count: 6,125 
  • Modeled Residue Count: 782 
  • Deposited Residue Count: 852 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trypsin
A, C
231Sus scrofaMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa)
Explore P00761 
Go to UniProtKB:  P00761
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00761
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KTI-A protein
B, D
195Solanum tuberosumMutation(s): 0 
Gene Names: KTI-A
UniProt
Find proteins for Q41448 (Solanum tuberosum)
Explore Q41448 
Go to UniProtKB:  Q41448
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41448
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.244 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.249α = 90
b = 85.887β = 90
c = 186.063γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentMexicoDGAPA - PAPIIT - UNAM IN226523

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references