9CSZ | pdb_00009csz

Crystallographic structure of M271 a new Kunitz-STI from potato


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.203 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KTI-A proteinA [auth B],
B [auth A]
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ETE
Query on ETE

Download Ideal Coordinates CCD File 
H [auth A]2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
I [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
F [auth B]
G [auth B]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
G [auth B],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.203 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.398α = 90
b = 76.711β = 90
c = 82.369γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentDGPA-PAPIIT-UNAM IN226523
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

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