9GRG | pdb_00009grg

StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with PMSF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.235 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.178 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Unveiling the structure, function and dynamics of StmPr1 in Stenotrophomonas maltophilia virulence.

Sommer, M.Negm, A.Outzen, L.Windhorst, S.Gabdulkhakov, A.Weber, W.Betzel, C.

(2025) Sci Rep 15: 20193-20193

  • DOI: https://doi.org/10.1038/s41598-025-06177-5
  • Primary Citation of Related Structures:  
    9G8V, 9GOI, 9GRG, 9I67, 9I6C

  • PubMed Abstract: 

    The increase in infections caused by multi-resistant Gram-negative bacteria, like Stenotrophomonas maltophilia, has become a growing health crisis worldwide. S. maltophilia poses a risk because of its tendency to opportunistically infecting patience for example through colonization of catheters in hospital environments using its intrinsic resistance against multiple antibiotics. Through the COVID-19 pandemic it gained more prominence by being a key pathogen in respiratory co-infections. This study will present a structural analysis of StmPr1, S. maltophilia's main virulence factor, an excreted serine protease. Our study outline structure and functional aspects of StmPr1, revealing a unique autoproteolytic activity resulting in a shortened version of the active enzyme. We also investigated the potential of two groups of peptide-based inhibitors, one being acetyl- and the other being boron-based inhibitors. The focus here lies on Bortezomib, a boron-based serine protease inhibitor, and its potential therapeutic use against S. maltophilia. We provide a structure-function analysis which includes X-ray crystallography data with resolutions ranging from 1.64 to 2.08 Å, molecular dynamic simulations and small-angle X-ray scattering (SAXS) experiments. These data provide a deeper understanding of StmPr1's resilience and mechanisms, while highlighting the relevance of StmPr1's C-terminal extension for correct folding and its stability. Moreover, it also shows that StmPr1 is promising target for further drug discovery investigations to identify compounds and drugs to treat S. maltophilia infections.


  • Organizational Affiliation

    Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603, Hamburg, Germany. m.sommer.92@gmx.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline serine protease356Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: StmPr1
UniProt
Find proteins for Q93IQ4 (Stenotrophomonas maltophilia)
Explore Q93IQ4 
Go to UniProtKB:  Q93IQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93IQ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMS (Subject of Investigation/LOI)
Query on PMS

Download Ideal Coordinates CCD File 
C [auth A]phenylmethanesulfonic acid
C7 H8 O3 S
NIXKBAZVOQAHGC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.902α = 90
b = 85.747β = 90
c = 130.747γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release