9SUQ | pdb_00009suq

Crystal structure of the zymogen of cathepsin D from Schistosoma mansoni

• PDB DOI: https://doi.org/10.2210/pdb9SUQ/pdb

• Classification: HYDROLASE
• Organism(s): Schistosoma mansoni
• Expression System: Leishmania donovani
• Mutation(s): No 


• Deposited: 2025-09-29 Released: 2026-10-07 
• Deposition Author(s): Busa, M., Brynda, J., Houstecka, R., Hanova, I., Mares, M.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the zymogen of cathepsin D from Schistosoma mansoni

Busa, M., Houstecka, R., Hanova, I., Mares, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 98.2 kDa 
• Atom Count: 6,159 
• Modeled Residue Count: 733 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin D (A01 family)	A, B	434	Schistosoma mansoni	Mutation(s): 0  EC: 3.4.23.1
UniProt
Find proteins for G4VEV6 (Schistosoma mansoni) Explore G4VEV6  Go to UniProtKB:  G4VEV6
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOE	G [auth A]	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL C7 H16 O4 JLGLQAWTXXGVEM-UHFFFAOYSA-N
SO4	H [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.727	α = 90
b = 112.807	β = 90
c = 114.235	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Busa, M., Brynda, J., Houstecka, R., Hanova, I., Mares, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LUAUS23050

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release