9HJY | pdb_00009hjy

Cathepsin L3 from Ixodes ricinus (IrCL3) inhibited by E-64

• PDB DOI: https://doi.org/10.2210/pdb9HJY/pdb

• Classification: HYDROLASE
• Organism(s): Ixodes ricinus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2024-12-02 Released: 2025-12-17 
• Deposition Author(s): Schenkmayerova, A., Orsaghova, K., Benova, M., Busa, M., Mares, M.
• Funding Organization(s): Czech Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: in silico

Literature

Cathepsin L3 from Ixodes ricinus (IrCL3) inhibited by E-64

Orsaghova, K., Benova, M., Busa, M., Schenkmayerova, A., Mares, M., Horn, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.06 kDa 
• Atom Count: 1,885 
• Modeled Residue Count: 219 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Late digestive cathepsin L	A	224	Ixodes ricinus	Mutation(s): 0  Gene Names: CL3
UniProt
Find proteins for A0A481Y5N4 (Ixodes ricinus) Explore A0A481Y5N4  Go to UniProtKB:  A0A481Y5N4
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64 (Subject of Investigation/LOI)	D [auth A]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.967	α = 90
b = 76.911	β = 90
c = 152.347	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Schenkmayerova, A., Orsaghova, K., Benova, M., Busa, M., Mares, M.

---

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	21-08826S

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release