8CD9

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 6

• PDB DOI: https://doi.org/10.2210/pdb8CD9/pdb

• Classification: HYDROLASE
• Organism(s): Schistosoma mansoni
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-01-30 Released: 2024-02-21 
• Deposition Author(s): Rubesova, P., Brynda, J., Fanfrlik, J., Gerwick, W.H., Mares, M.
• Funding Organization(s): Other government, Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.216 
• R-Value Work: 0.178 

Literature

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 6

Rubesova, P., Brynda, J., Fanfrlik, J., Gerwick, W.H., Mares, 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: homology

Macromolecule Content

• Total Structure Weight: 29.3 kDa 
• Atom Count: 2,368 
• Modelled Residue Count: 254 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B-like peptidase (C01 family)	A [auth AAA]	254	Schistosoma mansoni	Mutation(s): 2  Gene Names: cb1.1, Smp_103610
UniProt
Find proteins for Q8MNY2 (Schistosoma mansoni) Explore Q8MNY2  Go to UniProtKB:  Q8MNY2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UA9 (Subject of Investigation/LOI)	B [auth AAA]	[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-5-[(2~{S})-3-methoxy-5-oxidanylidene-2-(phenylmethyl)-2~{H}-pyrrol-1-yl]-5-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl] (2~{S})-2-(dimethylamino)-3-phenyl-propanoate C40 H56 N4 O7 WESAHNJMKCXPAC-WEHFJZMFSA-N
EDO	C [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.216 
• R-Value Work: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.062	α = 90
b = 78.87	β = 90
c = 90.139	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Rubesova, P., Brynda, J., Fanfrlik, J., Gerwick, W.H., Mares, M.

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Funding Organization	Location	Grant Number
Other government		NV18-05-00345
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LTAUSA19109

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release