8CCU

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 1

• PDB DOI: https://doi.org/10.2210/pdb8CCU/pdb

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


• Deposited: 2023-01-27 Released: 2024-02-07 
• Deposition Author(s): Rubesova, P., Brynda, 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: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.160 

Literature

Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 1

Rubesova, P., Brynda, 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: 29.17 kDa 
• Atom Count: 2,396 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U9X (Subject of Investigation/LOI)	B [auth AAA]	[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-5-[(2~{S})-3-methoxy-2-(2-methylpropyl)-5-oxidanylidene-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},3~{S})-2-(dimethylamino)-3-methyl-pentanoate C34 H60 N4 O7 QKERMDKGLIBAHM-VZNHIJNGSA-N
NA	C [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.081	α = 90
b = 79.031	β = 90
c = 90.584	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: 2024-02-07 
Deposition Author(s): Rubesova, P., Brynda, 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: 2024-02-07
  Type: Initial release