6UX6 | pdb_00006ux6

Cruzain covalently bound by a vinylsulfone compound

• PDB DOI: https://doi.org/10.2210/pdb6UX6/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-06 Released: 2020-11-25 
• Deposition Author(s): Zhai, X., Tang, S., Chenna, B.C., Meek, T.D., Sacchettini, J.C.
• Funding Organization(s): National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Cruzain covalently bound by a vinylsulfone compound

Zhai, X., Tang, S., Chenna, B.C., Meek, T.D., Sacchettini, J.C.

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)

Macromolecule Content 

• Total Structure Weight: 23.38 kDa 
• Atom Count: 1,706 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cruzipain	A	215	Trypanosoma cruzi	Mutation(s): 0  EC: 3.4.22.51
UniProt
Find proteins for P25779 (Trypanosoma cruzi) Explore P25779  Go to UniProtKB:  P25779

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TM8 (Subject of Investigation/LOI)	B [auth A]	Nalpha-[(benzyloxy)carbonyl]-N-[(2S)-1-phenyl-4-(phenylsulfonyl)butan-2-yl]-L-phenylalaninamide C33 H34 N2 O5 S RLNXSKBHINXQAP-VEEOACQBSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TM8	BindingDB:  6UX6	Ki: 3.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.509	α = 90
b = 122.127	β = 90
c = 34.585	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Zhai, X., Tang, S., Chenna, B.C., Meek, T.D., Sacchettini, J.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)	United States	--

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary