8HEI

Crystal structure of CTSB in complex with E64d

• PDB DOI: https://doi.org/10.2210/pdb8HEI/pdb

• Classification: ANTIVIRAL PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-08 Released: 2023-12-13 
• Deposition Author(s): Wang, H., Li, D., Sun, L., Yang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.173 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 

Literature

Crystal structure of CTSB in complex with E64d

Wang, H., Li, D., Sun, L., Yang, H.

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

Macromolecule Content

• Total Structure Weight: 28.82 kDa 
• Atom Count: 2,262 
• Modelled Residue Count: 255 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A	257	Homo sapiens	Mutation(s): 0  Gene Names: CTSB, CPSB EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens) Explore P07858  Go to UniProtKB:  P07858
PHAROS:  P07858 GTEx:  ENSG00000164733

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E6D (Subject of Investigation/LOI)	B [auth A]	ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate C17 H32 N2 O5 FGRTVYZNNRCSAS-KBPBESRZSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.173 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.115	α = 90
b = 81.509	β = 90
c = 94.106	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Wang, H., Li, D., Sun, L., Yang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92169109

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release