8HE9

Crystal structure of CTSB in complex with K777

• PDB DOI: https://doi.org/10.2210/pdb8HE9/pdb

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


• Deposited: 2022-11-07 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: 0.202 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Crystal structure of CTSB in complex with K777

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: 28.81 kDa 
• Atom Count: 2,128 
• Modelled Residue Count: 253 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A	255	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0IW (Subject of Investigation/LOI)	B [auth A]	Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide C32 H40 N4 O4 S VZSXPUDQSLKVIR-JDXGNMNLSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000325 (0IW)	B [auth A]	MePip-Phe-HphVSPh	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.202 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.432	α = 90
b = 70.497	β = 90
c = 93.739	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
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