9GJ2

Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b

• PDB DOI: https://doi.org/10.2210/pdb9GJ2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-08-20 Released: 2024-09-04 
• Deposition Author(s): Falke, S., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Reinke, P.Y.A., Guenther, S., Turk, D., Meents, A.
• Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research, Slovenian Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.162 
• R-Value Work: 0.151 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b

Falke, S., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Reinke, P.Y.A., Guenther, S., Turk, D., Meents, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.31 kDa 
• Atom Count: 4,041 
• Modelled Residue Count: 440 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	242	Homo sapiens	Mutation(s): 0  Gene Names: CTSS EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens) Explore P25774  Go to UniProtKB:  P25774
PHAROS:  P25774 GTEx:  ENSG00000163131

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KH0 (Subject of Investigation/LOI)	C [auth A], H [auth B]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C31 H41 N5 O7 FRACPXUHUTXLCX-LFBFJMOVSA-N
CIT	J [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
DMS	F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], I [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.162 
• R-Value Work: 0.151 
• R-Value Observed: 0.151 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.102	α = 90
b = 86.102	β = 90
c = 152.045	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Falke, S., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Reinke, P.Y.A., Guenther, S., Turk, D., Meents, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	FISCOV
Helmholtz Association	Germany	SFragX
German Federal Ministry for Education and Research	Germany	031B0405
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary