8A4X

Crystal structure of human Cathepsin L with covalently bound Calpain inhibitor III

• PDB DOI: https://doi.org/10.2210/pdb8A4X/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2022-06-13 Released: 2023-07-05 
• Deposition Author(s): Falke, S., Lieske, J., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Chapman, H.N., Hinrichs, W., 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: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Structural elucidation of antiviral cathepsin L inhibitors

Falke, S., Lieske, J., Herrmann, A., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Chapman, H.N., Hinrichs, W., 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 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 99.84 kDa 
• Atom Count: 7,332 
• Modelled Residue Count: 865 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L	A, B, C, D	220	Homo sapiens	Mutation(s): 1  Gene Names: CTSL, CTSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711  Go to UniProtKB:  P07711
PHAROS:  P07711 GTEx:  ENSG00000135047

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L3F (Subject of Investigation/LOI)	E [auth A], I [auth B], N [auth C], R [auth D]	(phenylmethyl) N-[(2S)-3-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]carbamate C22 H28 N2 O4 VLFHBNSJHLMKMM-PMACEKPBSA-N
P6G	Q [auth C], S [auth D]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	H [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	F [auth A], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.95	α = 105.472
b = 62.25	β = 93.522
c = 67.11	γ = 116.065

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
autoPROC	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Falke, S., Lieske, J., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Chapman, H.N., Hinrichs, W., 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
German Federal Ministry for Education and Research	Germany	16GW0277
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description