6PXF

Structure of human Cathepsin K with an ectosteric inhibitor at 1.85 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6PXF/pdb

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


• Deposited: 2019-07-25 Released: 2020-07-29 
• Deposition Author(s): Law, S., Aguda, A.H., Nguyen, N.T., Brayer, G.D., Bromme, D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structure of human Cathepsin K with an ectosteric inhibitor at 1.85 Angstrom resolution

Law, S., Aguda, A.H., Nguyen, N.T., Brayer, G.D., Bromme, D.

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)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 25.01 kDa 
• Atom Count: 1,887 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Homo sapiens	Mutation(s): 1  Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235  Go to UniProtKB:  P43235
PHAROS:  P43235 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J0V (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	1,6,6-trimethyl-10,11-dioxo-6,7,8,9,10,11-hexahydrophenanthro[1,2-b]furan-2-sulfonic acid C19 H18 O6 S UJCACMLMPLLRGW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.669	α = 90
b = 67.68	β = 90
c = 92.249	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Law, S., Aguda, A.H., Nguyen, N.T., Brayer, G.D., Bromme, D.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-89974
Canadian Institutes of Health Research (CIHR)	Canada	MOP-125866
Canadian Institutes of Health Research (CIHR)	Canada	MOP-125866
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-326803-13

Revision History  

• Version 1.0: 2020-07-29
  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