5QC2 | pdb_00005qc2

Crystal structure of human Cathepsin-S with bound ligand

• PDB DOI: https://doi.org/10.2210/pdb5QC2/pdb
• Deposition Group: G_1002040 | Explore  G_1002040  

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-08-04 Released: 2017-12-20 
• Deposition Author(s): Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Crystal structure of human Cathepsin-S with bound ligand

Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

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.

Macromolecule Content 

• Total Structure Weight: 50.45 kDa 
• Atom Count: 3,867 
• Modeled Residue Count: 438 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	223	Homo sapiens	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BQP	C [auth A], D [auth B]	2-[1-(cyclohexylmethyl)piperidin-4-yl]-1-{3-[3-{[2-(4-fluoropiperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-1-(3-hydroxypropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethan-1-one C37 H53 F4 N5 O2 S HHMNMVKIYRQSRB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.974	α = 70.6
b = 53.635	β = 72.11
c = 58.487	γ = 73.58

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Structure summary
• Version 2.0: 2018-06-06
  Changes: Atomic model, Data collection, Refinement description
• Version 2.1: 2021-02-10
  Changes: Database references, Structure summary
• Version 2.2: 2021-11-17
  Changes: Database references, Structure summary
• Version 2.3: 2024-11-06
  Changes: Data collection, Structure summary