5QCD | pdb_00005qcd

Crystal structure of human Cathepsin-S with bound ligand

• PDB DOI: https://doi.org/10.2210/pdb5QCD/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: 1.95 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.154 (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.

Macromolecule Content 

• Total Structure Weight: 25.32 kDa 
• Atom Count: 2,039 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BHJ	B [auth A]	{(3S)-7-[(2-chloro-5-{5-(methylsulfonyl)-1-[3-(morpholin-4-yl)propyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}phenyl)ethynyl]-1,2,3,4-tetrahydroisoquinolin-3-yl}(piperidin-1-yl)methanone C37 H45 Cl N6 O4 S BIYANWMTXPESQI-UMSFTDKQSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.952	α = 90
b = 73.329	β = 103.97
c = 44.594	γ = 90

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, Structure summary
• 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