4BPV | pdb_00004bpv

MOUSE CATHEPSIN S WITH COVALENT LIGAND

• PDB DOI: https://doi.org/10.2210/pdb4BPV/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-28 Released: 2014-06-11 
• Deposition Author(s): Banner, D.W., Benz, J., Gsell, B., Stihle, M., Ruf, A., Haap, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: other

Literature

Cathepsin S Nitrile Inhibitors

Haap, W., Banner, D.W.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.99 kDa 
• Atom Count: 10,276 
• Modeled Residue Count: 1,184 
• Deposited Residue Count: 1,350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATHEPSIN S	A, B, C, D, E, F [auth K]	225	Mus musculus	Mutation(s): 1  EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for O70370 (Mus musculus) Explore O70370  Go to UniProtKB:  O70370
IMPC:  MGI:107341

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OFH	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E]	(4R)-4-[(2-chloro-4-{[(2S)-1,1,1-trifluoropropan-2-yl]oxy}phenyl)sulfonyl]-N-{1-[(E)-iminomethyl]cyclopropyl}-1-{[1-(trifluoromethyl)cyclopropyl]carbonyl}-L-prolinamide C23 H24 Cl F6 N3 O5 S FXRUMLCPKBCVCA-YDWYZIHQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.855	α = 90
b = 128.917	β = 97.44
c = 97.132	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): Banner, D.W., Benz, J., Gsell, B., Stihle, M., Ruf, A., Haap, W.

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary