1CTE

CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design.

Jia, Z.Hasnain, S.Hirama, T.Lee, X.Mort, J.S.To, R.Huber, C.P.

(1995) J.Biol.Chem. 270: 5527-5533

  • Primary Citation of Related Structures:  1CPJ, 1THE

  • PubMed Abstract: 
  • The lysosomal cysteine proteinase cathepsin B (EC 3.4.22.1) plays an important role in protein catabolism and has also been implicated in various disease states. The crystal structures of two forms of native recombinant rat cathepsin B have been dete ...

    The lysosomal cysteine proteinase cathepsin B (EC 3.4.22.1) plays an important role in protein catabolism and has also been implicated in various disease states. The crystal structures of two forms of native recombinant rat cathepsin B have been determined. The overall folding of rat cathepsin B was shown to be very similar to that of the human liver enzyme. The structure of the native enzyme containing an underivatized active site cysteine (Cys29) showed the active enzyme conformation to be similar to that determined previously for the oxidized form. In a second structure Cys29 was derivatized with the reversible blocking reagent pyridyl disulfide. In this structure large side chain conformational changes were observed for the two key catalytic residues Cys29 and His199, demonstrating the potential flexibility of these side chains. In addition the structure of the complex between rat cathepsin B and the inhibitor benzyloxycarbonyl-Arg-Ser(O-Bzl) chloromethylketone was determined. The complex structure showed that very little conformational change occurs in the enzyme upon inhibitor binding. It also allowed visualization of the interaction between the enzyme and inhibitor. In particular the interaction between Glu245 and the P2 Arg residue was clearly demonstrated, and it was found that the benzyl group of the P1 substrate residue occupies a large hydrophobic pocket thought to represent the S'1 subsite. This may have important implications for structure-based design of cathepsin B inhibitors.


    Related Citations: 
    • Crystallization of Recombinant Rat Cathepsin B
      Lee, X.,Ahmed, F.R.,Hirama, T.,Huber, C.P.,Rose, D.R.,To, R.,Hasnain, S.,Tam, A.,Mort, J.S.
      (1990) J.Biol.Chem. 265: 5950


    Organizational Affiliation

    Institute for Biological Sciences, National Research Council of Canada, Ottawa.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN B
A, B
254Rattus norvegicusGene Names: Ctsb
EC: 3.4.22.1
Find proteins for P00787 (Rattus norvegicus)
Go to UniProtKB:  P00787
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYS
Query on PYS

Download SDF File 
Download CCD File 
A, B
2-PYRIDINETHIOL
C5 H5 N S
WHMDPDGBKYUEMW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.070α = 90.00
b = 90.190β = 97.43
c = 62.210γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
SDMSdata reduction
X-PLORmodel building
SDMSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-05-03 
  • Released Date: 1995-07-31 
  • Deposition Author(s): Huber, C.P., Jia, Z.

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance