1CSB

Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors.

Turk, D.Podobnik, M.Popovic, T.Katunuma, N.Bode, W.Huber, R.Turk, V.

(1995) Biochemistry 34: 4791-4797


  • PubMed Abstract: 
  • Crystals of cysteine protease human cathepsin B inhibited with CA030 (ethyl ester of epoxysuccinyl-Ile-Pro-OH) [Murata, M., et al. (1991) FEBS Lett. 280, 307-310; Towatari, T., et al. (1991) FEBS Lett. 280, 311-315] were isomorphous to a previous pub ...

    Crystals of cysteine protease human cathepsin B inhibited with CA030 (ethyl ester of epoxysuccinyl-Ile-Pro-OH) [Murata, M., et al. (1991) FEBS Lett. 280, 307-310; Towatari, T., et al. (1991) FEBS Lett. 280, 311-315] were isomorphous to a previous published structure of cathepsin B [Musil, D., et al. (1991) EMBO J. 10, 2321-2330]. The crystal structure of the complex was refined at 2.0-A resolution to an R-value of 0.194. CA030 is well-defined in the electron density. The Ile-Pro-OH part of CA030 mimics a substrate P1' and P2' residues. The structure thus reveals for the first time a substratelike interaction in the S1' and S2' sites of a papain-like cysteine protease. The CA030 ethyl ester group occupies the S2 site. The structure confirms the role of residues His 110 and His 111 as the receptors of a peptidic substrate C-terminal carboxylic group. The structure suggests that an epoxysuccinyl fragment can be used to extend binding into primed and nonprimed substrate binding sites of a papain-like cysteine protease.


    Related Citations: 
    • The Refined 2.15 Angstrom X-Ray Crystal Structure of Human Liver Cathepsin B: The Structural Basis for its Specificity
      Musil, D.,Zucic, D.,Turk, D.,Engh, R.A.,Mayr, I.,Huber, R.,Popovic, T.,Turk, V.,Towatari, T.,Katunuma, N.,Bode, W.
      (1991) Embo J. 10: 2321


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN B light chain
A, D
47Homo sapiensGene Names: CTSB (CPSB)
EC: 3.4.22.1
Find proteins for P07858 (Homo sapiens)
Go to Gene View: CTSB
Go to UniProtKB:  P07858
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN B heavy chain
B, E
205Homo sapiensGene Names: CTSB (CPSB)
EC: 3.4.22.1
Find proteins for P07858 (Homo sapiens)
Go to Gene View: CTSB
Go to UniProtKB:  P07858
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EP0
Query on EP0

Download SDF File 
Download CCD File 
A, E
N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline
epoxy succinyl inhibitor
C17 H28 N2 O7
XMBVSOIOHZNPHI-FMSGJZPZSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000310 (EP0)
Query on PRD_000310
A,ECA030, ethyl ester of epoxysuccinyl-Ile-Pro-OHPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.510α = 90.00
b = 34.150β = 103.10
c = 85.530γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
XDSdata scaling
X-PLORmodel building
X-PLORphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-12-09 
  • Released Date: 1996-04-03 
  • Deposition Author(s): Turk, D., Bode, W.

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2011-08-31
    Type: Non-polymer description
  • Version 1.4: 2012-12-12
    Type: Other