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: 2.00 Å
  • R-Value Work: 0.194 
  • R-Value Observed: 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

  • DOI: 10.1021/bi00014a037
  • Primary Citation of Related Structures:  
    1CSB

  • 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 published structure of cathepsin B [Musil, D ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN B light chainA,
C [auth D]		47Homo sapiensMutation(s): 0 
Gene Names: CTSB, CPSB
EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens)
Explore P07858 
Go to UniProtKB:  P07858
PHAROS:  P07858
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07858
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CATHEPSIN B heavy chainB,
D [auth E]		205Homo sapiensMutation(s): 0 
Gene Names: CTSB, CPSB
EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens)
Explore P07858 
Go to UniProtKB:  P07858
PHAROS:  P07858
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07858
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EP0
Query on EP0
Download Ideal Coordinates CCD File 
E [auth A],
F [auth E]		N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline
C17 H28 N2 O7
XMBVSOIOHZNPHI-FMSGJZPZSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000310 (EP0)
Query on PRD_000310		E [auth A],
F [auth E]		CA030, ethyl ester of epoxysuccinyl-Ile-Pro-OHPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.51α = 90
b = 34.15β = 103.1
c = 85.53γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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