1QDQ

X-RAY CRYSTAL STRUCTURE OF BOVINE CATHEPSIN B-CA074 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 

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This is version 1.5 of the entry. See complete history


Literature

Substrate specificity of bovine cathepsin B and its inhibition by CA074, based on crystal structure refinement of the complex.

Yamamoto, A.Tomoo, K.Hara, T.Murata, M.Kitamura, K.Ishida, T.

(2000) J Biochem 127: 635-643

  • DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a022651
  • Primary Citation of Related Structures:  
    1QDQ

  • PubMed Abstract: 

    The crystal structure of the bovine spleen cathepsin B (BSCB)-CA074 complex was refined to R = 0.152 using X-ray diffraction data up to 2.18 A resolution. BSCB is characterized by an extra Cys148-Cys252 disulfide bridge, as compared with rat and human CBs. Although the crystal structures of these enzymes showed similar overall folding, a difference was observed in the occluding loop, a structural element specific only to CB. Comparison of the torsion angles indicated the different flexibilities of their loop structures. The oxirane C6 atom of CA074 was covalently bonded to the Cys29 S(gamma) atom (C3-S(gamma)=1.81 A), where the S-configuration was transformed to the R-form. Concerning the oxirane carbon atom that participates in the covalent bonding with the Cys residue, an acceptable rule has been proposed. The substrate specificities at the Sn (n = 1-3) and Sn' (n=1 and 2) subsites of CB, together with the interaction features as to CA074, have been discussed in comparison with the crystal structure of the papain-CA028 (a CA074-related inhibitor) complex.


  • Organizational Affiliation

    Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara, Takatsuki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATHEPSIN B253Bos taurusMutation(s): 0 
EC: 3.4.22.1
UniProt
Find proteins for P07688 (Bos taurus)
Explore P07688 
Go to UniProtKB:  P07688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07688
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
074
Query on 074

Download Ideal Coordinates CCD File 
B [auth A][PROPYLAMINO-3-HYDROXY-BUTAN-1,4-DIONYL]-ISOLEUCYL-PROLINE
C18 H31 N3 O6
UDNIFTKCMDIXFC-ABHRYQDASA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.06α = 90
b = 73.06β = 90
c = 141.79γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2000-07-10 
  • Deposition Author(s): Yamamoto, A.

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.5: 2018-01-31
    Changes: Experimental preparation