1STF

THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction.

Stubbs, M.T.Laber, B.Bode, W.Huber, R.Jerala, R.Lenarcic, B.Turk, V.

(1990) EMBO J. 9: 1939-1947


  • PubMed Abstract: 
  • A stoichiometric complex of human stefin B and carboxymethylated papain has been crystallized in a trigonal crystal form. Data to 2.37 A resolution were collected using the area detector diffractometer FAST. The crystal structure of the complex has b ...

    A stoichiometric complex of human stefin B and carboxymethylated papain has been crystallized in a trigonal crystal form. Data to 2.37 A resolution were collected using the area detector diffractometer FAST. The crystal structure of the complex has been solved by Patterson search techniques using papain as search model. Starting from the structure of chicken cystatin, the stefin structure was elucidated through cycles of model building and crystallographic refinement. The current crystallographic R factor is 0.19. Like cystatin, the stefin molecule consists of a five stranded beta-sheet wrapped around a five turn alpha-helix, but with an additional carboxy terminal strand running along the convex side of the sheet. Topological equivalence of stefin and cystatin reveal the previous sequence alignment to be incorrect in part, through deletion of the intermediate helix. The conserved residues form a tripartite wedge, which slots into the papain active site as proposed through consideration of the tertiary structures of the individual components (Bode et al., 1988). The main interactions are provided by the amino terminal 'trunk' (occupying the 'unprimed' subsites of the enzyme), and by the first hairpin loop, containing the highly conserved QVVAG sequence, with minor contributions from the second hairpin loop. The carboxyl terminus of stefin provides an additional interaction region with respect to cystatin. The interaction is dominated by hydrophobic contacts. Inhibition by the cysteine proteinase inhibitors is fundamentally different to that observed for the serine proteinase inhibitors.


    Related Citations: 
    • Mutations in the Qvvag Region of the Cysteine Proteinase Inhibitor Stefin B
      Jerala, R.,Trstenjak-Prebanda, M.,Kroon-Zitko, L.,Lenarcic, B.,Turk, V.
      (1990) Biol.Chem.Hoppe-Seyler 371: 157
    • Minireview: The Cystatins: Protein Inhibitors of Cysteine Proteinases
      Turk, V.,Bode, W.
      (1991) FEBS Lett. 285: 213


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried bei München, FRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PAPAIN
E
212Carica papayaEC: 3.4.22.2
Find proteins for P00784 (Carica papaya)
Go to UniProtKB:  P00784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
STEFIN B (CYSTATIN B)
I
98Homo sapiensGene Names: CSTB (CST6, STFB)
Find proteins for P04080 (Homo sapiens)
Go to Gene View: CSTB
Go to UniProtKB:  P04080
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
E
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Work: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.000α = 90.00
b = 67.000β = 90.00
c = 169.300γ = 120.00
Software Package:
Software NamePurpose
EREFrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other