1PPP

CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites.

Kim, M.J.Yamamoto, D.Matsumoto, K.Inoue, M.Ishida, T.Mizuno, H.Sumiya, S.Kitamura, K.

(1992) Biochem.J. 287: 797-803


  • PubMed Abstract: 
  • In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) reso ...

    In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] were used for the structure solution and refinement. The papain structure was determined by means of the molecular replacement method, and then the inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference Fourier map. The complex structure was finally refined to R = 19.4% including 207 solvent molecules. Although this complex crystal (Form II) was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were significantly different from each other. By the calculation of accessible surface area for each complex atom, these two different binding modes were both shown to be tight enough to prevent the access of solvent molecules to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states which were derived from the crystal structures of Forms I and II. One of these, which corresponds to the binding mode simulated from Form I, was essentially the same as that observed in the crystal structure, and the other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the papain S subsites. The substrate specificity for the papain active site is discussed on the basis of the present results.


    Related Citations: 
    • Mode of Binding of E-64-C, a Potent Thiol Protease Inhibitor, to Papain as Determined by X-Ray Crystal Analysis of the Complex
      Matsumoto, K.,Yamamoto, D.,Ohishi, H.,Tomoo, K.,Ishida, T.,Inoue, M.,Sadatome, T.,Kitamura, K.,Mizuno, H.
      (1989) FEBS Lett. 245: 171
    • Refined X-Ray Structure of Papain(Dot)E-64-C Complex at 2.1-Angstroms Resolution
      Yamamoto, D.,Matsumoto, K.,Ohishi, H.,Ishida, T.,Inoue, M.,Kitamura, K.,Mizuno, H.
      (1991) J.Biol.Chem. 266: 14771
    • The Importance of Val-157 Hydrophobic Interaction for Papain Inhibitory Activity of an Epoxysuccinyl Amino Acid Derivative; a Structure-Activity Relationship Based on the Crystal Structure of the Papain-E-64-C Complex
      Yamamoto, D.,Matsumoto, K.,Ohishi, H.,Ishida, T.,Inoue, M.,Kitamura, K.,Mizuno, H.
      (1990) FEBS Lett. 253: 134


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PAPAIN
A
212Carica papayaEC: 3.4.22.2
Find proteins for P00784 (Carica papaya)
Go to UniProtKB:  P00784
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E6C
Query on E6C

Download SDF File 
Download CCD File 
A
N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE
C15 H28 N2 O5
KBIWEWPGBHKYML-RYUDHWBXSA-N
 Ligand Interaction
MOH
Query on MOH

Download SDF File 
Download CCD File 
A
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.370α = 90.00
b = 102.340β = 90.00
c = 49.950γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-03-17 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Ishida, T.

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: 2012-05-09
    Type: Other