1PE6

REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined x-ray structure of papain.E-64-c complex at 2.1-A resolution.

Yamamoto, D.Matsumoto, K.Ohishi, H.Ishida, T.Inoue, M.Kitamura, K.Mizuno, H.

(1991) J.Biol.Chem. 266: 14771-14777


  • PubMed Abstract: 
  • E-64-c, a synthetic cysteine protease inhibitor designed from E-64, binds to papain through a thioether covalent bond. The x-ray diffraction data for 2.1-A resolution were used to determine the three-dimensional structure of this complex and refined ...

    E-64-c, a synthetic cysteine protease inhibitor designed from E-64, binds to papain through a thioether covalent bond. The x-ray diffraction data for 2.1-A resolution were used to determine the three-dimensional structure of this complex and refined it to R = 0.159. 0.159. In the complex structure, the configurational conversion from S to R took place on the epoxy carbon of E-64-c, implying that the nucleophilic attack of the Cys-25 thiol group occurs at the opposite side of the epoxy oxygen atom. The leucyl and isoamylamide groups of E-64-c were strongly fixed to papain S subsites by specific interactions, including hydrogen bonding to the Gly-66 residue. The carboxyl-terminal anion of E-64-c formed an electrostatic interaction with the protonated His-159 imidazole ring (O-...HN+ = 3.76 A) and consequently prevented the participation of this residue in the hydrolytic charge-relay system. No significant distortion caused by the binding of E-64-c was shown in the secondary structure of papain. It is important to note that inhibitor and substrate have opposite binding modes for the peptide groups. The possible relationship between the binding mode and inhibitory activity is discussed on the basis of the crystal structure of this complex.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Osaka University of Pharmaceutical Science, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PAPAIN
A
212Carica papayaMutation(s): 0 
EC: 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: 2.1 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.900α = 90.00
b = 95.510β = 90.00
c = 49.990γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance