1F34

CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3 BOUND TO PORCINE PEPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the inhibition of porcine pepsin by Ascaris pepsin inhibitor-3.

Ng, K.K.Petersen, J.F.Cherney, M.M.Garen, C.Zalatoris, J.J.Rao-Naik, C.Dunn, B.M.Martzen, M.R.Peanasky, R.J.James, M.N.

(2000) Nat.Struct.Mol.Biol. 7: 653-657

  • DOI: 10.1038/77950
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structures of pepsin inhibitor-3 (PI-3) from Ascaris suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition by this uni ...

    The three-dimensional structures of pepsin inhibitor-3 (PI-3) from Ascaris suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition by this unique inhibitor. PI-3 has a new fold consisting of two domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3'). The molecular structure of the pepsin-PI-3 complex suggests new avenues for the rational design of proteinaceous aspartic proteinase inhibitors.


    Organizational Affiliation

    MRC of Canada, Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPSIN A
A
326Sus scrofaGene Names: PGA
EC: 3.4.23.1
Find proteins for P00791 (Sus scrofa)
Go to UniProtKB:  P00791
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MAJOR PEPSIN INHIBITOR PI-3
B
149Ascaris suum
Find proteins for P19400 (Ascaris suum)
Go to UniProtKB:  P19400
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 65.374α = 90.00
b = 97.593β = 90.00
c = 136.394γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection