Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51123.35 
• Atom Count: 3515 
• Residue Count: 475 
• Unique protein chains: 2

1F34

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

• DOI: 10.2210/pdb1F34/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa, Ascaris suum
• Expression System: Escherichia coli


• Deposited: 2000-05-31 Released: 2001-02-01 
• Deposition Author(s): Ng, K.K., Petersen, J.F., Cherney, M.M., Garen, C., James, M.N.

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Experimental Data Snapshot

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

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

• PubMed: 10932249 
• DOI: 10.1038/77950
• Primary Citation of Related Structures:  
  1F32


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
PEPSIN A	A	326	Sus scrofa	Mutation(s): 0  Gene Names: PGA EC: 3.4.23.1
Find proteins for P00791 (Sus scrofa) Go to UniProtKB:  P00791

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
MAJOR PEPSIN INHIBITOR PI-3	B	149	Ascaris suum	Mutation(s): 0
Find proteins for P19400 (Ascaris suum) Go to UniProtKB:  P19400

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

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 = 65.374	α = 90.00
b = 97.593	β = 90.00
c = 136.394	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
AMoRE	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-31 
• Released Date: 2001-02-01 
• Deposition Author(s): Ng, K.K., Petersen, J.F., Cherney, M.M., Garen, C., James, M.N.

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