Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 35.32 kDa 
• Atom Count: 2720 
• Residue Count: 332 
• Unique protein chains: 2

1PSO

The crystal structure of human pepsin and its complex with pepstatin

• DOI: 10.2210/pdb1PSO/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Streptomyces argenteolus subsp. toyonakensis
• Mutation(s): No 


• Deposited: 1995-01-23 Released: 1995-04-20 
• Deposition Author(s): Fujinaga, M., Chernaia, M.M., Tarasova, N., Mosimann, S.C., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.185 

Literature

Crystal structure of human pepsin and its complex with pepstatin.

Fujinaga, M., Chernaia, M.M., Tarasova, N.I., Mosimann, S.C., James, M.N.

(1995) Protein Sci 4: 960-972

• PubMed: 7663352 
• DOI: 10.1002/pro.5560040516
• Primary Citation of Related Structures:  
  1PSO, 1PSN


• PubMed Abstract: 
  

The three-dimensional crystal structure of human pepsin and that of its complex with pepstatin have been solved by X-ray crystallographic methods. The native pepsin structure has been refined with data collected to 2.2 A resolution to an R-factor of 19.7%. The pepsin:pepstatin structure has been refined with data to 2.0 A resolution to an R-factor of 18.5%. The hydrogen bonding interactions and the conformation adopted by pepstatin are very similar to those found in complexes of pepstatin with other aspartic proteinases. The enzyme undergoes a conformational change upon inhibitor binding to enclose the inhibitor more tightly. The analysis of the binding sites indicates that they form an extended tube without distinct binding pockets. By comparing the residues on the binding surface with those of the other human aspartic proteinases, it has been possible to rationalize some of the experimental data concerning the different specificities. At the S1 site, valine at position 120 in renin instead of isoleucine, as in the other enzymes, allows for binding of larger hydrophobic residues. The possibility of multiple conformations for the P2 residue makes the analysis of the S2 site difficult. However, it is possible to see that the specific interactions that renin makes with histidine at P2 would not be possible in the case of the other enzymes. At the S3 site, the smaller volume that is accessible in pepsin compared to the other enzymes is consistent with its preference for smaller residues at the P3 position.

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Related Citations: 

• Molecular and Crystal Structures of Monoclinic Porcine Pepsin Refined at 1.8 Angstroms Resolution
  Sielecki, A.R., Fedorov, A.A., Boodhoo, A., Andreeva, N.S., James, M.N.G.
  (1990) J Mol Biol 214: 143

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Organizational Affiliation: 

Department of Biochemistry, University of Alberta, Edmonton, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPSIN 3A	E	326	Homo sapiens	Mutation(s): 0  Gene Names: PGA4 EC: 3.4.23.1
Find proteins for P0DJD7 (Homo sapiens) Explore P0DJD7  Go to UniProtKB:  P0DJD7
NIH Common Fund Data Resources
PHAROS:  P0DJD7 GTEx:  ENSG00000229183

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPSTATIN	I	6	Streptomyces argenteolus subsp. toyonakensis	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000557	I	Pepstatin	Oligopeptide /  Enzyme inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.068	α = 90
b = 150.972	β = 90
c = 40.854	γ = 90

Software Package:

Software Name	Purpose
GROMOS	refinement
SAN	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-01-23 
• Released Date: 1995-04-20 
Deposition Author(s): Fujinaga, M., Chernaia, M.M., Tarasova, N., Mosimann, S.C., James, M.N.G.

Revision History 

• Version 1.0: 1995-04-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Changes: Other