Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23.79 kDa 
• Atom Count: 1840 
• Modelled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 2

1JRS

HEMIACETAL COMPLEX BETWEEN LEUPEPTIN AND TRYPSIN

• DOI: 10.2210/pdb1JRS/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bos taurus, Streptomyces roseus
• Mutation(s): No 


• Deposited: 1996-02-07 Released: 1996-10-14 
• Deposition Author(s): Kurinov, I.V., Harrison, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Literature

Two crystal structures of the leupeptin-trypsin complex.

Kurinov, I.V., Harrison, R.W.

(1996) Protein Sci 5: 752-758

• PubMed: 8845765 
• DOI: 10.1002/pro.5560050420
• Primary Citation of Related Structures:  
  1JRS, 1JRT


• PubMed Abstract: 
  

Three-dimensional structures of trypsin with the reversible inhibitor leupeptin have been determined in two different crystal forms. The first structure was determined at 1.7 A resolution with R-factor = 17.7% in the trigonal crystal space group P3(1)21, with unit cell dimensions of a = b = 55.62 A, c = 110.51 A. The second structure was determined at a resolution of 1.8 A with R-factor = 17.5% in the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 63.69 A, b = 69.37 A, c = 63.01 A. The overall protein structure is very similar in both crystal forms, with RMS difference for main-chain atoms of 0.27 A. The leupeptin backbone forms four hydrogen bonds with trypsin and a fifth hydrogen bond interaction is mediated by a water molecule. The aldehyde carbonyl of leupeptin forms a covalent bond of 1.42 A length with side-chain oxygen of Ser-195 in the active site. The reaction of trypsin with leupeptin proceeds through the formation of stable tetrahedral complex in which the hemiacetal oxygen atom is pointing out of the oxyanion hole and forming a hydrogen bond with His-57.

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Related Citations: 

• Prediction of New Serine Proteinase Inhibitors
  Kurinov, I.V., Harrison, R.W.
  (1994) Nat Struct Biol 1: 735

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Organizational Affiliation: 

Department of Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leupeptin	B	4	Streptomyces roseus	Mutation(s): 0  EC: 3.4.21.4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AR7	B	PEPTIDE-LIKE	C6 H17 N4 O2		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000216	B	LEUPEPTIN	Oligopeptide / Enzyme inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.686	α = 90
b = 69.373	β = 90
c = 63.013	γ = 90

Software Package:

Software Name	Purpose
PROCESS	data collection
X-PLOR	model building
X-PLOR	refinement
PROCESS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-02-07 
• Released Date: 1996-10-14 
Deposition Author(s): Kurinov, I.V., Harrison, R.W.

Revision History  

• Version 1.0: 1996-10-14
  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: 2012-12-12
  Changes: Other