1MCV | pdb_00001mcv

Crystal Structure Analysis of a Hybrid Squash Inhibitor in Complex with Porcine Pancreatic Elastase

• PDB DOI: https://doi.org/10.2210/pdb1MCV/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2002-08-06 Released: 2003-02-04 
• Deposition Author(s): Ay, J., Hilpert, K., Krauss, N., Schneider-Mergener, J., Hoehne, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.221 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure of a hybrid squash inhibitor in complex with porcine pancreatic elastase at 1.8 A resolution.

Ay, J., Hilpert, K., Krauss, N., Schneider-Mergener, J., Hohne, W.

(2003) Acta Crystallogr D Biol Crystallogr 59: 247-254

• PubMed: 12554935 
• DOI: https://doi.org/10.1107/s0907444902020887
• Primary Citation Related Structures: 
  1MCV


• PubMed Abstract: 
  

  The crystal structure of porcine pancreatic elastase in complex with a hybrid squash inhibitor (HEI-TOE I; 28 amino acids) has been determined to a resolution of 1.8 A. To construct the hybrid inhibitor, the trypsin-binding loop of the squash inhibitor from Ecballium elaterium was substituted by the sequence of a peptide that was derived from the third domain of the turkey ovomucoid inhibitor and was optimized to inhibit porcine pancreatic elastase. This modification of the squash inhibitor changed its specificity for trypsin to a specificity for porcine pancreatic elastase. Specific interactions of this hybrid inhibitor with porcine pancreatic elastase and the differences from the interactions of the ovomucoid inhibitor with human leukocyte elastase are discussed. The binding loop of the inhibitor adopts a 'canonical' conformation and the scissile bond Leu-Glu remains intact.

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Organizational Affiliation: 
• Institut für Biochemie, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Abteilung Proteinstrukturforschung, Monbijoustrasse 2, 10117 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 29.04 kDa 
• Atom Count: 2,457 
• Modeled Residue Count: 268 
• Deposited Residue Count: 268 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elastase 1	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEI-TOE I	B [auth I]	28	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.221 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.33	α = 90
b = 56.44	β = 90
c = 72.76	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-04 
Deposition Author(s): Ay, J., Hilpert, K., Krauss, N., Schneider-Mergener, J., Hoehne, W.

Revision History  

• Version 1.0: 2003-02-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary