1GEC

GLYCYL ENDOPEPTIDASE-COMPLEX WITH BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE COVALENTLY BOUND TO CYSTEINE 25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of glycyl endopeptidase from Carica papaya: a cysteine endopeptidase of unusual substrate specificity.

O'Hara, B.P.Hemmings, A.M.Buttle, D.J.Pearl, L.H.

(1995) Biochemistry 34: 13190-13195


  • PubMed Abstract: 
  • Glycyl endopeptidase is a cysteine endopeptidase of the papain family, characterized by specificity for cleavage C-terminal to glycyl residues only and by resistance to inhibition by members of the cystatin family of cysteine proteinase inhibitors. G ...

    Glycyl endopeptidase is a cysteine endopeptidase of the papain family, characterized by specificity for cleavage C-terminal to glycyl residues only and by resistance to inhibition by members of the cystatin family of cysteine proteinase inhibitors. Glycyl endopeptidase has been crystallized from high salt with a substrate-like inhibitor covalently bound to the catalytic Cys 25. The structure has been solved by molecular replacement with the structure of papain and refined at 2.1 A to an R factor of 0.196 (Rfree = 0.258) with good geometry. The structure of the S1 substrate binding site of glycyl endopeptidase differs from that of papain by the substitution of glycines at residues 23 and 65 in papain, with glutamic acid and arginine, respectively, in glycyl endopeptidase. The side chains of these residues form a barrier across the binding pocket, effectively excluding substrate residues with large side chains from the S1 subsite. The constriction of this subsite in glycyl endopeptidase explains the unique specificity of this enzyme for cleavage after glycyl residues and is a major component of its resistance to inhibition by cystatins.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University College London, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYL ENDOPEPTIDASE
E
216Carica papayaEC: 3.4.22.25
Find proteins for P05994 (Carica papaya)
Go to UniProtKB:  P05994
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE INHIBITOR
I
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000337
Query on PRD_000337
IBENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENEPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 55.780α = 90.00
b = 55.780β = 90.00
c = 64.430γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other