1YAL

CARICA PAPAYA CHYMOPAPAIN AT 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of chymopapain at 1.7 A resolution.

Maes, D.Bouckaert, J.Poortmans, F.Wyns, L.Looze, Y.

(1996) Biochemistry 35: 16292-16298

  • DOI: 10.1021/bi961491w
  • Primary Citation of Related Structures:  
    1YAL

  • PubMed Abstract: 
  • The X-ray structure of chymopapain, a cysteine proteinase isolated from the latex of the fruits of Carica papaya L., has been determined by molecular replacement methods and refined to a conventional R factor of 0.19 for all observed reflections in t ...

    The X-ray structure of chymopapain, a cysteine proteinase isolated from the latex of the fruits of Carica papaya L., has been determined by molecular replacement methods and refined to a conventional R factor of 0.19 for all observed reflections in the range from 9.5 to 1.7 A resolution. The crystals used in this study contained a unique molecular species of chymopapain with two moles of thiomethyl attached to the two free cysteines per mole of enzyme. A comparison is made with the other known papaya proteinase X-ray structures: papain, caricain, and glycyl endopeptidase. Their backbone conformations are extremely similar except for two loop regions. Both regions are located at the surface of the protein and far away of the active site cleft. In each X-ray structure the same water network was found at the interface between the two domains of the enzyme. A close examination of the active site groove showed that the specificity restrictions dictated by the S2 subsite did not differ significantly among the four proteinases.


    Related Citations: 
    • Preparation of Crystals of Chymopapain Diffracting to 1.4 Angstroms Resolution
      Azarkan, M., Maes, D., Bouckaert, J., Thi, M.-H.D., Wyns, L., Looze, Y.
      () To be published --: --

    Organizational Affiliation

    Ultrastructure Unit, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHYMOPAPAINA218Carica papayaMutation(s): 0 
EC: 3.4.22.6
Find proteins for P14080 (Carica papaya)
Explore P14080 
Go to UniProtKB:  P14080
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
AL-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.18α = 90
b = 32.35β = 98.37
c = 47.42γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Advisory, Data collection, Other
  • Version 1.4: 2018-04-18
    Changes: Data collection