Crystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Carribean sea anemone stichodactyla helianthus

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Structure of the recombinant BPTI/Kunitz-type inhibitor rShPI-1A from the marine invertebrate Stichodactyla helianthus.

Garcia-Fernandez, R.Pons, T.Meyer, A.Perbandt, M.Gonzalez-Gonzalez, Y.Gil, D.de los Angeles Chavez, M.Betzel, C.Redecke, L.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1289-1293

  • DOI: https://doi.org/10.1107/S1744309112039085
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The BPTI/Kunitz-type inhibitor family includes several extremely potent serine protease inhibitors. To date, the inhibitory mechanisms have only been studied for mammalian inhibitors. Here, the first crystal structure of a BPTI/Kunitz-type inhibitor from a marine invertebrate (rShPI-1A) is reported to 2.5 Å resolution. Crystallization of recombinant rShPI-1A required the salt-induced dissociation of a trypsin complex that was previously formed to avoid intrinsic inhibitor aggregates in solution. The rShPI-1A structure is similar to the NMR structure of the molecule purified from the natural source, but allowed the assignment of disulfide-bridge chiralities and the detection of an internal stabilizing water network. A structural comparison with other BPTI/Kunitz-type canonical inhibitors revealed unusual ϕ angles at positions 17 and 30 to be a particular characteristic of the family. A significant clustering of ϕ and ψ angle values in the glycine-rich remote fragment near the secondary binding loop was additionally identified, but its impact on the specificity of rShPI-1A and similar molecules requires further study.

  • Organizational Affiliation

    Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, Calle 25 No. 455, Havana 10400, Cuba.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kunitz-type proteinase inhibitor SHPI-160Stichodactyla helianthusMutation(s): 0 
Find proteins for P31713 (Stichodactyla helianthus)
Explore P31713 
Go to UniProtKB:  P31713
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31713
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.158α = 90
b = 37.158β = 90
c = 114.98γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2013-01-23
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description