1AVW

COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, ORTHORHOMBIC CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kunitz-type soybean trypsin inhibitor revisited: refined structure of its complex with porcine trypsin reveals an insight into the interaction between a homologous inhibitor from Erythrina caffra and tissue-type plasminogen activator.

Song, H.K.Suh, S.W.

(1998) J.Mol.Biol. 275: 347-363

  • DOI: 10.1006/jmbi.1997.1469
  • Primary Citation of Related Structures:  1AVU, 1AVX

  • PubMed Abstract: 
  • The Kunitz-type trypsin inhibitor from soybean (STI) consists of 181 amino acid residues with two disulfide bridges. Its crystal structures have been determined in complex with porcine pancreatic trypsin in two crystal forms (an orthorhombic form at ...

    The Kunitz-type trypsin inhibitor from soybean (STI) consists of 181 amino acid residues with two disulfide bridges. Its crystal structures have been determined in complex with porcine pancreatic trypsin in two crystal forms (an orthorhombic form at 1.75 A resolution and a tetragonal form at 1.9 A) and in the free state at 2.3 A resolution. They have been refined to crystallographic R-values of 18.9%, 21.6% and 19.8%, respectively. The three models of STI reported here represent a significant improvement over the partial inhibitor structure in the complex, which was previously determined at a nominal resolution of 2.6 A by the multiple isomorphous replacement method. This study provides the first high-resolution picture of the complex between a Kunitz-type proteinase inhibitor with its cognate proteinase. Many of the external loops of STI show high B-factors, both in the free and the complexed states, except the reactive site loop whose B-factors are dramatically reduced upon complexation. The reactive site loop of STI adopts a canonical conformation similar to those in other substrate-like inhibitors. The P1 carbonyl group displays no out-of-plane displacement and thus retains a nominal trigonal planar geometry. Modeling studies on the complex between a homologous Kunitz-type trypsin inhibitor DE-3 from Erythrina caffra and the human tissue-type plasminogen activator reveal a new insight into the specific interactions which could play a crucial role in their binding.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Crystallographic Study of Kunitz-Type Soybean Trypsin Inhibitor
      Lee, J.K.
      (1993) Thesis, Seoul National University --: --
    • Crystallization of Kunitz-Type Soybean Trypsin Inhibitor
      Lee, J.K.,Song, H.K.,Hwang, K.Y.,Kim, K.K.,Suh, S.W.
      (1993) Mol.Cells 3: 335
    • Crystal Structure Analyses of Human A1-Antitrypsin, Soybean Kunitz-Type Trypsin Inhibitor, and Barley Chitinase
      Song, H.K.
      (1997) Thesis, Seoul National University --: --


    Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Sus scrofaEC: 3.4.21.4
Find proteins for P00761 (Sus scrofa)
Go to UniProtKB:  P00761
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN INHIBITOR
B
177Glycine maxGene Names: KTI3
Find proteins for P01070 (Glycine max)
Go to UniProtKB:  P01070
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.910α = 90.00
b = 62.330β = 90.00
c = 151.460γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-09-21 
  • Released Date: 1998-10-28 
  • Deposition Author(s): Song, H.K., Suh, S.W.

Revision History 

  • Version 1.0: 1998-10-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance