1R0R

1.1 Angstrom Resolution Structure of the Complex Between the Protein Inhibitor, OMTKY3, and the Serine Protease, Subtilisin Carlsberg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and energetics of protein-protein interactions: the role of conformational heterogeneity in OMTKY3 binding to serine proteases

Horn, J.R.Ramaswamy, S.Murphy, K.P.

(2003) J.Mol.Biol. 331: 497-508


  • PubMed Abstract: 
  • Proteins with flexible binding surfaces can interact with numerous binding partners. However, this promiscuity is more difficult to understand in "rigid-body" proteins, whose binding results in little, or no, change in the position of backbone atoms. ...

    Proteins with flexible binding surfaces can interact with numerous binding partners. However, this promiscuity is more difficult to understand in "rigid-body" proteins, whose binding results in little, or no, change in the position of backbone atoms. The binding of Kazal inhibitors to serine proteases is considered a classic case of rigid-body binding, although they bind to a wide range of proteases. We have studied the thermodynamics of binding of the Kazal serine protease inhibitor, turkey ovomucoid third domain (OMTKY3), to the serine protease subtilisin Carlsberg using isothermal titration calorimetry and have determined the crystal structure of the complex at very high resolution (1.1A). Comparison of the binding energetics and structure to other OMTKY3 interactions demonstrates that small changes in the position of side-chains can make significant contributions to the binding thermodynamics, including the enthalpy of binding. These effects emphasize that small, "rigid-body" proteins are still dynamic structures, and these dynamics make contributions to both the enthalpy and entropy of binding interactions.


    Organizational Affiliation

    Department of Biochemistry, College of Medicine, University of Iowa, Iowa City, IA 52242, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
subtilisin carlsberg
E
274Bacillus licheniformisGene Names: apr
EC: 3.4.21.62
Find proteins for P00780 (Bacillus licheniformis)
Go to UniProtKB:  P00780
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ovomucoid
I
51Meleagris gallopavo
Find proteins for P68390 (Meleagris gallopavo)
Go to UniProtKB:  P68390
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.329α = 90.00
b = 70.810β = 90.00
c = 127.476γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
HKL-2000data reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance