1YU6

Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.

Maynes, J.T.Cherney, M.M.Qasim, M.A.Laskowski Jr, M.James, M.N.

(2005) Acta Crystallogr.,Sect.D 61: 580-588

  • DOI: 10.1107/S0907444905004889

  • PubMed Abstract: 
  • One of the most studied protein proteinase inhibitors is the turkey ovomucoid third domain, OMTKY3. This inhibitor contains a reactive-site loop (Lys13I-Arg21I) that binds in a nearly identical manner to all studied serine proteinases, regardless of ...

    One of the most studied protein proteinase inhibitors is the turkey ovomucoid third domain, OMTKY3. This inhibitor contains a reactive-site loop (Lys13I-Arg21I) that binds in a nearly identical manner to all studied serine proteinases, regardless of their clan or specificity. The crystal structure of OMTKY3 bound to subtilisin Carlsberg (CARL) has been determined. There are two complete copies of the complexes in the crystallographic asymmetric unit. Whereas the two enzyme molecules are virtually identical [0.16 A root-mean-square difference (r.m.s.d.) for 274 C(alpha) atoms], the two inhibitor molecules show dramatic differences between one another (r.m.s.d. = 2.4 A for 50 C(alpha) atoms). When compared with other proteinase-bound OMTKY3 molecules, these inhibitors show even larger differences. This work facilitates a re-evaluation of the importance of certain ovomucoid residues in proteinase binding and explains why additivity and sequence-based binding-prediction methods fail for the CARL-OMTKY3 complex.


    Organizational Affiliation

    Canadian Institutes of Health Research, Group in Protein Structure and Function, Department of Biochemistry, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada. jason@biochem.ualberta.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subtilisin Carlsberg
A, B
275Bacillus licheniformisMutation(s): 0 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00780 (Bacillus licheniformis)
Go to UniProtKB:  P00780
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ovomucoid
C, D
185Meleagris gallopavoMutation(s): 0 
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 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 110.256α = 90.00
b = 100.971β = 90.00
c = 115.785γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance