1Z7K

Crystal Structure of Trypsin- Ovomucoid turkey egg white inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of trypsin-turkey egg white inhibitor complex

Syed Ibrahim, B.Pattabhi, V.

(2004) Biochem Biophys Res Commun 313: 8-16

  • DOI: 10.1016/j.bbrc.2003.11.082
  • Primary Citation of Related Structures:  
    1Z7K

  • PubMed Abstract: 
  • Crystal structure of the complex between porcine beta-trypsin and the second domain of the Kazal-type ovomucoid turkey egg white trypsin inhibitor (OMTKY2) has been determined at 1.9A resolution. A peptide fragment from the first domain has been crys ...

    Crystal structure of the complex between porcine beta-trypsin and the second domain of the Kazal-type ovomucoid turkey egg white trypsin inhibitor (OMTKY2) has been determined at 1.9A resolution. A peptide fragment from the first domain has been crystallized with the complex. Restrained-refinement of the structure led to an R-factor of 0.19 for the 32206 reflections. OMTKY2 exhibits the canonical Kazal-type fold with a central alpha-helix and a short two-stranded anti-parallel beta-sheet. The carbonyl carbon of the reactive site prefers trigonal geometry. The reactive site loop geometry of the inhibitor is complementary to the surface and charge of the binding site in beta-trypsin.


    Organizational Affiliation

    Department of crystallography and Biophysics, University of Madras, Chennai 600 025, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TrypsinA223Sus scrofaMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00761 (Sus scrofa)
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Go to UniProtKB:  P00761
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
OvomucoidB62Meleagris gallopavoMutation(s): 0 
Find proteins for P68390 (Meleagris gallopavo)
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Go to UniProtKB:  P68390
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
OvomucoidC4Meleagris gallopavoMutation(s): 0 
Find proteins for P68390 (Meleagris gallopavo)
Explore P68390 
Go to UniProtKB:  P68390
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2 N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.575α = 90
b = 98.575β = 90
c = 73.724γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
DENZOdata reduction
CNSrefinement
XDSdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary