Experimental Data Snapshot

  • Resolution: 0.81 Å
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 

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Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.

Rypniewski, W.R.Ostergaard, P.R.Norregaard-Madsen, M.Dauter, M.Wilson, K.S.

(2001) Acta Crystallogr D Biol Crystallogr 57: 8-19

  • DOI: https://doi.org/10.1107/s0907444900014116
  • Primary Citation of Related Structures:  
    1FN8, 1FY4, 1FY5, 1GDN, 1GDQ, 1GDU

  • PubMed Abstract: 

    The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 A resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 A resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1-S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's beta-protein precursor, with some differences in the S1 site.

  • Organizational Affiliation

    European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. wojtek@embl-hamburg.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRYPSIN224Fusarium oxysporumMutation(s): 0 
Find proteins for P35049 (Fusarium oxysporum)
Explore P35049 
Go to UniProtKB:  P35049
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35049
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLY-ALA-ARG3N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.81 Å
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.146α = 102.09
b = 36.696β = 104.75
c = 39.556γ = 103.01
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance