1FY4

FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.81 Å
  • R-Value Work: 0.108 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 57: 8-19

  • Primary Citation of Related Structures:  1FN8, 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 ...

    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.


    Related Citations: 
    • Structure of inhibited trypsin from Fusarium oxysporum at 1.55A
      Rypniewski, W.R.,Dambmann, C.,von der Osten, C.,Dauter, M.,Wilson, K.S.
      (1995) Acta Crystallogr.,Sect.D 51: 73


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
224Fusarium oxysporumEC: 3.4.21.4
Find proteins for P35049 (Fusarium oxysporum)
Go to UniProtKB:  P35049
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLY-ALA-ARG
B
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.81 Å
  • R-Value Work: 0.108 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.132α = 102.24
b = 36.774β = 104.75
c = 39.639γ = 102.85
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance