1GDN: FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION

Citation:
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.
PDB ID: 1GDNDownload
MMDB ID: 163379
PDB Deposition Date: 2000/9/28
Updated in MMDB: 2018/06
Experimental Method:
x-ray diffraction
Resolution: 0.81  Å
Source Organism:
Fusarium oxysporum
Similar Structures:
Biological Unit for 1GDN: dimeric; determined by author and by software (PISA)
Molecular Components in 1GDN
Label Count Molecule
Proteins (2 molecules)
1
Trypsin
Molecule annotation
1
Gly-ala-lys
Molecule annotation
Chemicals (5 molecules)
1
1
2
4
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.