PDBsum entry 1gdn

Go to PDB code: 
protein ligands links
Hydrolase/hydrolase substrate PDB id
Protein chain
224 a.a. *
GOL ×4
Waters ×432
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase substrate
Title: Fusarium oxysporum trypsin at atomic resolution
Structure: Trypsin. Chain: a. Gly-ala-lys. Chain: b. Engineered: yes
Source: Fusarium oxysporum. Organism_taxid: 5507. Synthetic: yes
Biol. unit: Dimer (from PQS)
0.81Å     R-factor:   0.108    
Authors: W.R.Rypniewski,P.Oestergaard,M.Noerregaard-Madsen,M.Dauter,K
Key ref:
W.R.Rypniewski et al. (2001). Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding. Acta Crystallogr D Biol Crystallogr, 57, 8. PubMed id: 11134922 DOI: 10.1107/S0907444900014116
28-Sep-00     Release date:   07-Feb-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P35049  (TRYP_FUSOX) -  Trypsin
248 a.a.
224 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1107/S0907444900014116 Acta Crystallogr D Biol Crystallogr 57:8 (2001)
PubMed id: 11134922  
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, K.S.Wilson.
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.
  Selected figure(s)  
Figure 3.
Figure 3 Schematic representation of TRY-N. Secondary-structure elements forming the N-terminal domain are marked A1-F1 and the C-terminal domain A2-F2 as defined previously (Rypniewski, Mangani et al., 1995[Rypniewski, W. R., Mangani, S., Bruni, B., Orioli, P. L., Casati, M. & Wilson, K. S. (1995). J. Mol. Biol. 251, 282-296.]). The active site is indicated by the side chains of the `catalytic triad': Ser195, His57 and Asp102. The side chain of Asp189 is also shown at the bottom of the `specificity pocket' defining the tryptic substrate specificity. The peptide bound in sites S1 to S3 is indicated by a ball-and-stick model with dark bonds.
Figure 6.
Figure 6 Ligand binding in TRY-LYS2. (a) `Omit' maps calculated as for Fig. 4-(a), at the same contour levels and with similar colouring scheme. Sites 2004-2006 are not occupied in this structure, as shown by the absence of difference density. There is an indication of a double conformation of the Lys side chain, not modelled because of weak density level for refinement. The water at 2102 has been modelled in two alternative conformations: 2102b is at a bonding distance to Lys N , whilst 2102a is at clashing distance, binding in the absence of the peptide ligand. (b) Geometry of the binding site. The labelling scheme is similar to Fig. 4-(b). Some atoms have been omitted for clarity.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 8-0) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18814299 P.Labute (2009).
Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures.
  Proteins, 75, 187-205.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
16237016 E.Matsuda, N.Abe, H.Tamakawa, J.Kaneko, and Y.Kamio (2005).
Gene cloning and molecular characterization of an extracellular poly(L-lactic acid) depolymerase from Amycolatopsis sp. strain K104-1.
  J Bacteriol, 187, 7333-7340.  
16114036 L.R.Forrest, and B.Honig (2005).
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.
  Proteins, 61, 296-309.  
15146478 E.I.Howard, R.Sanishvili, R.E.Cachau, A.Mitschler, B.Chevrier, P.Barth, V.Lamour, M.Van Zandt, E.Sibley, C.Bon, D.Moras, T.R.Schneider, A.Joachimiak, and A.Podjarny (2004).
Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.
  Proteins, 55, 792-804.
PDB code: 1us0
12937176 A.Schmidt, C.Jelsch, P.Ostergaard, W.Rypniewski, and V.S.Lamzin (2003).
Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis.
  J Biol Chem, 278, 43357-43362.
PDB codes: 1ppz 1pq5 1pq7 1pq8 1pqa
11896054 G.Katona, R.C.Wilmouth, P.A.Wright, G.I.Berglund, J.Hajdu, R.Neutze, and C.J.Schofield (2002).
X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution.
  J Biol Chem, 277, 21962-21970.
PDB code: 1gvk
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.