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PDBsum entry 1dpo
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Serine protease PDB id
1dpo

 

 

 

 

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Contents
Protein chain
223 a.a. *
Ligands
SO4 ×2
BEN ×3
Metals
_CA
Waters ×217
* Residue conservation analysis
PDB id:
1dpo
Name: Serine protease
Title: Structure of rat trypsin
Structure: Trypsin. Chain: a. Engineered: yes. Mutation: yes. Other_details: anionic trypsin
Source: Rattus rattus. Black rat. Organism_taxid: 10117. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.59Å     R-factor:   0.174    
Authors: R.M.Stroud
Key ref: T.Earnest et al. (1991). 1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures. Proteins, 10, 171-187. PubMed id: 1881877
Date:
31-Mar-97     Release date:   07-Jul-97    
PROCHECK
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 Headers
 References

Protein chain
P00763  (TRY2_RAT) -  Anionic trypsin-2 from Rattus norvegicus
Seq:
Struc: 		246 a.a.
223 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.4  - trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

 

 
Proteins 10:171-187 (1991)
PubMed id: 1881877  
 
 
1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures.
T.Earnest, E.Fauman, C.S.Craik, R.Stroud.
 
  ABSTRACT  
 
The structure of a rat trypsin mutant [S195C] at a temperature of 120 K has been refined to a crystallographic R factor of 17.4% between 12.0 and 1.59 A and is compared with the structure of the D102N mutant at 295 K. A reduction in the unit cell dimensions in going from room temperature to low temperature is accompanied by a decrease in molecular surface area and radius of gyration. The overall structure remains similar to that at room temperature. The attainable resolution appears to be improved due to the decrease in the fall off of intensities with resolution [reduction of the temperature factor]. This decreases the uncertainty in the atomic positions and allows the localization of more protein atoms and solvent molecules in the low temperature map. The largest differences between the two models occur at residues with higher than average temperature factors. Several features can be localized in the solvent region of the 120 K map that are not seen in the 295 K map. These include several more water molecules as well as an interstitial sulfate ion and two interstitial benzamidine molecules.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16204896 L.Jin, P.Pandey, R.E.Babine, D.T.Weaver, S.S.Abdel-Meguid, and J.E.Strickler (2005).
Mutation of surface residues to promote crystallization of activated factor XI as a complex with benzamidine: an essential step for the iterative structure-based design of factor XI inhibitors.
  Acta Crystallogr D Biol Crystallogr, 61, 1418-1425.
PDB codes: 1zhm 1zhp 1zhr
15537660 M.T.Fiorillo, C.Rückert, M.Hülsmeyer, R.Sorrentino, W.Saenger, A.Ziegler, and B.Uchanska-Ziegler (2005).
Allele-dependent similarity between viral and self-peptide presentation by HLA-B27 subtypes.
  J Biol Chem, 280, 2962-2971.
PDB codes: 1uxs 1uxw
15578663 O.Guvench, D.J.Price, and C.L.Brooks (2005).
Receptor rigidity and ligand mobility in trypsin-ligand complexes.
  Proteins, 58, 407-417.  
11927576 J.Funahashi, K.Takano, Y.Yamagata, and K.Yutani (2002).
Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability.
  J Biol Chem, 277, 21792-21800.
PDB codes: 1gf8 1gf9 1gfa 1gfe 1gfg 1gfh 1gfj 1gfk 1gfr 1gft 1gfu 1gfv 1inu
11856832 S.Kriminski, C.L.Caylor, M.C.Nonato, K.D.Finkelstein, and R.E.Thorne (2002).
Flash-cooling and annealing of protein crystals.
  Acta Crystallogr D Biol Crystallogr, 58, 459-471.  
10842337 A.A.Gorfe, B.O.Brandsdal, H.K.Leiros, R.Helland, and A.O.Smalås (2000).
Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: qualitative evaluation of electrostatic differences at the substrate binding site.
  Proteins, 40, 207-217.  
10672012 H.K.Leiros, N.P.Willassen, and A.O.Smalås (2000).
Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation.
  Eur J Biochem, 267, 1039-1049.  
10651279 N.Ota, C.Stroupe, J.M.Ferreira-da-Silva, S.A.Shah, M.Mares-Guia, and A.T.Brunger (1999).
Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine.
  Proteins, 37, 641-653.
PDB codes: 1ce5 2bza
10089359 O.Carugo, and D.Bordo (1999).
How many water molecules can be detected by protein crystallography?
  Acta Crystallogr D Biol Crystallogr, 55, 479-483.  
  9792092 P.C.Sanschagrin, and L.A.Kuhn (1998).
Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.
  Protein Sci, 7, 2054-2064.  
  9232638 S.D.Rader, and D.A.Agard (1997).
Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.
  Protein Sci, 6, 1375-1386.
PDB codes: 1tal 2ull
7704524 D.W.Rodgers (1994).
Cryocrystallography.
  Structure, 2, 1135-1140.  
1557349 J.S.Finer-Moore, A.A.Kossiakoff, J.H.Hurley, T.Earnest, and R.M.Stroud (1992).
Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.
  Proteins, 12, 203-222.
PDB code: 5ptp
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 codes are shown on the right.

 

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