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PDBsum entry 1krn

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Serine protease PDB id
1krn
Jmol
Contents
Protein chain
79 a.a. *
Ligands
SO4
Waters ×249
* Residue conservation analysis
PDB id:
1krn
Name: Serine protease
Title: Structure of kringle 4 at 4c temperature and 1.67 angstroms resolution
Structure: Plasminogen. Chain: a. Fragment: kringle 4 domain. Ec: 3.4.21.7
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood
Resolution:
1.67Å     R-factor:   0.147     R-free:   0.232
Authors: B.Stec,M.M.Teeter,M.Whitlow,A.Yamano
Key ref:
B.Stec et al. (1997). Structure of human plasminogen kringle 4 at 1.68 a and 277 K. A possible structural role of disordered residues. Acta Crystallogr D Biol Crystallogr, 53, 169-178. PubMed id: 15299951 DOI: 10.1107/S0907444996012267
Date:
21-Jun-95     Release date:   11-Jan-97    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00747  (PLMN_HUMAN) -  Plasminogen
Seq:
Struc:
 
Seq:
Struc:
810 a.a.
79 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.7  - Plasmin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Lys-|-Xaa > Arg-|-Xaa; higher selectivity than trypsin. Converts fibrin into soluble products.

 

 
DOI no: 10.1107/S0907444996012267 Acta Crystallogr D Biol Crystallogr 53:169-178 (1997)
PubMed id: 15299951  
 
 
Structure of human plasminogen kringle 4 at 1.68 a and 277 K. A possible structural role of disordered residues.
B.Stec, A.Yamano, M.Whitlow, M.M.Teeter.
 
  ABSTRACT  
 
Despite considerable effort to elucidate the functional role of the kringle domains, relatively little is known about interactions with other protein domains. Most of the crystal structures describe the interactions at the kringle active site. This study suggests a novel way to interpret structural results such as disorder located away from an active site. The crystal structure of human plasminogen kringle 4 (PGK4) has been refined against 10-1.68 A resolution X-ray data (R(merge) = 3.7%) to the standard crystallographic R = 14.7% using the program X-PLOR. The crystals of PGK4 showed significant instability in cell dimensions (changes more than 1.5 A) even at 277 K. The refinement revealed structural details not observed before [Mulichak, Tulinsky & Ravichandran (1991). Biochemistry, 30, 10576-10588], such as clear density for additional side chains and more extensive disorder. Discrete disorder was detected for residues S73, S78, T80, S89, S91, S92, Ml12, S132, C138 and K142. Most of the disordered residues form two patches on the surface of the protein. This localized disorder suggests that these residues may play a role in quaternary interactions and possibly form an interface with the other domains of proteins that contain kringles, such as plasminogen. Although, an additional residue D65 was refined at the beginning of the sequence, still more residues near the peptide cleavage site must be disordered in the crystal.
 
  Selected figure(s)  
 
Figure 10.
Fig. 10. Bifurcated hydrogen bond of His96NE2. Close contacts are also provided by carbonyl O atoms to the carbon H atoms of the imidazole ring. The 2Fo- Fc electron density is contoured at the 1.5cr level.
Figure 11.
Fig. 11. Trifurcated hydrogen bond of His98 (H98) NE2. The hydrogen bond between Met93 (M93) SD and the carbonyl O atom is also depicted, as are short contacts to CE1.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1997, 53, 169-178) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19662173 J.A.Kornblatt, T.A.Barretto, K.Chigogidze, and B.Chirwa (2007).
Canine plasminogen: spectral responses to changes in 6-aminohexanoate and temperature.
  Anal Chem Insights, 2, 17-29.  
16991168 F.Grandi, M.Sandal, G.Guarguaglini, E.Capriotti, R.Casadio, and B.Samorì (2006).
Hierarchical mechanochemical switches in angiostatin.
  Chembiochem, 7, 1774-1782.  
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.