1PKR

THE STRUCTURE OF RECOMBINANT PLASMINOGEN KRINGLE 1 AND THE FIBRIN BINDING SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of recombinant plasminogen kringle 1 and the fibrin binding site.

Wu, T.P.Padmanabhan, K.P.Tulinsky, A.

(1994) Blood Coagulation Fibrinolysis 5: 157-166


  • PubMed Abstract: 
  • The structure of recombinant (Hoover et al. Biochemistry, 1993; 32:10936-10944) plasminogen (PG) kringle 1 (K1) has been determined and refined at 2.48 A resolution to a crystallographic R value of 0.159. In addition, 71 water molecules and two chlor ...

    The structure of recombinant (Hoover et al. Biochemistry, 1993; 32:10936-10944) plasminogen (PG) kringle 1 (K1) has been determined and refined at 2.48 A resolution to a crystallographic R value of 0.159. In addition, 71 water molecules and two chloride ions have been located. The folding of PGK1 is very similar to that of PGK4. The lysine/fibrin binding site, however, differs from that of both PGK4 and tissue-type PG activator (t-PA) K2 at the cationic centre. Although PGK1 can potentially have a doubly charged cationic centre utilizing Arg34 and Arg71, the side chain of Arg34 is outside of Arg71 in a solvent region and its guanidino group is flexibly disordered. Moreover, site specific mutagenesis studies show unequivocally that Arg34 can be changed to glutamine without affecting the binding ability of PGK1. Thus, PGK1 only has Arg71 at the cationic site, PGK4 has Lys35/Arg71 and t-PAK2 has only Lys33. The cationic site differences may result in subtle responses in the binding affinities of the kringles. The two chloride ions are located in the lysine binding site and effectively compensate the positive charges of the region. They also appear to be involved intermolecularly in a complex way in the crystal structure. Such intermolecular anionic interactions are also found in PGK4 and t-PAK2.


    Related Citations: 
    • The Amino Acids of the Recombinant Kringle 1 Domain of Human Plasminogen that Stabilize its Interaction with W-Amino Acids
      Hoover, G.J.,Menhart, N.,Martin, A.,Warder, S.,Castellino, F.J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing 48824.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN
A
82Homo sapiensMutation(s): 0 
Gene Names: PLG
EC: 3.4.21.7
Find proteins for P00747 (Homo sapiens)
Go to Gene View: PLG
Go to UniProtKB:  P00747
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.930α = 90.00
b = 58.930β = 90.00
c = 54.640γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other