1PK4

CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN PLASMINOGEN KRINGLE 4 REFINED AT 1.9-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal and molecular structure of human plasminogen kringle 4 refined at 1.9-A resolution.

Mulichak, A.M.Tulinsky, A.Ravichandran, K.G.

(1991) Biochemistry 30: 10576-10588

  • DOI: 10.1021/bi00107a029
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the bovine prothrombin kringle 1 (PTK1) structure as a model and refined by restrained least-squares methods to an R factor of 14.2% at 1.9-A r ...

    The crystal structure of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the bovine prothrombin kringle 1 (PTK1) structure as a model and refined by restrained least-squares methods to an R factor of 14.2% at 1.9-A resolution. The K4 structure is similar to that of PTK1, and an insertion of one residue at position 59 of the latter has minimal effect on the protein folding. The PGK4 structure is highly stabilized by an internal hydrophobic core and an extensive hydrogen-bonding network. Features new to this kringle include a cis peptide bond at Pro30 and the presence of two alternate, perpendicular, and equally occupied orientations for the Cys75 side chain. The K4 lysine-binding site consists of a hydrophobic trough formed by the Trp62 and Trp72 indole rings, with anionic (Asp55/Asp57) and cationic (Lys35/Arg71) charge pairs at either end. With the adjacent Asp5 and Arg32 residues, these result in triply charged anionic and cationic clusters (pH of crystals at 6.0), which, in addition to the unusually high accessibility of the Trp72 side chain, serve as an obvious marker of the binding site on the K4 surface. A complex intermolecular interaction occurs between the binding sites of symmetry-related molecules involving a highly ordered sulfate anion of solvation in which the Arg32 side chain of a neighboring kringle occupies the binding site.


    Related Citations: 
    • Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution
      Seshadri, T.P., Tulinsky, A., Skrzypczak-Jankun, E., Park, C.H.
      (1991) J Mol Biol 220: 481
    • Structure of the Lysine-Fibrin Binding Subsite of Human Plasminogen Kringle 4
      Mulichak, A.M., Tulinsky, A.
      (1990) Blood Coagul Fibrinolysis 1: 673
    • Lysine(Slash)Fibrin Binding Sites of Kringles Modeled After the Structure of Kringle 1 of Prothrombin
      Tulinsky, A., Park, C.H., Mao, B., Llinas, M.
      (1988) Proteins 3: 85
    • Structure of Prothrombin Fragment 1 Refined at 2.8 Angstroms Resolution
      Tulinsky, A., Park, C.H., Skrzypczak-Jankun, E.
      (1988) J Mol Biol 202: 885

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN KRINGLE 4
A
79Homo sapiensMutation(s): 0 
Gene Names: PLG
EC: 3.4.21.7
Find proteins for P00747 (Homo sapiens)
Go to UniProtKB:  P00747
NIH Common Fund Data Resources
PHAROS  P00747
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.11α = 90
b = 49.09β = 90
c = 49.39γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other