1PML

KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Kringle-kringle interactions in multimer kringle structures.

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

(1994) Protein Sci. 3: 898-910

  • DOI: 10.1002/pro.5560030605
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorthombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% ...

    The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorthombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% at 2.25 A resolution. The X-PLOR structure of kringle 2 of tissue plasminogen activator (t-PAK2) has been refined further using PROFFT (R = 14.5% at 2.38 A resolution). The PGK4 structure has 2 and t-PAK2 has 3 independent molecules in the asymmetric unit. There are 5 different noncrystallographic symmetry "dimers" in PGK4. Three make extensive kringle-kringle interactions related by noncrystallographic 2(1) screw axes without blocking the lysine binding site. Such associations may occur in multikringle structures such as prothrombin, hepatocyte growth factor, plasminogen (PG), and apolipoprotein [a]. The t-PAK2 structure also has noncrystallographic screw symmetry (3(1)) and mimics fibrin binding mode by having lysine of one molecule interacting electrostatically with the lysine binding site of another kringle. This ligand-like binding interaction may be important in kringle-kringle interactions involving non-lysine binding kringles with lysine or pseudo-lysine binding sites. Electrostatic intermolecular interactions involving the lysine binding site are also found in the crystal structures of PGK1 and orthorhombic PGK4. Anions associate with the cationic centers of these and t-PAK2 that appear to be more than occasional components of lysine binding site regions.


    Related Citations: 
    • Crystal and Molecular Structure of Human Plasminogen Kringle 4 Refined to 1.9A Resolution
      Mulichak, A.M.,Tulinsky, A.,Ravichandran, K.G.
      (1991) Biochemistry 30: 10576
    • Crystal Structure of the Kringle 2 Domain of Tissue Plasminogen Activator at 2.4 A Resolution
      De Vos, A.M.,Ultsch, M.H.,Kelly, R.F.,Padmanabhan, K.,Tulinsky, A.,Westbrook, M.L.,Kossiakoff, A.A.
      (1992) Biochemistry 31: 270
    • The Refined Structure of the Epsilon-Aminocaproic Acid Complex of Human Plasminogen Kringle 4
      Wu, T.-P.,Padmanabhan, K.,Tulinsky, A.,Mulichak, A.M.
      (1991) Biochemistry 30: 10589


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
A, B, C
86Homo sapiensMutation(s): 0 
Gene Names: PLAT
EC: 3.4.21.68
Find proteins for P00750 (Homo sapiens)
Go to Gene View: PLAT
Go to UniProtKB:  P00750
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.800α = 90.00
b = 63.580β = 106.70
c = 46.580γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    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