1CEA

THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH EACA (EPSILON-AMINOCAPROIC ACID)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of the recombinant kringle 1 domain of human plasminogen in complexes with the ligands epsilon-aminocaproic acid and trans-4-(aminomethyl)cyclohexane-1-carboxylic Acid.

Mathews, I.I.Vanderhoff-Hanaver, P.Castellino, F.J.Tulinsky, A.

(1996) Biochemistry 35: 2567-2576

  • DOI: 10.1021/bi9521351
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystal structures of the complexes of the recombinant kringle 1 domain of human plasminogen (Klpg) with the ligands epsilon-aminocaproic acid (EACA) and trans-4-(aminomethyl)cyclohexane-1-carboxylic acid (AMCHA), which are representative o ...

    The X-ray crystal structures of the complexes of the recombinant kringle 1 domain of human plasminogen (Klpg) with the ligands epsilon-aminocaproic acid (EACA) and trans-4-(aminomethyl)cyclohexane-1-carboxylic acid (AMCHA), which are representative of a class of in vivo antifibrinolytic agents, have been determined at 2.1 angstroms resolution. Each Klpg/ligand unit cell contained a dimer of the complexes, and some small differences were noted in the kringle/ligand interatomic distances within the monomeric components of the dimers. The structures obtained allowed predictions to be made of the amino acid residues of Klpg that are likely important to ligand binding. In the crystal structure, the anionic center of Klpg responsible for coordinating the amino group of the ligands is composed of both Asp54 and Asp56, and the cationic center that stabilizes binding of the carboxylate moiety of the ligands is Arg70, with a possible contribution from Arg34. A hydrogen bond between the carboxylate of the ligand to the hydroxyl group of Tyr63 also appears to contribute to the kringle/ligand binding energies. The methylene groups of the ligand are stablized in the binding pocket by van der Waals contacts with side-chain atoms of Trp61 and Tyr71. These conclusions are in general agreement with site-directed mutagenesis results that implicate many of the same amino acid residues in the binding process, thus showing that the crystal and solution structures are in basic accord with each other. Further comparisons of the X-ray crystal structures of the Klpg/ligand complexes with each other and with apo-Klpg show that while small differences in Klpg side-chain geometries may exist in the three structures, the binding pocket can be considered to be preformed in the apokringle and not substantially altered by the nature of the omega-amino acid ligand that is inserted into the site. From the similar geometries of the binding of EACA and AMCHA, it appears that the kon is an important component to the tighter binding of AMCHA to Klpg, as compared to EACA. Ordered solvation effects of the bound AMCHA may contribute to its longer lifetime on Klpg, thereby retarding koff, both effects thus accounting for the higher binding energy of AMCHA as compared to EACA.


    Related Citations: 
    • 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
    • 1H-NMR Assignments and Secondary Structure of Human Plasminogen Kringle 1
      Rejante, M.R.,Llinas, M.
      (1994) Eur.J.Biochem. 221: 939
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN
A, B
88Homo 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
ACA
Query on ACA

Download SDF File 
Download CCD File 
A, B
6-AMINOHEXANOIC ACID
AMINOCAPROIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ACAIC50: 40000 - 105000 nM (100) BINDINGDB
ACAKd: ~11000 nM BINDINGMOAD
ACAKd: 11000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.500α = 90.00
b = 51.600β = 112.00
c = 46.500γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata reduction
RAXISdata collection
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-04-03
    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