2PK4

THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF HUMAN PLASMINOGEN KRINGLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10589-10594

  • DOI: 10.1021/bi00107a030
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystallographic structure of the plasminogen kringle 4-epsilon-aminocaproic acid (ACA) complex (K4-ACA) has been solved by molecular replacement rotation-translation methods utilizing the refined apo-K4 structure as a search model (Mulichak et a ...

    The crystallographic structure of the plasminogen kringle 4-epsilon-aminocaproic acid (ACA) complex (K4-ACA) has been solved by molecular replacement rotation-translation methods utilizing the refined apo-K4 structure as a search model (Mulichak et al., 1991), and it has been refined to an R value of 0.148 at 2.25-A resolution. The K4-ACA structure consists of two interkringle residues, the kringle along with the ACA ligand, and 106 water molecules. The lysine-binding site has been confirmed to be a relatively open and shallow depression, lined by aromatic rings of Trp62, Phe64, and Trp72, which provide a highly nonpolar environment between doubly charged anionic and cationic centers formed by Asp55/Asp57 and Lys35/Arg71. A zwitterionic ACA ligand molecule is held by hydrogen-bonded ion pair interactions and van der Waals contacts between the charged centers. The lysine-binding site of apo-K4 and K4-ACA have been compared: the rms differences in main-chain and side-chain positions are 0.25 and 0.69 A, respectively, both practically within error of the determinations. The largest deviations in the binding site are due to different crystal packing interactions. Thus, the lysine-binding site appears to be preformed, and lysine binding does not require conformational changes of the host. The results of NMR studies of lysine binding with K4 are correlated with the structure of K4-ACA and agree well.


    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
HUMAN PLASMINOGEN KRINGLE 4
A
80Homo 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
ACA
Query on ACA

Download CCD File 
A
6-AMINOHEXANOIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ACAIC50:  105000   nM  BindingDB
ACAIC50:  40000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.21α = 90
b = 35.46β = 102.94
c = 25.43γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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