Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.79 kDa 
• Atom Count: 1489 
• Residue Count: 168 
• Unique protein chains: 1

5HPG

STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN

• DOI: 10.2210/pdb5HPG/pdb

• Classification: SERINE PROTEASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-09-19 Released: 1998-03-25 
• Deposition Author(s): Tulinsky, A., Mochalkin, I., Castellino, F.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Work: 0.166 

Literature

Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen.

Chang, Y., Mochalkin, I., McCance, S.G., Cheng, B., Tulinsky, A., Castellino, F.J.

(1998) Biochemistry 37: 3258-3271

• PubMed: 9521645 
• DOI: 10.1021/bi972284e
• Primary Citation of Related Structures:  
  5HPG


• PubMed Abstract: 
  

The X-ray crystal structure of the recombinant (r) kringle 5 domain of human plasminogen (K5HPg) has been solved by molecular replacement methods using K1HPg as a model and refined at 1.7 A resolution to an R factor of 16.6%. The asymmetric unit of K5HPg is composed of two molecules related by a noncrystallographic 2-fold rotation axis approximately parallel to the z-direction. The lysine binding site (LBS) is defined by the regions His33-Thr37, Pro54-Val58, Pro61-Tyr64, and Leu71-Tyr74 and is occupied in the apo-form by water molecules. A unique feature of the LBS of apo-K5HPg is the substitution by Leu71 for the basic amino acid, arginine, that in other kringle polypeptides forms the donor cationic center for the carboxylate group of omega-amino acid ligands. While wild-type (wt) r-K5HPg interacted weakly with these types of ligands, replacement by site-directed mutagenesis of Leu71 by arginine led to substantially increased affinity of the ligands for the LBS of K5HPg. As a result, binding of omega-amino acids to this mutant kringle (r-K5HPg[L71R]) was restored to levels displayed by the companion much stronger affinity HPg kringles, K1HPg and K4HPg. Correspondingly, alkylamine binding to r-K5HPg[L71R] was considerably attenuated from that shown by wtr-K5HPg. Thus, employing a rational design strategy based on the crystal structure of K5HPg, successful remodeling of the LBS has been accomplished, and has resulted in the conversion of a weak ligand binding kringle to one that possesses an affinity for omega-amino acids that is similar to K1HPg and K4HPg.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Notre Dame, Indiana 46556, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMINOGEN	A, B	84	Homo sapiens	Mutation(s): 0  Gene Names: PLG EC: 3.4.21.7
Find proteins for P00747 (Homo sapiens) Explore P00747  Go to UniProtKB:  P00747
NIH Common Fund Data Resources
PHAROS:  P00747 GTEx:  ENSG00000122194

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Work: 0.166 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.43	α = 90
b = 79.2	β = 90
c = 30.78	γ = 90

Software Package:

Software Name	Purpose
RIGAKU	data collection
RIGAKU	data reduction
AMoRE	phasing
PROFFT	refinement
R-AXIS	data reduction
R-AXIS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-09-19 
• Released Date: 1998-03-25 
Deposition Author(s): Tulinsky, A., Mochalkin, I., Castellino, F.J.

Revision History 

• Version 1.0: 1998-03-25
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance