1QRZ

CATALYTIC DOMAIN OF PLASMINOGEN

• PDB DOI: https://doi.org/10.2210/pdb1QRZ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 1999-06-16 Released: 1999-10-14 
• Deposition Author(s): Peisach, E., Wang, J., de los Santos, T., Reich, E., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.294 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 

Literature

Crystal structure of the proenzyme domain of plasminogen.

Peisach, E., Wang, J., de los Santos, T., Reich, E., Ringe, D.

(1999) Biochemistry 38: 11180-11188

• PubMed: 10460175 
• DOI: https://doi.org/10.1021/bi991130r
• Primary Citation of Related Structures:  
  1QRZ


• PubMed Abstract: 
  

  We have solved the X-ray crystal structure of the proenzyme form of the catalytic domain of plasminogen, with the nonessential mutations M585Q, V673M, and M788L, to 2.0 A resolution. The structure presents an inactive protease characterized by Asp740 (chymotrypsinogen 194) hydrogen bonded to His586 (chymotrypsinogen 40), preventing proper formation of the oxyanion hole and S1 specificity pocket. In addition, the catalytic triad residues are misplaced relative to the active conformation adopted by serine proteases in the chymotrypsin family. Finally, a unique form of zymogen inactivation is observed, characterized by a "foot-in-mouth" mechanism in which Trp761 (chymotrypsinogen 215) is folded into the S1 specificity pocket preventing substrate binding.

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Organizational Affiliation: 

Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.08 kDa 
• Atom Count: 8,097 
• Modelled Residue Count: 984 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMINOGEN	A, B, C, D	246	Homo sapiens	Mutation(s): 3  EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens) Explore P00747  Go to UniProtKB:  P00747
PHAROS:  P00747 GTEx:  ENSG00000122194

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.294 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.658	α = 90
b = 73.575	β = 108.73
c = 81.363	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-14 
Deposition Author(s): Peisach, E., Wang, J., de los Santos, T., Reich, E., Ringe, D.

Revision History  

• Version 1.0: 1999-10-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-09-25
  Changes: Derived calculations
• Version 1.4: 2021-11-03
  Changes: Database references
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary