3EOX | pdb_00003eox

High quality structure of cleaved PAI-1-stab

• PDB DOI: https://doi.org/10.2210/pdb3EOX/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-09-29 Released: 2009-02-17 
• Deposition Author(s): Dewilde, M., Declerck, P.J., Rabijns, A., Strelkov, S.V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.256 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

High quality structure of cleaved PAI-1-stab.

Dewilde, M., Strelkov, S.V., Rabijns, A., Declerck, P.J.

(2009) J Struct Biol 165: 126-132

• PubMed: 19059484 
• DOI: https://doi.org/10.1016/j.jsb.2008.11.001
• Primary Citation Related Structures: 
  3EOX


• PubMed Abstract: 
  

  Here we report the crystal structure of a stablilized plasminogen activator inhibitor-1 variant (PAI-1-N150H-K154T-Q301P-Q319L-M354I (PAI-1-stab)) that shows a cleavage within the reactive centre loop. The new structure is of superior quality compared to the previously determined structure of the cleaved PAI-1-A335P mutant. We present a detailed comparison of the two structures and also compare them with the structure of the active PAI-1-stab. The structural data give important insights into the working mechanism of PAI-1 and also explain the role of various stabilizing mutations.

---

Organizational Affiliation: 
• Katholieke Universiteit Leuven, Belgium.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.75 kDa 
• Atom Count: 3,084 
• Modeled Residue Count: 370 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator inhibitor 1	A	379	Homo sapiens	Mutation(s): 5  Gene Names: SERPINE1, PAI1, PLANH1
UniProt & NIH Common Fund Data Resources
Find proteins for P05121 (Homo sapiens) Explore P05121  Go to UniProtKB:  P05121
PHAROS:  P05121 GTEx:  ENSG00000106366

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.256 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.174	α = 90
b = 71.174	β = 90
c = 141.664	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
detector	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Dewilde, M., Declerck, P.J., Rabijns, A., Strelkov, S.V.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2021-11-10
  Changes: Advisory, Data collection, Database references
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description