3UT3 | pdb_00003ut3

A novel PAI-I inhibitor and its structural mechanism

• PDB DOI: https://doi.org/10.2210/pdb3UT3/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-25 Released: 2013-02-06 
• Deposition Author(s): Lin, Z.H., Hong, Z.B., Shi, X.L., Hu, L.H., Andreasen, P.A., Huang, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Models: experimental

Literature

A novel PAI-I inhibitor and its structural mechanism

Lin, Z.H., Hong, Z.B., Shi, X.L., Hu, L.H., Andreasen, P.A., Huang, M.D.

To be published.

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: 169.53 kDa 
• Atom Count: 11,638 
• Modeled Residue Count: 1,455 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator inhibitor 1	A, B, C, D	375	Homo sapiens	Mutation(s): 4  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMJ	E [auth B]	2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione C17 H26 O4 IRSFLDGTOHBADP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.252	α = 90.89
b = 74.953	β = 93.33
c = 103.775	γ = 115.72

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Lin, Z.H., Hong, Z.B., Shi, X.L., Hu, L.H., Andreasen, P.A., Huang, M.D.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description