5ZLZ | pdb_00005zlz

Structure of tPA and PAI-1

• PDB DOI: https://doi.org/10.2210/pdb5ZLZ/pdb

• Classification: HYDROLASE INHIBITOR/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: prokaryotic environmental samples
• Mutation(s): Yes 


• Deposited: 2018-03-31 Released: 2019-04-03 
• Deposition Author(s): Min, L., Huang, M.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 
  0.312 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Models: experimental

Literature

Development of a PAI-1 trapping agent (PAItrap2) based on inactivated tPA-SPD and the crystal structure of PAItrap2 in complex with PAI-1

Min, L., Huang, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.41 kDa 
• Atom Count: 4,891 
• Modeled Residue Count: 620 
• Deposited Residue Count: 625 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator inhibitor 1	A [auth I]	374	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue-type plasminogen activator	B [auth E]	251	Homo sapiens	Mutation(s): 4  Gene Names: PLAT EC: 3.4.21.68
UniProt & NIH Common Fund Data Resources
Find proteins for P00750 (Homo sapiens) Explore P00750  Go to UniProtKB:  P00750
PHAROS:  P00750 GTEx:  ENSG00000104368

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth E], D [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free:  0.312 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.852	α = 90
b = 67.186	β = 90
c = 212.591	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Min, L., Huang, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370737
National Natural Science Foundation of China	China	31400637
National Natural Science Foundation of China	China	31570745
National Natural Science Foundation of China	China	31670739
National Natural Science Foundation of China	China	U1405229

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary