2O8W

Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator (C122A/N145Q/S195A) in complex with Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2O8W/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2006-12-12 Released: 2007-12-25 
• Deposition Author(s): Zhao, G., Yuan, C., Jiang, L., Huang, Z., Huang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.255 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Literature

Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator (C122A/N145Q/S195A) in complex with Inhibitors

Zhao, G., Yuan, C., Jiang, L., Huang, Z., Huang, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.85 kDa 
• Atom Count: 2,252 
• Modelled Residue Count: 245 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator	A	253	Homo sapiens	Mutation(s): 3  EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens) Explore P00749  Go to UniProtKB:  P00749
PHAROS:  P00749 GTEx:  ENSG00000122861

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PL0	D [auth A]	1-phenylguanidine C7 H9 N3 QRJZGVVKGFIGLI-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
PL0	BindingDB:  2O8W	Ki: min: 2.06e+4, max: 2.06e+4 (nM) from 2 assay(s)
		IC50: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.255 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.875	α = 90
b = 120.875	β = 90
c = 42.591	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Zhao, G., Yuan, C., Jiang, L., Huang, Z., Huang, M.

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-12-27
  Changes: Data collection