2O8U | pdb_00002o8u

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

• PDB DOI: https://doi.org/10.2210/pdb2O8U/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: 1.70 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

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: 29.06 kDa 
• Atom Count: 2,126 
• Modeled Residue Count: 238 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
BEN	C [auth A], D [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.073	α = 90
b = 120.073	β = 90
c = 42.252	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
• Version 1.4: 2024-11-13
  Changes: Structure summary