6AG9 | pdb_00006ag9

Crystal structure of uPA in complex with 3,5-bis(azanyl)-6-(1-benzofuran-2-yl)-N-carbamimidoyl-pyrazine-2- carboxamide

• PDB DOI: https://doi.org/10.2210/pdb6AG9/pdb

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


• Deposited: 2018-08-09 Released: 2019-09-18 
• Deposition Author(s): Buckley, B., Jiang, L.G., Majed, H., Huang, M.D., Kelso, M., Ranson, M.
• Funding Organization(s): National Health and Medical Research Council (Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

uPA-HMA

Buckley, B., Jiang, L.G., Huang, M.D., Kelso, M., Ranson, M.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.85 kDa 
• Atom Count: 2,110 
• Modeled Residue Count: 245 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	253	Homo sapiens	Mutation(s): 2  Gene Names: PLAU 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9XF (Subject of Investigation/LOI)	B [auth U]	3,5-bis(azanyl)-6-(1-benzofuran-2-yl)-N-carbamimidoyl-pyrazine-2-carboxamide C14 H13 N7 O2 ZKLNPUKNSARQMG-UHFFFAOYSA-N
SO4	C [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.56	α = 90
b = 120.56	β = 90
c = 42.35	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Buckley, B., Jiang, L.G., Majed, H., Huang, M.D., Kelso, M., Ranson, M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (Australia)	Australia	APP1100432

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary