6JYP

Crystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb6JYP/pdb

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


• Deposited: 2019-04-27 Released: 2020-05-13 
• Deposition Author(s): Buckley, B., Jiang, L.G., Huang, M.D., Kelso, M., Ranson, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.254 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

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: 28.15 kDa 
• Atom Count: 2,020 
• Modelled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	246	Homo sapiens	Mutation(s): 3  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
HMX (Subject of Investigation/LOI)	B [auth U]	3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide C12 H18 Cl N7 O RQQJJXVETXFINY-UHFFFAOYSA-N
SO4	C [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.254 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.242	α = 90
b = 121.242	β = 90
c = 42.174	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Buckley, B., Jiang, L.G., Huang, M.D., Kelso, M., Ranson, M.

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

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary