6L04 | pdb_00006l04

Crystal structure of uPA_H99Y in complex with 31F

• PDB DOI: https://doi.org/10.2210/pdb6L04/pdb

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


• Deposited: 2019-09-26 Released: 2020-09-30 
• 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: 2.21 Å
• R-Value Free: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of uPA_H99Y in complex with 31F

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.03 kDa 
• Atom Count: 2,037 
• Modeled Residue Count: 245 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	245	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
32I (Subject of Investigation/LOI)	B [auth U]	3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide C18 H25 N9 O3 GYTXWTOJZQGKDP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.95	α = 90
b = 119.95	β = 90
c = 42.31	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-30 
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: 2020-09-30
  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