4ZKR | pdb_00004zkr

The crystal structure of upain-1-W3A in complex with uPA at pH9.0

• PDB DOI: https://doi.org/10.2210/pdb4ZKR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2015-04-30 Released: 2016-05-18 
• Deposition Author(s): Jiang, L., Andreasen, P.A., Huang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.234 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of mupain-1-IG in complex with murinised human uPA at pH7.4

Jiang, L., Andreasen, P.A., Huang, 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)

Macromolecule Content 

• Total Structure Weight: 29.6 kDa 
• Atom Count: 2,168 
• Modeled Residue Count: 247 
• Deposited Residue Count: 259 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	247	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
upain-1-W3A	B [auth P]	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth U]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	C [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.234 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.122	α = 90
b = 121.122	β = 90
c = 43.062	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Jiang, L., Andreasen, P.A., Huang, M.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary