7ZRR | pdb_00007zrr

Crystal structure of human Urokinase-type plasminogen activator in complex with bicycle peptide inhibitor UK965

• PDB DOI: https://doi.org/10.2210/pdb7ZRR/pdb

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


• Deposited: 2022-05-05 Released: 2023-11-15 
• Deposition Author(s): Caregnato, A., Angela, P., Mazzoccato, Y., Frasson, N., Angelini, A., Cendron, L.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Urokinase-type plasminogen activator in complex with bicycle peptide inhibitor UK965

Caregnato, A., Angela, P., Mazzoccato, Y., Frasson, N., Angelini, A., Cendron, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 34.33 kDa 
• Atom Count: 2,277 
• Modeled Residue Count: 263 
• Deposited Residue Count: 300 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A	284	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
synthetic peptide UK965	B	16	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZBR (Subject of Investigation/LOI)	G [auth B]	1,3,5-tris(bromomethyl)benzene C9 H9 Br3 GHITVUOBZBZMND-UHFFFAOYSA-N
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NH2 (Subject of Investigation/LOI)	F [auth B]	AMINO GROUP H2 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.906	α = 90
b = 120.906	β = 90
c = 42.716	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Caregnato, A., Angela, P., Mazzoccato, Y., Frasson, N., Angelini, A., Cendron, L.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary