8W31

Crystal structure of parkin (R0RB):2pUb with activator compound

• PDB DOI: https://doi.org/10.2210/pdb8W31/pdb

• Classification: LIGASE
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-21 Released: 2024-08-21 
• Deposition Author(s): Sauve, V., Gehring, K.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

Starting Model: experimental

Literature

Activation of Parkin by a Molecular Glue

Sauve, V., Gehring, K.

(2024) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 44.58 kDa 
• Atom Count: 3,051 
• Modelled Residue Count: 380 
• Deposited Residue Count: 390 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	A	240	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkn, Park2 EC: 2.3.2.31
UniProt
Find proteins for Q9JK66 (Rattus norvegicus) Explore Q9JK66  Go to UniProtKB:  Q9JK66

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, C	75	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AE9 (Subject of Investigation/LOI)	J [auth A]	(S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one C31 H30 N4 O2 ZYSMPORNWLASGT-MHZLTWQESA-N
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B, C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.54	α = 90
b = 83.54	β = 90
c = 258.77	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Sauve, V., Gehring, K.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN 159903

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release